SRX695793 RNA-seq analysis of Phaseolus vulgaris cv. Negro jamapa SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS696906 SAMN02226068 YL RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695829 PvL5 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS696938 SAMN02226069 PvL5 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695830 PvLF SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS696939 SAMN02226070 PvLF RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695874 PvLE SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS696983 SAMN02226071 PvLE RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695875 PvLI SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS696984 SAMN02226072 PvLI RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695876 PvYS SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS696985 SAMN02226073 PvYS RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695905 PvST SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS697014 SAMN02226074 PvST RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695906 PvYF SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS697015 SAMN02226075 PvYF RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695908 PvPY SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools SRS697017 SAMN02226076 PvPY RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695909 PvPH SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697018 SAMN02226077 PvPH RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695911 PvP1 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697020 SAMN02226078 PvP1 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695912 PvP2 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697021 SAMN02226079 PvP2 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695913 PvSH SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697022 SAMN02226080 PvSH RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695914 PvS1 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697023 SAMN02226081 PvS1 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695915 PvS2 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697024 SAMN02226082 PvS2 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695916 PvRT SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697025 SAMN02226083 PvRT RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695917 PvYR SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697026 SAMN02226084 PvYR RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695918 PvR5 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697027 SAMN02226085 PvR5 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695919 PvRF SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697028 SAMN02226086 PvRF RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695920 PvRE SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697029 SAMN02226087 PvRE RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695921 PvRI SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697030 SAMN02226088 PvRI RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695927 PvN5 SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697036 SAMN02226089 PvN5 RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695929 PvNE SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697038 SAMN02226090 PvNE RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000 SRX695931 PvNI SRP046307 PRJNA210619 Total RNA was purified using RNeasy Plant Mini Kit (Qiagen, Valencia, CA, USA). RNA samples were shipped on dry ice overnight to National Center for Genome Resources (NCGR, Santa Fe, NM) for sequencing. Poly-A RNA samples were isolated from total RNA using oligo-dT25 magnetic beads (Dynabeads; Invitrogen, Carlsbad, CA). Poly-A RNA was denatured and used in a random-priming cDNA synthesis followed by end repair by T4 DNA polymerase, Klenow polymerase, and dNTPs. End-repaired fragments are phosphorylated by T4 polynucleotide kinase followed by the addition of a single ‘A’ base to the 3’ end of the blunt end phosphorylated DNA fragments. Illumina adapters were added to DNA fragments by ligation and size selected (500bp) by electrophoresis. DNA libraries were amplified for 15 cycles. Two picomoles of the cDNA library were loaded on an Illunina single-end flow cell using the Illunina Cluster Station (Illunina, Inc., San Diego, CA). 36bp reads were collected on an Illunina Genome Analyzer using sequencing by synthesis. Sequenced reads were aligned to the Phaseolus vulgaris v1.0 genome (www.phytozome.net) using Bowtie. Alignment files were sorted using Samtools. SRS697040 SAMN02226091 PvNI RNA-Seq TRANSCRIPTOMIC PolyA 36 0 Application Read Forward 1 Illumina HiSeq 1000