Prunus ferganensis Whole Genome v2.0 Assembly & Annotation

Overview
Analysis NamePrunus ferganensis Whole Genome v2.0 Assembly & Annotation
MethodALLPATHS-LG
SourceIllumina, PacBio and Hi-C Reads
Date performed2021-09-23

Publication

Pan-genome analyses of peach and its wild relatives provide insights into the genetics of disease resistance and species adaptation. Ke Cao, Zhen Peng, Xing Zhao, Yong Li, Kuozhan Liu, Pere Arus, Shuhan Deng, Weichao Fang, Changwen Chen, Xinwei Wang, Jinlong Wu, Zhangjun Fei. To be submitted to Molecular Plant. Availalbe in bioRxiv.

Abstract

As a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis. Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica. Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis, was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca. We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.

Homology Analysis

Homology of the Prunus ferganensis genome v2.0 proteins was determined by pairwise sequence comparison using the blastp algorithm against various protein databases. An expectation value cutoff less than 1e-9 was used for the NCBI nr (Release 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Prunus ferganensis v2.0 proteins with NCBI nr homologs (EXCEL file) pferganensis_v2.0_vs_nr.xlsx.gz
Prunus ferganensis v2.0 proteins with NCBI nr (FASTA file) pferganensis_v2.0_vs_nr_hit.fasta.gz
Prunus ferganensis v2.0 proteins without NCBI nr (FASTA file) pferganensis_v2.0_vs_nr_noHit.fasta.gz
Prunus ferganensis v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pferganensis_v2.0_vs_arabidopsis.xlsx.gz
Prunus ferganensis v2.0 proteins with arabidopsis (Araport11) (FASTA file) pferganensis_v2.0_vs_arabidopsis_hit.fasta.gz
Prunus ferganensis v2.0 proteins without arabidopsis (Araport11) (FASTA file) pferganensis_v2.0_vs_arabidopsis_noHit.fasta.gz
Prunus ferganensis v2.0 proteins with SwissProt homologs (EXCEL file) pferganensis_v2.0_vs_swissprot.xlsx.gz
Prunus ferganensis v2.0 proteins with SwissProt (FASTA file) pferganensis_v2.0_vs_swissprot_hit.fasta.gz
Prunus ferganensis v2.0 proteins without SwissProt (FASTA file) pferganensis_v2.0_vs_swissprot_noHit.fasta.gz
Prunus ferganensis v2.0 proteins with TrEMBL homologs (EXCEL file) pferganensis_v2.0_vs_trembl.xlsx.gz
Prunus ferganensis v2.0 proteins with TrEMBL (FASTA file) pferganensis_v2.0_vs_trembl_hit.fasta.gz
Prunus ferganensis v2.0 proteins without TrEMBL (FASTA file) pferganensis_v2.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Prunus ferganensis Genome v2.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) pferganensis_v2.0.fasta.gz

 

Gene Predictions

The Prunus ferganensis v2.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) pferganensis_v2.0.proteins.fasta.gz
Genes (GFF3 file) pferganensis_v2.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus ferganensis genome v2.0 are available for download below. The Prunus ferganensis genome v2.0 proteins were analyzed using InterProScan in order to assign InterPro domains and Gene Ontology (GO) terms. Pathways analysis was performed using the KEGG Automatic Annotation Server (KAAS).

Downloads

GO assignments from InterProScan pferganensis_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pferganensis_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pferganensis_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pferganensis_v2.0_KEGG-pathways.xlsx.gz

 

Transcript Alignments
Transcript alignments were performed by the GDR Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Prunus ferganensis genome assembly. Alignments with an alignment length of 97% and 97% identify were preserved. The available files are in GFF3 format.

 

Fragaria x ananassa GDR RefTrans v1 Prunus ferganensis_v2.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Prunus ferganensis_v2.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Prunus ferganensis_v2.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Prunus ferganensis_v2.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Prunus ferganensis_v2.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Prunus ferganensis_v2.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Prunus ferganensis_v2.0_rubus_GDR_reftransV2