Pyrus ussuriensis x communis Zhongai 1 v1.0 Whole Genome Assembly & Annotation

Overview
Analysis NamePyrus ussuriensis x communis Zhongai 1 v1.0 Whole Genome Assembly & Annotation
MethodCanu (1.5)
SourceIllumina and PacBio
Date performed2019-12-11

Publication:

Ou C, Wang F, Wang J, Li S, Zhang Y, Fang M, Ma L, Zhao Y, Jiang S. A de novo genome assembly of the dwarfing pear rootstock Zhongai 1. Scientific data. 2019 Nov 25; 6(1):281.

Overview:

'Zhongai 1' [(Pyrus ussuriensis × communis) × spp.] is an excellent pear dwarfing rootstock common in China. It is dwarf itself and has high dwarfing efficiency on most of main Pyrus cultivated species when used as inter-stock. Here we describe the draft genome sequences of 'Zhongai 1' which was assembled using PacBio long reads, Illumina short reads and Hi-C technology. We estimated the genome size is approximately 511.33 Mb by K-mer analysis and obtained a final genome of 510.59 Mb with a contig N50 size of 1.28 Mb. Next, 506.31 Mb (99.16%) of contigs were clustered into 17 chromosomes with a scaffold N50 size of 23.45 Mb. We further predicted 309.86 Mb (60.68%) of repetitive sequences and 43,120 protein-coding genes. The assembled genome will be a valuable resource and reference for future pear breeding, genetic improvement, and comparative genomics among related species. Moreover, it will help identify genes involved in dwarfism, early flowering, stress tolerance, and commercially desirable fruit characteristics.

Homology

Homology of the Pyrus ussuriensis x communis Zhongai 1 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 ussuriensis x communis Zhongai 1 v1.0 proteins with NCBI nr homologs (EXCEL file) pZhongai1_v1.0_vs_nr.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with NCBI nr (FASTA file) pZhongai1_v1.0_vs_nr_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without NCBI nr (FASTA file) pZhongai1_v1.0_vs_nr_noHit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) pZhongai1_v1.0_vs_arabidopsis.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with arabidopsis (Araport11) (FASTA file) pZhongai1_v1.0_vs_arabidopsis_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without arabidopsis (Araport11) (FASTA file) pZhongai1_v1.0_vs_arabidopsis_noHit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with SwissProt homologs (EXCEL file) pZhongai1_v1.0_vs_swissprot.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with SwissProt (FASTA file) pZhongai1_v1.0_vs_swissprot_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without SwissProt (FASTA file) pZhongai1_v1.0_vs_swissprot_noHit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with TrEMBL homologs (EXCEL file) pZhongai1_v1.0_vs_trembl.xlsx.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins with TrEMBL (FASTA file) pZhongai1_v1.0_vs_trembl_hit.fasta.gz
Pyrus ussuriensis x communis Zhongai 1 v1.0 proteins without TrEMBL (FASTA file) pZhongai1_v1.0_vs_trembl_noHit.fasta.gz

 

Download

All assembly and 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 to download.  Alternatively, you can browse all available files on the FTP repository.

Assembly

The Pyrus ussuriensis x communis Zhongai 1 Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) pZhongai1_v1.0.fasta.gz

 

Gene Predictions

The Pyrus ussuriensis x communis Zhongai 1 v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) pZhongai1_v1.0.proteins.fasta.gz
CDS (FASTA file) pZhongai1_v1.0.CDs.fasta.gz
Genes (GFF3 file) pZhongai1_v1.0.genes.gff3.gz

 

Functional Analysis

Functional annotation for the Pyrus ussuriensis x communis Zhongai 1 genome v1.0 are available for download below. The Pyrus ussuriensis x communis Zhongai 1 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 pZhongai1_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan pZhongai1_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways pZhongai1_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs pZhongai1_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 ussuriensis x communis Zhongai 1 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 ussuriensis x communis Zhongai 1_v1.0_f.x.ananassa_GDR_reftransV1
Malus_x_domestica GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_m.x.domestica_GDR_reftransV1
Prunus avium GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_p.avium_GDR_reftransV1
Prunus persica GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_p.persica_GDR_reftransV1
Pyrus GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_p.persica_GDR_reftransV1
Rosa GDR RefTrans v1 Pyrus ussuriensis x communis Zhongai 1_v1.0_rosa_GDR_reftransV1
Rubus GDR RefTrans v2 Pyrus ussuriensis x communis Zhongai 1_v1.0_rubus_GDR_reftransV2