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

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 c...

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Autores: Alioto, Tyler, Cruz, Fernando, Frias, Leonor, Gómez Garrido, Jèssica, Gut, Marta, Julca, Irene, Ribeca, Paolo, Vlasova, Anna, Gabaldón Estevan, Juan Antonio, 1973-, Arús, Pere
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2020
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/44361
Acceso en línea:http://hdl.handle.net/10230/44361
http://dx.doi.org/10.1111/tpj.14538
Access Level:acceso abierto
Palabra clave:Transposons
Genomes
Genòmica
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spelling Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequenceAlioto, TylerCruz, FernandoFrias, LeonorGómez Garrido, JèssicaGut, MartaJulca, IreneRibeca, PaoloVlasova, AnnaGabaldón Estevan, Juan Antonio, 1973-Arús, PereTransposonsGenomesGenòmicaWe 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.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-2014-00062Wiley-VCH Verlag202020202020info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/44361http://dx.doi.org/10.1111/tpj.14538reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésThe Plant Journal. 2020 Jan;101(2):455-72info:eu-repo/grantAgreement/ES/3PN/AGL2012-40228-C02-01info:eu-repo/grantAgreement/ES/1PE/AGL2015-68329-Rinfo:eu-repo/grantAgreement/ES/1PE/AGL2016-78992-Rinfo:eu-repo/grantAgreement/ES/1PE/RTA2015-00050-00-00© 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 citedhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/443612026-05-29T05:05:01Z
dc.title.none.fl_str_mv Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
title Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
spellingShingle Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
Alioto, Tyler
Transposons
Genomes
Genòmica
title_short Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
title_full Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
title_fullStr Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
title_full_unstemmed Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
title_sort Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
dc.creator.none.fl_str_mv Alioto, Tyler
Cruz, Fernando
Frias, Leonor
Gómez Garrido, Jèssica
Gut, Marta
Julca, Irene
Ribeca, Paolo
Vlasova, Anna
Gabaldón Estevan, Juan Antonio, 1973-
Arús, Pere
author Alioto, Tyler
author_facet Alioto, Tyler
Cruz, Fernando
Frias, Leonor
Gómez Garrido, Jèssica
Gut, Marta
Julca, Irene
Ribeca, Paolo
Vlasova, Anna
Gabaldón Estevan, Juan Antonio, 1973-
Arús, Pere
author_role author
author2 Cruz, Fernando
Frias, Leonor
Gómez Garrido, Jèssica
Gut, Marta
Julca, Irene
Ribeca, Paolo
Vlasova, Anna
Gabaldón Estevan, Juan Antonio, 1973-
Arús, Pere
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Transposons
Genomes
Genòmica
topic Transposons
Genomes
Genòmica
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/44361
http://dx.doi.org/10.1111/tpj.14538
url http://hdl.handle.net/10230/44361
http://dx.doi.org/10.1111/tpj.14538
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv The Plant Journal. 2020 Jan;101(2):455-72
info:eu-repo/grantAgreement/ES/3PN/AGL2012-40228-C02-01
info:eu-repo/grantAgreement/ES/1PE/AGL2015-68329-R
info:eu-repo/grantAgreement/ES/1PE/AGL2016-78992-R
info:eu-repo/grantAgreement/ES/1PE/RTA2015-00050-00-00
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley-VCH Verlag
publisher.none.fl_str_mv Wiley-VCH Verlag
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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