Transposons played a major role in the diversification between the closely related almond ( Prunus dulcis ) and peach ( P. persica ) genomes: Results from the almond genome sequence
Transposons played a major role in the diversification between the closely related almond ( Prunus dulcis ) and peach ( P. persica ) genomes: Results from the almond genome sequence
Abstract Combining both short and long-read sequencing, we have estimated the almond Prunus dulcis cv. Texas genome size in 235 Mbp and assembled 227.6 Mb of its sequence. The highly heterozygous compact genome of Texas comprises eight chromosomes, to which we have anchored over 91% of the assembly. We annotated 27,042 protein-coding genes and 6,800 non-coding transcripts. High levels of genetic variability were characterized after resequencing a collection of ten almond accessions. Phylogenomic comparison with the genomes of 16 other close and distant species allowed estimating that almond and peach diverged around 5.88 Mya. Comparison between peach and almond genomes confirmed the high synteny between these close relatives, but also revealed high numbers of presence-absence variants, many attributable to the movement of transposable elements (TEs). The number and distribution of TEs between peach and almond was similar, but the history of TE movement was distinct, with peach having a larger proportion of recent transpositions and almond preserving a higher level of polymorphism in the older TEs. When focusing on specific genes involved in key characters such as the bitter vs. sweet kernel taste and the formation of a fleshy mesocarp, we found that for one gene associated with the biosynthesis of amygdalin that confers the bitter kernel taste, several TEs were inserted in its vicinity only in sweet almond cultivars but not in bitter cultivars and Prunus bitter kernel relatives, including P. webbii, P. mume, and other species like peach and cherry. TE insertions likely to produce affects in the expression of six more genes involved in the formation of the fleshy mesocarp were also identified. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond with respect to peach.
Vlasova Anna、Garcia Jos¨| L.、Cruz Fernando、Howad Werner、Castanera Ra¨2l、Duval Henri、Fern¨￠ndez i Mart¨a ¨￠ngel、Frias Leonor、Gal¨￠n Beatriz、Garrido J¨¨ssica G¨?mez、Gut Marta、Julca Irene、Ribeca Paolo、Wirthensohn Michelle、Garcia-Mas Jordi、Ar¨2s Pere、Barteri Fabio、Alioto Tyler、Puigdom¨¨nech Pere、Rubio Cabetas Mar¨aa Jos¨|、Bardil Am¨|lie、Dhingra Amit、Casacuberta Josep M.、Alexiou Konstantinos、Morata Jordi、Gabald¨?n Toni
Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG)Department of Environmental Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)||Universitat Pompeu Fabra (UPF)IRTA||Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBCentre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBINRA, UR1052, Unit¨| de G¨|n¨|tique et Am¨|lioration des Fruits et L¨|gumes (GAFL)Unidad de Fruticultura||Genome Center, University of CaliforniaCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)||Universitat Pompeu Fabra (UPF)Department of Environmental Biology, Center for Biological Research (CIB-CSIC), Spanish National Research Council (CSIC)CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)||Universitat Pompeu Fabra (UPF)CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)||Universitat Pompeu Fabra (UPF)Universitat Pompeu Fabra (UPF)||Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG)CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)||Universitat Pompeu Fabra (UPF)||The Pirbright InstituteUniversity of Adelaide, Waite Research Institute, School of AgricultureIRTA||Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBIRTA||Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBCentre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBCNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST)||Universitat Pompeu Fabra (UPF)Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBUnidad de FruticulturaCentre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBDepartment of Horticulture, Washington State UniversityCentre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBIRTA||Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBCentre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UBUniversitat Pompeu Fabra (UPF)||Bioinformatics and Genomics Programme. Centre for Genomic Regulation (CRG)||Instituci¨? Catalana de Recerca i Estudis Avan?ats (ICREA)
植物学遗传学园艺
Almondvariabilityindelstransposable elementscrop evolutionPrunusrosaceous crops
Vlasova Anna,Garcia Jos¨| L.,Cruz Fernando,Howad Werner,Castanera Ra¨2l,Duval Henri,Fern¨￠ndez i Mart¨a ¨￠ngel,Frias Leonor,Gal¨￠n Beatriz,Garrido J¨¨ssica G¨?mez,Gut Marta,Julca Irene,Ribeca Paolo,Wirthensohn Michelle,Garcia-Mas Jordi,Ar¨2s Pere,Barteri Fabio,Alioto Tyler,Puigdom¨¨nech Pere,Rubio Cabetas Mar¨aa Jos¨|,Bardil Am¨|lie,Dhingra Amit,Casacuberta Josep M.,Alexiou Konstantinos,Morata Jordi,Gabald¨?n Toni.Transposons played a major role in the diversification between the closely related almond ( Prunus dulcis ) and peach ( P. persica ) genomes: Results from the almond genome sequence[EB/OL].(2025-03-28)[2025-05-24].https://www.biorxiv.org/content/10.1101/662676.点此复制
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