Pyrus pyrifolia Cuiguan Whole Genome v1.0 Assembly & Annotation

Overview
Analysis NamePyrus pyrifolia Cuiguan Whole Genome v1.0 Assembly & Annotation
MethodCanu (1.5)
SourcePacBio 124.6
Date performed2021-09-03

Publication

Gao Y, Yang Q, Yan X, Wu X, Yang F, Li J, Wei J, Ni J, Ahmad M, Bai S, and Teng Y. High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy. Hortic Res 8, 197 (2021)

Abstract

Dormancy-associated MADS-box (DAM) genes serve as crucial regulators of the endodormancy cycle in rosaceous plants. Although pear DAM genes have been identified previously, the lack of a high-quality reference genome and techniques to study gene function have prevented accurate genome-wide analysis and functional verification of such genes. Additionally, the contribution of other genes to the regulation of endodormancy release remains poorly understood. In this study, a high-quality genome assembly for 'Cuiguan' pear (Pyrus pyrifolia), which is a leading cultivar with a low chilling requirement cultivated in China, was constructed using PacBio and Hi-C technologies. Using this genome sequence, we revealed that pear DAM genes were tandemly clustered on Chr8 and Chr15 and were differentially expressed in the buds between 'Cuiguan' and the high-chilling-requirement cultivar 'Suli' during the dormancy cycle. Using a virus-induced gene silencing system, we determined the repressive effects of DAM genes on bud break. Several novel genes potentially involved in the regulation of endodormancy release were identified by RNA sequencing and H3K4me3 chromatin immunoprecipitation sequencing analyses of 'Suli' buds during artificial chilling using the new reference genome. Our findings enrich the knowledge of the regulatory mechanism underlying endodormancy release and chilling requirements and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.

Homology Analysis

Homology of the Pyrus pyrifolia Cuiguan 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 2018-05) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Pyrus pyrifolia v1.0 proteins with NCBI nr homologs (EXCEL file) ppyrifolia_Cuiguan_v1.0_vs_nr.xlsx.gz
Pyrus pyrifolia v1.0 proteins with NCBI nr (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_nr_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without NCBI nr (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_nr_noHit.fasta.gz
Pyrus pyrifolia v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) ppyrifolia_Cuiguan_v1.0_vs_arabidopsis.xlsx.gz
Pyrus pyrifolia v1.0 proteins with arabidopsis (Araport11) (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_arabidopsis_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without arabidopsis (Araport11) (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_arabidopsis_noHit.fasta.gz
Pyrus pyrifolia v1.0 proteins with SwissProt homologs (EXCEL file) ppyrifolia_Cuiguan_v1.0_vs_swissprot.xlsx.gz
Pyrus pyrifolia v1.0 proteins with SwissProt (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_swissprot_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without SwissProt (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_swissprot_noHit.fasta.gz
Pyrus pyrifolia v1.0 proteins with TrEMBL homologs (EXCEL file) ppyrifolia_Cuiguan_v1.0_vs_trembl.xlsx.gz
Pyrus pyrifolia v1.0 proteins with TrEMBL (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_trembl_hit.fasta.gz
Pyrus pyrifolia v1.0 proteins without TrEMBL (FASTA file) ppyrifolia_Cuiguan_v1.0_vs_trembl_noHit.fasta.gz

 

Assembly

The Pyrus pyrifolia Cuiguan Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) ppyrifolia_Cuiguan_v1.0.fasta.gz

 

Gene Predictions

The Pyrus pyrifolia Cuiguan v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) ppyrifolia_Cuiguan_v1.0.proteins.fasta.gz
CDS  (FASTA file) ppyrifolia_Cuiguan_v1.0.cds.fasta.gz
RNA sequences  (FASTA file) ppyrifolia_Cuiguan_v1.0.rnas.fasta.gz
Genes (GFF3 file) ppyrifolia_Cuiguan_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Pyrus pyrifolia Cuiguan Genome v1.0 are available for download below. The Pyrus pyrifolia 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 ppyrifolia_Cuiguan_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan ppyrifolia_Cuiguan_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways ppyrifolia_Cuiguan_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs ppyrifolia_Cuiguan_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 Pyrus pyrifolia 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 ppyrifolia_Cuiguan_v1.0_f.x.ananassa_GDR_reftransV1
fragaria avium GDR RefTrans v1 ppyrifolia_Cuiguan_v1.0_p.avium_GDR_reftransV1
fragaria persica GDR RefTrans v1 ppyrifolia_Cuiguan_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 ppyrifolia_Cuiguan_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 ppyrifolia_Cuiguan_v1.0_rubus_GDR_reftransV2
Malus_x_domestica GDR RefTrans v1 ppyrifolia_Cuiguan_v1.0_m.x.domestica_GDR_reftransV1
Pyrus GDR RefTrans v1 ppyrifolia_Cuiguan_v1.0_pyrus_GDR_reftransV1