Prunus mandshurica CH264_4 Whole Genome v1.0 Assembly & Annotation

Overview

Analysis Name Prunus mandshurica CH264_4 Whole Genome v1.0 Assembly & Annotation
Sequencing technology Long-reads(Oxford Nanopore Technologies or Pacific Biosciences)and Illumina
Assembly method Falcon/Falcon-Unzip/SMARTdenovo
Release Date 2021-03-09
Reference Publication(s)

Groppi A, Liu S, Cornille A, Decroocq S, Bui QT, Tricon D, Cruaud C, Arribat S, Belser C, Marande W, Salse J, Huneau C, Rodde N, Rhalloussi W, Cauet S, Istace B, Denis E, Carrère S, Audergon JM, Roch G, Lambert P, Zhebentyayeva T, Liu WS, Bouchez O, Lopez-Roques C, Serre RF, Debuchy R, Tran J, Wincker P, Chen X, Pétriacq P, Barre A, Nikolski M, Aury JM, Abbott AG, Giraud T, Decroocq V. Population genomics of apricots unravels domestication history and adaptive events. Nat Commun. 2021 Jun 25;12(1):3956. doi: 10.1038/s41467-021-24283-6.

Abstract

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding.

Assembly statistics

Assembly

The Prunus mandshurica CH264_4 Whole Genome v1.0 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Prunus_Mandshurica.fasta.gz

Gene Predictions

The Prunus mandshurica CH264_4 Whole Genome v1.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Prunus_Mandshurica.gff3.gz
CDS sequences (FASTA file) Prunus_Mandshurica_CDS.fasta.gz
Protein sequences (FASTA file) Prunus_Mandshurica_peptide.fasta.gz

Functional Analysis

Functional annotation for the Prunus mandshurica CH264_4 Whole Genome v1.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Prunus_mandshurica.Pfam.tsv.gz

S genes

Prunus S genes Nucleotide

Prunus S genes Protein

© 2023 National Genomics Data Center, China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences