SRX697846 GSM1500790 SRP046740 SRS699449 GSM1500790 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500790 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500790 gds 301500790 GEO Accession GSM1500790 SRX697847 GSM1500791 SRP046740 SRS699450 GSM1500791 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500791 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500791 gds 301500791 GEO Accession GSM1500791 SRX697848 GSM1500792 SRP046740 SRS699451 GSM1500792 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500792 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500792 gds 301500792 GEO Accession GSM1500792 SRX697849 GSM1500793 SRP046740 SRS699452 GSM1500793 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500793 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500793 gds 301500793 GEO Accession GSM1500793 SRX697850 GSM1500794 SRP046740 SRS699453 GSM1500794 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500794 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500794 gds 301500794 GEO Accession GSM1500794 SRX697851 GSM1500795 SRP046740 SRS699454 GSM1500795 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500795 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500795 gds 301500795 GEO Accession GSM1500795 SRX697852 GSM1500796 SRP046740 SRS699455 GSM1500796 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500796 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500796 gds 301500796 GEO Accession GSM1500796 SRX697853 GSM1500797 SRP046740 SRS699456 GSM1500797 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500797 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500797 gds 301500797 GEO Accession GSM1500797 SRX697854 GSM1500798 SRP046740 SRS699457 GSM1500798 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500798 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500798 gds 301500798 GEO Accession GSM1500798 SRX697855 GSM1500799 SRP046740 SRS699458 GSM1500799 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500799 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500799 gds 301500799 GEO Accession GSM1500799 SRX697856 GSM1500800 SRP046740 SRS699459 GSM1500800 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500800 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500800 gds 301500800 GEO Accession GSM1500800 SRX697857 GSM1500801 SRP046740 SRS699460 GSM1500801 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500801 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500801 gds 301500801 GEO Accession GSM1500801 SRX697858 GSM1500802 SRP046740 SRS699461 GSM1500802 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500802 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500802 gds 301500802 GEO Accession GSM1500802 SRX697859 GSM1500803 SRP046740 SRS699462 GSM1500803 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500803 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500803 gds 301500803 GEO Accession GSM1500803 SRX697860 GSM1500804 SRP046740 SRS699463 GSM1500804 RNA-Seq TRANSCRIPTOMIC cDNA total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2500 GEO Sample GSM1500804 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500804 gds 301500804 GEO Accession GSM1500804 SRX697861 GSM1500805 SRP046740 SRS699464 GSM1500805 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500805 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500805 gds 301500805 GEO Accession GSM1500805 SRX697862 GSM1500806 SRP046740 SRS699466 GSM1500806 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500806 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500806 gds 301500806 GEO Accession GSM1500806 SRX697863 GSM1500807 SRP046740 SRS699465 GSM1500807 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500807 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500807 gds 301500807 GEO Accession GSM1500807 SRX697864 GSM1500808 SRP046740 SRS699467 GSM1500808 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500808 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500808 gds 301500808 GEO Accession GSM1500808 SRX697865 GSM1500809 SRP046740 SRS699468 GSM1500809 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500809 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500809 gds 301500809 GEO Accession GSM1500809 SRX697866 GSM1500810 SRP046740 SRS699469 GSM1500810 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500810 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500810 gds 301500810 GEO Accession GSM1500810 SRX697867 GSM1500811 SRP046740 SRS699471 GSM1500811 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500811 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500811 gds 301500811 GEO Accession GSM1500811 SRX697868 GSM1500812 SRP046740 SRS699470 GSM1500812 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500812 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500812 gds 301500812 GEO Accession GSM1500812 SRX697869 GSM1500813 SRP046740 SRS699472 GSM1500813 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500813 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500813 gds 301500813 GEO Accession GSM1500813 SRX697870 GSM1500814 SRP046740 SRS699473 GSM1500814 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500814 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500814 gds 301500814 GEO Accession GSM1500814 SRX697871 GSM1500815 SRP046740 SRS699474 GSM1500815 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500815 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500815 gds 301500815 GEO Accession GSM1500815 SRX697872 GSM1500816 SRP046740 SRS699475 GSM1500816 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500816 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500816 gds 301500816 GEO Accession GSM1500816 SRX697873 GSM1500817 SRP046740 SRS699476 GSM1500817 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500817 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500817 gds 301500817 GEO Accession GSM1500817 SRX697874 GSM1500818 SRP046740 SRS699477 GSM1500818 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500818 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500818 gds 301500818 GEO Accession GSM1500818 SRX697875 GSM1500819 SRP046740 SRS699478 GSM1500819 miRNA-Seq TRANSCRIPTOMIC size fractionation total RNA was extracted from larval samples using Trizol reagent, following the manufacturer’s protocol (Invitrogen (Life Technologies), Melgrave, Vic, Australia). Briefly, larval samples were homogenised in 500µl of Trizol reagent (3:1 Trizol to sample ratio). One hundred microliters of chloroform were then added and allowed to incubate for 3min at room temperature, before the samples were centrifuged at 12,000g for 10min at 4°C. Following centrifugation, the upper phase was collected, with total RNA precipitated using isopropanol. The pellet was washed briefly in 75% ethanol and dissolved in 50µL double-distilled water by incubating for 2-3 min at 80oC. RNA purity was determined by gel electrophoresis and quantified using a nanodrop spectrophotometer. Small RNA libraries were constructed using a NEBNext Multiplex Small RNA Library prep kit for Illumina Sequencing (#E7300S/L, New England BioLabs (NEB), Genesearch, Arundel, Qld, Australia). Briefly, small RNAs were size selected and purified from 10µg of total RNA (n=5 per caste) using a 15% acrylamide:bis-acrylamide PAGE, 8M urea gel with the aid of a microRNA Marker (#N2102S, NEB). The size selected small RNAs were eluted from the gel by incubation in a 0.3M NaCl solution over night at 4°C, before precipitation using the isopropanol/ethanol. The precipitated pellet was dissolved in 6.5µL RNAase free, DEPC-treated, distilled water. Library preparation, which involved adaptor ligation, reverse transcription and PCR amplification, were carried out following the manufactures protocol for small RNA library preparations (#E7300S/L, NEB). Product verification and size selection of amplified cDNA libraries was undertaken using a 6% PAGE gel. Gel bands corresponding to 140-150 nucleotides in size, which corresponds to adaptor-ligated constructs formed from 21-30 nucleotide RNA fragments, were cut from the gel and extracted by overnight incubation in 0.3M NaCl at 4°C. Library constructs were then precipitated with 3M NaOAc, chilled isopropanol, before being washed in 75% ethanol, with the final pellet dissolved in 10μl 10mM Tris‐HCI, pH 8.5. Libraries were validated on a 2100 Bioanalyser (Agilent Technologies, Integrated Sciences, Chatswood, Australia), using a high sensitivity DNA LabChip. Illumina HiSeq 2000 GEO Sample GSM1500819 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1500819 gds 301500819 GEO Accession GSM1500819