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Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence

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dc.contributor.author Alioto, Tyler
dc.contributor.author Cruz, Fernando
dc.contributor.author Frias, Leonor
dc.contributor.author Gómez Garrido, Jèssica
dc.contributor.author Gut, Marta
dc.contributor.author Julca, Irene
dc.contributor.author Ribeca, Paolo
dc.contributor.author Vlasova, Anna
dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
dc.contributor.author Arús, Pere
dc.date.accessioned 2020-04-28T10:42:54Z
dc.date.available 2020-04-28T10:42:54Z
dc.date.issued 2020
dc.identifier.citation Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F et al. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J. 2020 Jan; 101(2): 455-472. DOI: 10.1111/tpj.14538
dc.identifier.issn 0960-7412
dc.identifier.uri http://hdl.handle.net/10230/44361
dc.description.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 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.
dc.description.sponsorship This research was supported in part by grants from the Spanish Ministry of Economy and Competitiveness (MINECO/FEDER projects AGL2012-40228-C02-01, AGL2015-68329-R, AGL2016-78992-R and RTA2015-00050-00-00), Severo Ochoa Program for Centres of Excellence in R&D 201-2019 SEV-2015-0533 and CERCA Programme-Generalitat de Catalunya. MJR acknowledges grant support from the Spanish Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA) project no. RTA-2014-00062
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Wiley-VCH Verlag
dc.relation.ispartof The Plant Journal. 2020 Jan;101(2):455-72
dc.rights © 2019 Tyler Alioto et al. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Transposons
dc.subject.other Genomes
dc.subject.other Genòmica
dc.title Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1111/tpj.14538
dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/AGL2012-40228-C02-01
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/AGL2015-68329-R
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/AGL2016-78992-R
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/RTA2015-00050-00-00
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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