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 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chrom...

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Detalles Bibliográficos
Autores: Alioto, Tyler S., Alexiou, Konstantinos G., Bardil, Amélie, Barteri, Fabio, Castanera, Raúl, Cruz, Fernando, Dhingra, Amit, Duval, Henri, Fernández i Marti, Ángel, Frías, Leonor, Galán, Beatriz, García, José Luis, Howad, Werner, Gómez-Garrido, Jèssica, Gut, Marta, Julca, Irene, Morata, Jordi, Puigdomènech, Pere, Ribeca, Paolo, Rubio-Cabetas, María José, Vlasova, Anna, Wirthensohn, Michelle G., García-Mas, Jordi, Gabaldón, Toni, Casacuberta, Josep M., Arús, Pere
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/191606
Acceso en línea:http://hdl.handle.net/10261/191606
Access Level:acceso abierto
Palabra clave:Almonds
Variability
Indels
Transposable elements
Crop evolution
Prunus
Rosaceous crops
Descripción
Sumario: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 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein-coding genes and 6,747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (P. persica) diverged around 5.88 Mya. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions/kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). TEs 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. TEs 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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