Prunus persica Zhongyoutao 14 Genome v1.0 Assembly & Annotation

Overview
Analysis NamePrunus persica Zhongyoutao 14 Genome v1.0 Assembly & Annotation
MethodCANU (1.9)
SourcePacbio
Date performed2022-03-03

Publication

Lian X, Zhang H, Jiang C, Gao F, Yan L, Zheng X, Cheng J, Wang W, Wang X, Ye X, Li J, Zhang L, Li Z, Tan B, Feng J. De novo chromosome-level genome of a semi-dwarf cultivar of Prunus persica identifies the aquaporin PpTIP2 as responsible for temperature-sensitive semi-dwarf trait and PpB3-1 for flower type and size.. Plant biotechnology journal. 2021 Dec 17.

Abstract

Peach (Prunus persica) is one of the most important fruit crops globally, but its cultivation can be hindered by large tree size. 'Zhongyoutao 14' (CN14) is a temperature-sensitive semi-dwarf (TSSD) cultivar which might be useful as breeding stock. The genome of CN14 was sequenced and assembled de novo using single-molecule real-time sequencing and chromosome conformation capture assembly. A high-quality genome was assembled and annotated, with 228.82 Mb mapped to eight chromosomes. Eighty-six re-sequenced F1 individuals and 334 previously re-sequenced accessions were used to identify candidate genes controlling TSSD and flower type and size. An aquaporin tonoplast intrinsic protein (PpTIP2) was a strong candidate gene for control of TSSD. Sequence variations in the upstream regulatory region of PpTIP2 correlated with different transcriptional activity at different temperatures. PpB3-1, a candidate gene for flower type (SH) and flower size, contributed to petal development and promoted petal enlargement. The locus of another twelve agronomic traits were identified through genome-wide association study. Most of these loci exhibited consistent and precise association signals, except for flesh texture and flesh adhesion. A 6015-bp insertion in exon 3 and a 26-bp insertion upstream of PpMYB25 were associated with fruit hairless. Along with a 70.5-Kb gap at the F-M locus in CN14, another two new alleles were identified in peach accessions. Our findings will not only promote genomic research and agronomic breeding in peach, but also provide a foundation for the peach pan-genome.

Homology

Homology of the Prunus persica Zhongyoutao 14 Genome v1.0 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 persica v1.0 proteins with NCBI nr homologs (EXCEL file) ppersica_Zhongyoutao14_v1.0_vs_nr.xlsx.gz
Prunus persica v1.0 proteins with NCBI nr (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_nr_hit.fasta.gz
Prunus persica v1.0 proteins without NCBI nr (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_nr_noHit.fasta.gz
Prunus persica v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) ppersica_Zhongyoutao14_v1.0_vs_arabidopsis.xlsx.gz
Prunus persica v1.0 proteins with arabidopsis (Araport11) (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_arabidopsis_hit.fasta.gz
Prunus persica v1.0 proteins without arabidopsis (Araport11) (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_arabidopsis_noHit.fasta.gz
Prunus persica v1.0 proteins with SwissProt homologs (EXCEL file) ppersica_Zhongyoutao14_v1.0_vs_swissprot.xlsx.gz
Prunus persica v1.0 proteins with SwissProt (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_swissprot_hit.fasta.gz
Prunus persica v1.0 proteins without SwissProt (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_swissprot_noHit.fasta.gz
Prunus persica v1.0 proteins with TrEMBL homologs (EXCEL file) ppersica_Zhongyoutao14_v1.0_vs_trembl.xlsx.gz
Prunus persica v1.0 proteins with TrEMBL (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_trembl_hit.fasta.gz
Prunus persica v1.0 proteins without TrEMBL (FASTA file) ppersica_Zhongyoutao14_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Prunus persica Zhongyoutao 14 Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) pp_Zhongyoutao14_v1.0.fasta.gz

 

Gene Predictions

The Prunus persica Zhongyoutao 14 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) pp_Zhongyoutao14_v1.0.proteins.fasta.gz
CDS  (FASTA file) pp_Zhongyoutao14_v1.0.cds.fasta.gz
Gene sequences  (FASTA file) pp_Zhongyoutao14_v1.0.genes.fasta.gz
Genes (GFF3 file) pp_Zhongyoutao14_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Prunus persica Zhongyoutao 14 Genome v1.0 are available for download below. The Prunus persica Genome v1.0 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 ppersica_Zhongyoutao14_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan ppersica_Zhongyoutao14_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways ppersica_Zhongyoutao14_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs ppersica_Zhongyoutao14_v1.0_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 persica 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 ppersica_Zhongyoutao14_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 ppersica_Zhongyoutao14_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 ppersica_Zhongyoutao14_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 ppersica_Zhongyoutao14_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 ppersica_Zhongyoutao14_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 ppersica_Zhongyoutao14_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 ppersica_Zhongyoutao14_v1.0_pyrus_GDR_reftransV1