Journal article
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
The Plant journal : for cell and molecular biology, Vol.101(2), pp.455-472
01/2020
Handle:
https://hdl.handle.net/2376/105285
PMCID: PMC7004133
PMID: 31529539
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.
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Details
- Title
- Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
- Creators
- Tyler Alioto - Centro de Regulación GenómicaKonstantinos Alexiou - Centro de Regulación GenómicaAmélie Bardil - Centro de Regulación GenómicaFabio Barteri - Centro de Regulación GenómicaRaúl Castanera - Centro de Regulación GenómicaFernando Cruz - Centro de Regulación GenómicaAmit Dhingra - Centro de Regulación GenómicaHenri Duval - Génétique et Amélioration des Fruits et LégumesAngel Fernandez i Marti - Genome CenterLeonor Frias - Centre for Genomic Regulation [Barcelona]Beatriz Galán - Consejo Superior de Investigaciones Científicas [Spain]José García - Consejo Superior de Investigaciones Científicas [Spain]Werner Howad - Centre for Research in Agricultural GenomicsJèssica Gómez‐Garrido - Centre for Genomic Regulation [Barcelona]Marta Gut - Centre for Genomic Regulation [Barcelona]Irene Julca - Centre for Genomic Regulation [Barcelona]Jordi Morata - Centre for Genomic Regulation [Barcelona]Pere Puigdomènech - Centre for Genomic Regulation [Barcelona]Paolo Ribeca - Centre for Genomic Regulation [Barcelona]María Rubio Cabetas - University of Zaragoza - Universidad de Zaragoza [Zaragoza]Anna Vlasova - Centre for Genomic Regulation [Barcelona]Michelle Wirthensohn - University of AdelaideJordi Garcia‐Mas - Institute of Agrifood Research and TechnologyToni Gabaldón - ICREA Infection Biology LaboratoryJosep Casacuberta - Centre for Research in Agricultural GenomicsPere Arús - Centre for Research in Agricultural Genomics
- Publication Details
- The Plant journal : for cell and molecular biology, Vol.101(2), pp.455-472
- Academic Unit
- Horticulture, Department of
- Publisher
- Wiley
- Identifiers
- 99900546764001842
- Language
- English
- Resource Type
- Journal article