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Title: Transposons played a major role in the diversification between the closely related almond and peach genomes: Results from the almond genome sequence
Authors: Alioto, Tyler
Alexiou, Konstantinos G.
Bardil, Amelie
Barteri, Fabio
Castanera, Raúl
Cruz, Fernando
Dhingra, Amit
Duval, Henri
Fernández i Martí, Angel V.
Frías, Leonor
Galán, Beatriz
García, José Luis
Howad, Werner
Gómez Garrido, Jéssica
Gut, Marta
Julca, Irene
Morata, Jordi
Puigdomenech, Pere
Ribeca, Paolo
Rubio Cabetas, María José
Vlasova, Anna
Wirthensohn, Michelle
García Más, Jordi
Gabaldón, Toni
Casacuberta, Josep M.
Arús, Pere
Issue Date: 2020
Citation: The Plant Journal, vol. 101, pp. 455-472, (2020)
Abstract: We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein-coding genes and 6,747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (P. persica) diverged around 5.88 Mya. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions/kb). However, they also exhibit a high 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 seems markedly 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 and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in 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.
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