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Combining both short and long-read sequencing, we have estimated the almond Prunusdulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. Thehighly heterozygous compact genome of Texas comprises eight chromosomes, to whichwe have anchored over 91% of the assembly. We annotated 27,042 protein-coding genesand 6,800 non-coding transcripts. High levels of genetic variability were characterizedafter resequencing a collection of ten almond accessions. Phylogenomic comparison withthe genomes of 16 other close and distant species allowed estimating that almond andpeach diverged around 5.88 Mya. Comparison between peach and almond genomesconfirmed the high synteny between these close relatives, but also revealed high numbersof presence-absence variants, many attributable to the movement of transposableelements (TEs). The number and distribution of TEs between peach and almond wassimilar, but the history of TE movement was distinct, with peach having a largerproportion of recent transpositions and almond preserving a higher level of polymorphismin the older TEs. When focusing on specific genes involved in key characters such as thebitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for onegene associated with the biosynthesis of amygdalin that confers the bitter kernel taste,several TEs were inserted in its vicinity only in sweet almond cultivars but not in bittercultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and otherspecies like peach and cherry. TE insertions likely to produce affects in the expression ofsix more genes involved in the formation of the fleshy mesocarp were also identified.Altogether, our results suggest a key role of TEs in the recent history and diversificationof almond with respect to peach. |