Pyrus bretschneideri ‘DangshanSuli’ Genome Assembly v1.1

Overview
Analysis NamePyrus bretschneideri ‘DangshanSuli’ Genome Assembly v1.1
MethodALLMAPS
SourceIllumina reads
Date performed2019-01-04

 

Publication

Xue H, Wang S, Yao JL, Deng CH, Wang L, Su Y, Zhang H, Zhou H, Sun M, Li X, Yang J. et al. (2018)  Chromosome level high-density integrated genetic maps improve the Pyrus bretschneideri 'DangshanSuli' v1.0 genome. BMC genomics, 7. (GDR | Journal)

 

Abstract

BACKGROUND:
Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the European (Pyrus communis) and Chinese (P. bretschneideri) pear genomes have not been published in public databases so far.

RESULTS:
To anchor the scaffolds of P. bretschneideri 'DangshanSuli' (DS) v1.0 genome into pseudo-chromosomes, two genetic maps (MH and YM maps) were constructed using half sibling populations of Chinese pear crosses, 'Mantianhong' (MTH) × 'Hongxiangsu' (HXS) and 'Yuluxiang' (YLX) × MTH, from 345 and 162 seedlings, respectively, which were prepared for SNP discovery using genotyping-by-sequencing (GBS) technology. The MH and YM maps, each with 17 linkage groups (LGs), were constructed from 2606 and 2489 SNP markers and spanned 1847 and 1668 cM, respectively, with average marker intervals of 0.7. The two maps were further merged with a previously published genetic map (BD) based on the cross 'Bayuehong' (BYH) × 'Dangshansuli' (DS) to build a new integrated MH-YM-BD map. By using 7757 markers located on the integrated MH-YM-BD map, 898 scaffolds (400.57 Mb) of the DS v1.0 assembly were successfully anchored into 17 pseudo-chromosomes, accounting for 78.8% of the assembled genome size. About 88.31% of them (793 scaffolds) were directionally anchored with two or more markers on the pseudo-chromosomes. Furthermore, the errors in each pseudo-chromosome (especially 1, 5, 7 and 11) were manually corrected and pseudo-chromosomes 1, 5 and 7 were extended by adding 19, 12 and 14 scaffolds respectively in the newly constructed DS v1.1 genome. Synteny analyses revealed that the DS v1.1 genome had high collinearity with the apple genome, and the homologous fragments between pseudo-chromosomes were similar to those found in previous studies. Moreover, the red-skin trait of Asian pear was mapped to an identical locus as identified previously.

CONCLUSIONS:
The accuracy of DS v1.1 genome was improved by using larger mapping populations and merged genetic map. With more than 400 MB anchored to 17 pseudo-chromosomes, the new DS v1.1 genome provides a critical tool that is essential for studies of pear genetics, genomics and molecular breeding.

Assembly

The Pyrus x bretschneideri genome v1.1 file is available in FASTA format.

Downloads

Chromosome (FASTA file) P.bretschneideri_v1.1.chr.fa.gz

 

Gene Predictions

The Pyrus x bretschneideri genome v1.1 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) P.bretschneideri_v1.1.proteins.fasta.gz
Genes (GFF3 file) P.bretschneideri_v1.1.genes.gff3.gz

 

Downloads

All annotation files are available for download by selecting the desired data type in the left-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 x bretschneideri  Genome v1.1 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 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Pyrus x bretschneideri v1.1 proteins with NCBI nr homologs (EXCEL file) P.bretschneideri_v1.1_vs_nr.xlsx.gz
Pyrus x bretschneideri v1.1 proteins with NCBI nr (FASTA file) P.bretschneideri_v1.1_vs_nr_hit.fasta.gz
Pyrus x bretschneideri v1.1 proteins without NCBI nr (FASTA file) P.bretschneideri_v1.1_vs_nr_noHit.fasta.gz
Pyrus x bretschneideri v1.1 proteins with arabidopsis (TAIR10) homologs (EXCEL file) P.bretschneideri_v1.1_vs_tair.xlsx.gz
Pyrus x bretschneideri v1.1 proteins with arabidopsis (TAIR10) (FASTA file) P.bretschneideri_v1.1_vs_tair_hit.fasta.gz
Pyrus x bretschneideri v1.1 proteins without arabidopsis (TAIR10) (FASTA file) P.bretschneideri_v1.1_vs_tair_noHit.fasta.gz
Pyrus x bretschneideri v1.1 proteins with SwissProt homologs (EXCEL file) P.bretschneideri_v1.1_vs_swissprot.xlsx.gz
Pyrus x bretschneideri v1.1 proteins with SwissProt (FASTA file) P.bretschneideri_v1.1_vs_swissprot_hit.fasta.gz
Pyrus x bretschneideri v1.1 proteins without SwissProt (FASTA file) P.bretschneideri_v1.1_vs_swissprot_noHit.fasta.gz
Pyrus x bretschneideri v1.1 proteins with TrEMBL homologs (EXCEL file) P.bretschneideri_v1.1_vs_trembl.xlsx.gz
Pyrus x bretschneideri v1.1 proteins with TrEMBL (FASTA file) P.bretschneideri_v1.1_vs_trembl_hit.fasta.gz
Pyrus x bretschneideri v1.1 proteins without TrEMBL (FASTA file) P.bretschneideri_v1.1_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Pyrus x bretschneideri Genome v1.1 are available for download below. The Pyrus x bretschneideri Genome v1.1 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 P.bretschneideri_v1.1_genes2GO.xlsx.gz
IPR assignments from InterProScan P.bretschneideri_v1.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways P.bretschneideri_v1.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs P.bretschneideri_v1.1_KEGG-pathways.xlsx.gz