Gossypium arboreum (A2) 'SXY1' genome CGP-BGI_v2_a1

Overview
Analysis NameGossypium arboreum (A2) 'SXY1' genome CGP-BGI_v2_a1
MethodSOAPdenovo
Source (G. arboreum A genome)
Date performed2014-05-31

About the Assembly

The Gossypium arboreum diploid genome is a putative contributor of the A subgenome of tetraploid cotton species. A highly homozygous single-seed descendant, derived from 18 successive generations of self-fertilization, of the cultivated diploid cotton Shixiya1 (SXY1) was used for DNA sequencing. Paired-end reads obtained from the Illumina HiSeq 2000 platform were obtained from various libraries of different insert sizes. The assembly was performed using SoapDenovo to generate contigs and scaffolds.

The work was performed by researchers from the Cotton Research Institute (CRI) of the Chinese Academy of Agricultural Sciences, the Beijing Genomics Institute (BGI) at Shenzhen, Peking University, Agricultural University of Hebei, USDA-ARS, the University of Copenhagen, King Adbulaziz University, Macau University of Science and Technology, and University of Hong Kong.

The predicted genes and proteins for the G. arboreum assembly were identified in the original genome assembly, all other annotation was performed by CottonGen.

 

 Summary
 Number of pseudomolecules (chromosomes) 13
 Total scaffolds (≥ 2kb) 7,914
 Number of Gene models 41,330
 Number of miRNA 431
 Number of rRNA 10,464
 Number of tRNA 2,289
 Number of snRNA 7,619

 


Publication
Li et. al., Genome sequence of the cultivated cotton Gossypium arboreumNature Genetics. 46, 567–572. 2014 

 

 

Assembly

The pseudomolecules (putative chromosomes & scaffolds) for the G. arboreum assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Li et al., 2014.

Assembly (chromosomes & scaffolds) (FASTA format) G.arboreum_BGI-A2_assembly.fasta.gz
G.arboreum_BGI-A2_assembly.fasta.gz.md5
Assembly (chromosomes & scaffolds)  (GFF3 format) G.arboreum_BGI-A2_assembly.gff3.gz
Assembly (chromosomes only)  (FASTA format) G.arboreum_BGI-A2_chromosomes_only.fas.gz
G.arboreum_BGI-A2_chromosomes_only.fas.gz.md5
Assembly (scaffolds only)  (FASTA format) G.arboreum_BGI-A2_scaffolds_only.fas.gz

 

Downloads

All assembly and annotation files are available for download by selecting the desired data type in the left-hand side bar.  Each data type page will provide a description of the available files and links to download.

Functional Annotation
G. arboreum proteins were analyzed using InterProScan and the KEGG Automated  Annotation Server (KAAS) in order to assign InterPro domains,  Gene Ontology (GO) terms,  KEGG pathways and KEGG orthologs.  This work was performed by the Main Bioinformatics Lab at Washington State University.  Term assignments to genes are available in compressed text files and KEGG hier files and maps are available for browsing with the KeggHier tool.
 

 

Genes

The predicted genes and proteins for the G. arboreum assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Li et al., 2014.
 

Predicted genes coding sequences (CDS)  (FASTA format) G.arboreum_BGI-A2_v1.0_CDS.fasta.gz
Predicted genes proteins (FASTA format) G.arboreum_BGI-A2_v1.0_protein.fasta.gz
Predicted genes aligned to genome (GFF3 format) G.arboreum_BGI-A2_v1.0_transcripts.gff3.gz

 

Markers
Marker alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map marker sequences from CottonGen to the G. barbadense genome assembly. Markers required 90% identity over 97% of their length. For SSRs & RFLPs, gap size was restricted to 1000bp or less with less than 2 gaps. For dbSNPs and Indels gap size was restricted to 2bp with less than 2 gaps. The available files are in GFF3 format. Markers available in CottonGen and CMap are linked to JBrowse.
 
CottonGen SNP markers mapped to genome G.arboreum_CGP-BGI_v2.0_SNP
CottonGen RFLP markers mapped to genome G.arboreum_CGP-BGI_v2.0_RFLP
CottonGen SSR markers mapped to genome G.arboreum_CGP-BGI_v2.0_SSR
CottonGen InDel markers mapped to genome G.arboreum_CGP-BGI_v2.0_Indels
Protein Homology
Homology of the Gossypium.arboreum BGI_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. 
G.arboreum CGP-BGI_v1.0 proteins with NCBI nr homologs (EXCEL file) G.arboreum-BGI_v1.0_vs_nr.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with NCBI nr (FASTA file) G.arboreum-BGI_v1.0_vs_nr_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without NCBI nr (FASTA file) G.arboreum-BGI_v1.0_vs_nr_noHit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) G.arboreum-BGI_v1.0_vs_tair.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with arabidopsis (Araport11) (FASTA file) G.arboreum-BGI_v1.0_vs_tair_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without arabidopsis (Araport11) (FASTA file) G.arboreum-BGI_v1.0_vs_tair_noHit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins with SwissProt homologs (EXCEL file) G.arboreum-BGI_v1.0_vs_swissprot.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with SwissProt (FASTA file) G.arboreum-BGI_v1.0_vs_swissprot_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without SwissProt (FASTA file) G.arboreum-BGI_v1.0_vs_swissprot_noHit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins with TrEMBL homologs (EXCEL file) G.arboreum-BGI_v1.0_vs_trembl.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with TrEMBL (FASTA file) G.arboreum-BGI_v1.0_vs_trembl_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without TrEMBL (FASTA file) G.arboreum-BGI_v1.0_vs_trembl_noHit.fasta.gz
Publication
Authors Fuguang Li, Guangyi Fan, Kunbo Wang, Fengming Sun, Youlu Yuan, Guoli Song, Qin Li, Zhiying Ma, Cairui Lu, Changsong Zou, Wenbin Chen, Xinming Liang, Haihong Shang, Weiqing Liu, Chengcheng Shi, Guanghui Xiao, Caiyun Gou, Wuwei Ye, Xun Xu, Xueyan Zhang, Hengling Wei, Zhifang Li, Guiyin Zhang, Junyi Wang, Kun Liu, Russell J Kohel, Richard G Percy, John Z Yu, Yu-Xian Zhu, Jun Wang & Shuxun Yu
Title  Genome sequence of the cultivated cotton Gossypium arboreum
Journal Nature Genetics
Issue 46
Pages 567-572
Year 2014

 

Transcript Alignments
Transcript alignments were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the G. arboreum genome assembly. Alignments with an alignment length of 97% and 98% identify were preserved. The available files are in GFF3 format.

 

G. arboreum CottonGen RefTrans v1 G.arboreum_CGP-BGI_v2.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.arboreum_CGP-BGI_v2.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.arboreum_CGP-BGI_v2.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.arboreum_CGP-BGI_v2.0_g.raimondii_cottongen_reftransV1