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

 

Non-coding RNA
Non coding RNA 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.  The available files are in GFF3 format.
 
Ribosomal RNA aligned to genome G.raimondii_BGI-CGP_v1.0_rRNA.gff3.gz
snRNA aligned to genome G.raimondii_BGI-CGP_v1.0_snRNA.gff3.gz
tRNA aligned to genome G.raimondii_BGI-CGP_v1.0_tRNA.gff3.gz
miRNA aligned to genome  G.raimondii_BGI-CGP_v1.0_miRNA.gff3.gz

 

Repeats
Repeats for the G. raimondii assembly were identified for the original genome assembly. Details can be found in the Nature Genetics paper by Wang et al., 2012.  The available files are in GFF3 format.
 
De novo repeats G.raimondii_BGI-CGP_v1.0_denovo.gff.gz
Repeats identified using RepeatMasker ProteinMask G.raimondii_BGI-CGP_v1.0_proteinmask.gff.gz
Repeats identified using RepeatMasker G.raimondii_BGI-CGP_v1.0_repeatmasker.gff.gz
Repeats identified using 'trf' G.raimondii_BGI-CGP_v1.0_trf.gff.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. raimondii genome assembly.  Markers required 90% identify over 97% of their length.  For SSRs & RFLPs, gap size was restricted to 1000bp or less with less than 2 gaps.  For dbSNPs, CottonGen SNPs 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.
 
NCBI cotton dbSNPs mapped to genome G.raimondii_BGI-CGP_v1.0_dbSNP.gff.gz
CottonGen RFLP markers mapped to genome G.raimondii_BGI-CGP_v1.0_RFLP.gff.gz
CottonGen SSR markers mapped to genome G.raimondii_BGI-CGP_v1.0_SSR_update1.gff.gz
CottonGen SNP markers mapped to genome G.raimondii_BGI-CGP_v1.0_CTG_SNP.gff.gz
CottonGen InDel markers mapped to genome G.raimondii_BGI-CGP_v1.0_CTG_Indels.gff.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. raimondii 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.raimondii_BGI-CGP_v1.0_dbEST.gff.gz
dbEST for G. arboreum G.raimondii_BGI-CGP_v1.0_dbEST_G-arboreum.gff.gz
dbEST for G. barbadense G.raimondii_BGI-CGP_v1.0_dbEST_G-barbadense.gff.gz
dbEST for G. herbaceum G.raimondii_BGI-CGP_v1.0_dbEST_G-herbaceum.gff.gz
dbEST for G. hirsutum G.raimondii_BGI-CGP_v1.0_dbEST_G-hirsutum.gff.gz
dbEST for G. raimondii G.raimondii_BGI-CGP_v1.0_dbEST_G-raimondii.gff.gz
mRNA from NCBI for all Gossypium G.raimondii_BGI-CGP_v1.0_NCBI-mRNA.gff.gz
CottonGen unigene v1.0 G.raimondii_BGI-CGP_v1.0_cottongen-unigenes.gff.gz
J. Udall 2012 Unigene contigs G.raimondii_BGI-CGP_v1.0_Udall2012-unigenes.gff.gz
PlantGDB Gossypium unigenes G.raimondii_BGI-CGP_v1.0_PlantGDB_Gossypium.gff.gz
PlantGDB G. arboreum unigenes G.raimondii_BGI-CGP_v1.0_PlantGDB_arboreum.gff.gz
PlantGDB G. barbadense unigenes G.raimondii_BGI-CGP_v1.0_PlantGDB_barbadense.gff.gz
PlantGDB G. hirsutum unigenes G.raimondii_BGI-CGP_v1.0_PlantGDB_hirsutum.gff.gz
PlantGDB G. raimondii unigenes G.raimondii_BGI-CGP_v1.0_PlantGDB_raimondii.gff.gz

 

Protein Homology
Protein homology was performed by the CottonGen Team of Main Bioinformatics Lab at WSU. Proteins from the G. raimondii assembly  were mapped against proteins from other genomes and databases using blastp with an e-value cutoff of 1e-6.  Only the best 10 matches were kept.   The available files are in Excel 2007 format.
 
Cacao theobroma v0.9 proteins G.raimondii_BGI-CGP_v1.0_vs_Cacao.xlsx
Arabidopsis thaliana TAIR10 proteins G.raimondii_BGI-CGP_v1.0_vs_TAIR10.xlsx
Oryza sativa MSU v7.0 proteins G.raimondii_BGI-CGP_v1.0_vs_Rice.xlsx
Poplar trichocarpa v2.0 proteins G.raimondii_BGI-CGP_v1.0_vs_Poplar.xlsx
Vitis vinifera proteins G.raimondii_BGI-CGP_v1.0_vs_Grape.xlsx
Prunus persica v1.0 proteins G.raimondii_BGI-CGP_v1.0_vs_Peach.xlsx
Fragaria vesca v1.0 proteins G.raimondii_BGI-CGP_v1.0_vs_Strawberry.xlsx
Uniprot SwissProt (Oct 2012) proteins G.raimondii_BGI-CGP_v1.0_vs_SwissProt.xlsx
Uniprot TrEMBL (Oct 2012) proteins G.raimondii_BGI-CGP_v1.0_vs_TrEMBL.xlsx
NCBI nr protein homology (Oct 2012) G.raimondii_BGI-CGP_v1.0_vs_nr.xlsx

 

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