Gossypium arboreum (A2) Genome BGI Assembly v2.0 & Annotation v1.0

Genome Overview
Analysis NameGossypium arboreum (A2) Genome BGI Assembly v2.0 & Annotation v1.0
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. 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 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
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
Assembly (scaffolds only)  (FASTA format) G.arboreum_BGI-A2_scaffolds_only.fas.gz

 

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. arboreum 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 GBrowse.
 
CottonGen SNP markers mapped to genome G.arboreum_BGI-CGP_v1.0_SNP.gff3.gz
CottonGen RFLP markers mapped to genome G.arboreum_BGI-CGP_v1.0_RFLP.gff3.gz
CottonGen SSR markers mapped to genome G.arboreum_BGI-CGP_v1.0_SSR.gff3.gz
CottonGen InDel markers mapped to genome G.arboreum_BGI-CGP_v1.0_CTG_Indels.gff3.gz

 

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 90% identify were preserved.  The available files are in GFF3 format.

 

dbEST for all Gossypium G.arboreum_BGI-CGP_v1.0_dbEST.gff3.gz
dbEST for G. arboreum G.arboreum_BGI-CGP_v1.0_dbEST_G-arboreum.gff3.gz
dbEST for G. barbadense G.arboreum_BGI-CGP_v1.0_dbEST_G-barbadense.gff3.gz
dbEST for G. herbaceum G.arboreum_BGI-CGP_v1.0_dbEST_G-herbaceum.gff3.gz
dbEST for G. hirsutum G.arboreum_BGI-CGP_v1.0_dbEST_G-hirsutum.gff3.gz
dbEST for G. raimondii G.arboreum_BGI-CGP_v1.0_dbEST_G-raimondii.gff3.gz
Unigene from NCBI for all Gossypium G.arboreum_BGI-CGP_v1.0_NCBI-unigenes.gff3.gz
Unigene from NCBI for  G. hirsutum G.arboreum_BGI-CGP_v1.0_NCBI_G-hirsutum-unigene.gff3.gz
Unigene from NCBI for  G. raimondii G.arboreum_BGI-CGP_v1.0_NCBI_G-raimondii-unigene.gff3.gz
CottonGen unigene v1.0 G.arboreum_BGI-CGP_v1.0_cottongen-unigenes.gff3.gz
J. Udall 2012 Unigene contigs G.arboreum_BGI-CGP_v1.0_Udall2012-unigenes.gff3.gz
J. Udall 2012 Unigene contigs (CDS) G.arboreum_BGI-CGP_v1.0_Udall2012-unigenes_cds.gff3.gz
PlantGDB Gossypium unigenes G.arboreum_BGI-CGP_v1.0_PlantGDB_Gossypium.gff3.gz
PlantGDB G. arboreum unigenes G.arboreum_BGI-CGP_v1.0_PlantGDB_arboreum.gff3.gz
PlantGDB G. barbadense unigenes G.arboreum_BGI-CGP_v1.0_PlantGDB_barbadense.gff3.gz
PlantGDB G. hirsutum unigenes G.arboreum_BGI-CGP_v1.0_PlantGDB_hirsutum.gff3.gz
PlantGDB G. raimondii unigenes G.arboreum_BGI-CGP_v1.0_PlantGDB_raimondii.gff3.gz
TIGR CGI unigenes G.arboreum_BGI-CGP_v1.0_TIGR_CGI.gff3.gz

 

Protein Alignments
Protein alignments available below were performed by the CottonGen Team of the Main Bioinformatics Lab at WSU.  The alignment tool 'exonerate' was used to map protein sequences onto the G. arboreum   JGI v2.0 genome.  Only alignments with a percent identity of 90% were retained.
 

 

Protein Homology
Protein homology was performed by the CottonGen Team of Main Bioinformatics Lab at WSU. Proteins from the G. arboreum assembly  were mapped against proteins from other genomes and databases using blastp with an e-value cutoff of 1e-6.  Only the best match was kept.   The available files are in Excel 2007 format.
 
Cacao theobroma v0.9 proteins G.arboreum_BGI-CGP_v1.0_vs_Cacao.xlsx
Arabidopsis thaliana TAIR10 proteins G.arboreum_BGI-CGP_v1.0_vs_TAIR10.xlsx
Oryza sativa MSU v7.0 proteins G.arboreum_BGI-CGP_v1.0_vs_Rice.xlsx
Poplar trichocarpa v2.0 proteins G.arboreum_BGI-CGP_v1.0_vs_Poplar.xlsx
Vitis vinifera proteins G.arboreum_BGI-CGP_v1.0_vs_Grape.xlsx
Glycine max v1.0 proteins G.arboreum_BGI-CGP_v1.0_vs_Soybean.xlsx
Uniprot SwissProt (Oct 2012) proteins G.arboreum_BGI-CGP_v1.0_vs_SwissProt.xlsx
Uniprot TrEMBL (Oct 2012) proteins G.arboreum_BGI-CGP_v1.0_vs_TrEMBL.xlsx
NCBI nr protein homology (Oct 2012) G.arboreum_BGI-CGP_v1.0_vs_nr.xlsx

 

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.
 

 

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

 

Downloads

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