Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence.
Prunus dulcis
Prunus persica
crop evolution
divergence
genome sequence
indels
seed bitterness
transposable elements
variability
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
01 2020
01 2020
Historique:
received:
11
06
2019
revised:
29
08
2019
accepted:
02
09
2019
pubmed:
19
9
2019
medline:
16
12
2020
entrez:
19
9
2019
Statut:
ppublish
Résumé
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 almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements 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. Transposable elements 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.
Identifiants
pubmed: 31529539
doi: 10.1111/tpj.14538
pmc: PMC7004133
doi:
Substances chimiques
DNA Transposable Elements
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
455-472Informations de copyright
© 2019 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.
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