Gossypium raimondii (D5) Draft Genome BGI-CGP v1.0 Assembly & Annotation

Genome Overview
Analysis NameGossypium raimondii (D5) Draft Genome BGI-CGP v1.0 Assembly & Annotation
MethodSOAPdenovo & SSPACE
Source (G. raimondii draft D genome)
Date performed2012-01-11

About the Assembly

The Gossypium raimondii diploid genome is considered the contributor of the D subgenome of economical important tetraploid cotton (Gossypium hirsutum and Gossypium barbadense).  Paired-end reads obtained FROM chado.the Illumina HiSeq 2000 platform were obtained FROM chado.various libraries with different insert sizes.  The assembly was performed using SoapDenovo to generate contigs and SSPACE was used to scaffold the contigs using the paired-end reads. 

The work was performed by researchers FROM chado.the Cotton Research Institute of the Chinese Academy of Agricultural Sciences, the Beijing Genomics Institute (BGI) at Shenzhen, Peking University, USDA-ARS, and the University of Copenhagen

 

 

 Assembly Summary
 Number of pseudomolecules (chromsomes) 13
 Number of scaffolds not in pseudomolecules 4,434
 Number of Gene models 40,976
 Number of miRNA 348
 Number of denovo repeats 753,866
 Number of repeats derived FROM chado.RepBase 178,739

 


Publication
Wang et. al., The draft genome of a diploid cotton Gossypium raimondiiNature Genetics. 44, 1098–1103. 2012 

 

 

 

Assembly

The pseudomolecules (putative chromosomes & scaffolds) for the G. raimondii assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012.

Assembly pseudomolecules (FASTA format) G.raimondii_BGI-CGP_v1.0_pseudomolecules.fasta.gz
Assembly pseudomolecules (chromosomes & scaffolds)  (GFF3 format) G.raimondii_BGI-CGP_v1.0_pseudomolecules.gff3.gz
 

 

Genes

The predicted genes and proteins for the G. raimondii assembly were identified in the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012.
 

Predicted genes coding sequences (CDS)  (FASTA format) G.raimondii_BGI-CGP_v1.0_CDS.fasta.gz
Predicted genes proteins (FASTA format) G.raimondii_BGI-CGP_v1.0_protein.fasta.gz
Predicted genes aligned to genome (GFF3 format) G.raimondii_BGI-CGP_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.raimondii_CGP-BGI_v2.0_SNP
CottonGen RFLP markers mapped to genome G.raimondii_CGP-BGI_v2.0_RFLP
CottonGen SSR markers mapped to genome G.raimondii_CGP-BGI_v2.0_SSR
CottonGen InDel markers mapped to genome G.raimondii_CGP-BGI_v2.0_Indels
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. raimondii 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.raimondii_CGP-BGI_v2.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.raimondii_CGP-BGI_v2.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.raimondii_CGP-BGI_v2.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.raimondii_CGP-BGI_v2.0_g.raimondii_cottongen_reftransV1
Protein Homology
Homology of the Gossypium raimondiiCGP-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.raimondii_CGP-BGI_v1.0_vs_nr.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with NCBI nr (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_nr_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without NCBI nr (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_nr_noHit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) G.raimondii_CGP-BGI_v1.0_vs_Araport11.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with arabidopsis (Araport11) (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_Araport11_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without arabidopsis (Araport11) (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_Araport11_noHit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins with SwissProt homologs (EXCEL file) G.raimondii_CGP-BGI_v1.0_vs_swissprot.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with SwissProt (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_swissprot_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without SwissProt (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_swissprot_noHit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins with TrEMBL homologs (EXCEL file) G.raimondii_CGP-BGI_v1.0_vs_trembl.xlsx.gz
G.arboreum CGP-BGI_v1.0 proteins with TrEMBL (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_trembl_hit.fasta.gz
G.arboreum CGP-BGI_v1.0 proteins without TrEMBL (FASTA file) G.raimondii_CGP-BGI_v1.0_vs_trembl_noHit.fasta.gz
Functional Annotation
G. raimondii 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 CottonGen Team of 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 Kunbo Wang,  Zhiwen Wang,  Fuguang Li,  Wuwei Ye,  Junyi Wang,  Guoli Song,  Zhen Yue,  Lin Cong,  Haihong Shang,  Shilin Zhu,  Changsong Zou,  Qin Li,  Youlu Yuan,  Cairui Lu,  Hengling Wei,  Caiyun Gou,  Zequn Zheng,  Ye Yin,  Xueyan Zhang,  Kun Liu,  Bo Wang,  Chi Song,  Nan Shi,  Russell J Kohel,  Richard G Percy,  John Z Yu,  Yu-Xian Zhu,  Jun Wang  & Shuxun Yu
Title  The draft genome of a diploid cotton Gossypium raimondii
Journal Nature Genetics
Issue 44
Pages 1098-1103
Year 2012

 

Acknowledgements

CottonGen acknowledges with thanks the provision of the draft cotton D genome by Drs. Shuxun Yu, Jun Wang and Yu-Xian Zhu as presented in the Wang et al., 2012 Nature Genetics publication.

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