Pyrus betulifolia Genome v1.0 Assembly & Annotation

Overview
Analysis NamePyrus betulifolia Genome v1.0 Assembly & Annotation
MethodFalcon,Canu and HGAP3 (Falcon(v0.3.0),Canu (v1.6))
SourcePyrus betulifolia Genome v1.0 Assembly & Annotation
Date performed2019-09-03

Summary

China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia‐Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi‐C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein‐coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide‐binding site (NBS)‐type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR‐NBS‐LRR (TNL)‐type genes, which represented the greatest number of TNL‐type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism‐related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high‐quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.

Publication

Dong X, Wang Z, Tian L, Zhang Y, Qi D, Huo H, Xu J, Li Z, Liao R, Shi M, Ali WS, Liu C, Zhang S, Tian Z, Cao Y. De novo assembly of a wild pear (Pyrus betuleafolia) genome. Plant biotechnology journal. 2019 Aug 01. https://doi.org/10.1111/pbi.13226. Journal | GDR

Assembly

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

Downloads

Chromosomes (FASTA file) pbetulifolia-v1.0.fasta.gz

 

Gene Predictions

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

Downloads

Protein sequences  (FASTA file) pbetulifolia-v1.0.proteins.fasta.gz
CDS (FASTA file) pbetulifolia-v1.0.CDs.fasta.gz
Genes (GFF3 file) pbetulifolia-v1.0.genes.gff3.gz

 

Downloads

All assembly and annotation files are available for download by selecting the desired data type in the right-hand "Resources" side bar.  Each data type page will provide a description of the available files and links do download.  Alternatively, you can use the FTP repository for bulk download.

Homology

Homology of the Pyrus betulifolia 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 (TAIR10), 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 betulifolia v1.0 proteins with NCBI nr homologs (EXCEL file) pbetulifolia-v1.0_vs_nr.xlsx.gz
Pyrus betulifolia v1.0 proteins with NCBI nr (FASTA file) pbetulifolia-v1.0_vs_nr_hit.fasta.gz
Pyrus betulifolia v1.0 proteins without NCBI nr (FASTA file) pbetulifolia-v1.0_vs_nr_noHit.fasta.gz
Pyrus betulifolia v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pbetulifolia-v1.0_vs_arabidopsis.xlsx.gz
Pyrus betulifolia v1.0 proteins with arabidopsis (Araport11) (FASTA file) pbetulifolia-v1.0_vs_arabidopsis_hit.fasta.gz
Pyrus betulifolia v1.0 proteins without arabidopsis (Araport11) (FASTA file) pbetulifolia-v1.0_vs_arabidopsis_noHit.fasta.gz
Pyrus betulifolia v1.0 proteins with SwissProt homologs (EXCEL file) pbetulifolia-v1.0_vs_swissprot.xlsx.gz
Pyrus betulifolia v1.0 proteins with SwissProt (FASTA file) pbetulifolia-v1.0_vs_swissprot_hit.fasta.gz
Pyrus betulifolia v1.0 proteins without SwissProt (FASTA file) pbetulifolia-v1.0_vs_swissprot_noHit.fasta.gz
Pyrus betulifolia v1.0 proteins with TrEMBL homologs (EXCEL file) pbetulifolia-v1.0_vs_trembl.xlsx.gz
Pyrus betulifolia v1.0 proteins with TrEMBL (FASTA file) pbetulifolia-v1.0_vs_trembl_hit.fasta.gz
Pyrus betulifolia v1.0 proteins without TrEMBL (FASTA file) pbetulifolia-v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation for the Pyrus betulifolia genome v1.0 are available for download below. The Pyrus betulifolia 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 pbetulifolia-v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pbetulifolia-v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pbetulifolia-v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pbetulifolia-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 betulifolia 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 Pyrus betulifolia_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Pyrus betulifolia_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pyrus betulifolia_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pyrus betulifolia_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pyrus betulifolia_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pyrus betulifolia_v1.0_rubus_GDR_reftransV2