| description |
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long-read sequencing. We have assembled 227.6 Mb of the estimated 235 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement. By phylogenomic comparison with the genomes of 16 close and distant species we estimate that almond and peach diverged around 5.88 Mya. These two genomes are highly syntenic and show a high degree of sequence conservation (20 substitutions per kb). However, they also exhibit a large number of presence-absence variants, many attributable to the movement of transposable elements (TEs). TEs have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement is different between them. TEs may also be at the origin of important phenotypic differences between both species, and in particular, for the sweet kernel phenotype, a key agronomic character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene of the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach. |