Prunus mira Whole Genome v2.0 Assembly & Annotation

Overview

Analysis Name Prunus mira Whole Genome v2.0 Assembly & Annotation
Sequencing technology HiFi, Hi-C, Illumina HiSeq X Ten platform
Assembly method Hifiasm (v0.13-r308)
Release Date 2021-09-23
Reference Publication(s)

Cao K, Peng Z, Zhao X, Li Y, Liu K, Arus P, Fang W, Chen C, Wang X, Wu J, Fei Z, Wang L. Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance. BMC Biol. 2022 Jun 13;20(1):139. doi: 10.1186/s12915-022-01342-y.

Abstract

Background: Peach (Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated in temperate and subtropical regions, emerging as an excellent material to study the interaction between plant and environment. During its genus, there are four wild species of peach, all living in harsh environments. For example, one of the wild species, P. mira, originates from the Qinghai-Tibet Plateau (QTP) and exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses in the gene discovery of fruit quality-related traits in peach using previous assembled genome were obtained, genomic basis of the response of these wild species to different geographical environments remains unclear.

Results: To uncover key genes regulating adaptability in different species and analyze the role of genetic variations in resistance formation, we performed de novo genome assembling of four wild relatives of peach (P. persica), P. mira, P. davidiana, P. kansuensis, and P. ferganensis and resequenced 175 peach varieties. The phylogenetic tree showed that the divergence time of P. mira and other wild relatives of peach was 11.5 million years ago, which was consistent with the drastic crustal movement of QTP. Abundant genetic variations were identified in four wild species when compared to P. persica, and the results showed that plant-pathogen interaction pathways were enriched in genes containing small insertions and deletions and copy number variations in all four wild relatives of peach. Then, the data were used to identify new genes and variations regulating resistance. For example, presence/absence variations which result from a hybridization event that occurred between P. mira and P. dulcis enhanced the resistance of their putative hybrid, P. davidiana. Using bulked segregant analysis, we located the nematode resistance locus of P. kansuensis in chromosome 2. Within the mapping region, a deletion in the promoter of one NBS-LRR gene was found to involve the resistance by regulating gene expression. Furthermore, combined with RNA-seq and selective sweeps analysis, we proposed that a deletion in the promoter of one CBF gene was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature.

Conclusions: In general, the reference genomes assembled in the study facilitate our understanding of resistance mechanism of perennial fruit crops, and provide valuable resources for future breeding and improvement.

Assembly statistics

Assembly

The Prunus mira Whole Genome v2.0 Assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Pmi.genome.update.fa.gz

Gene Predictions

The Prunus mira Whole Genome v2.0 genome gene prediction files are available in GFF3 and FASTA format.

Downloads

Genes (GFF3 file) Pmi.update.gff3.gz
CDS sequences (FASTA file) -
Protein sequences (FASTA file) Pmi.update.pep.gz

Functional Analysis

Functional annotation for the Prunus mira Whole Genome v2.0 is available for download below. The proteins were analyzed using InterProScan to assign InterPro domains(Pfam).

Downloads

Domain from InterProScan Prunus_mira_Whole_Genome_v2.0.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