Gossypium arboreum (A2) genome CRI-Updated Assembly v1.0 & Annotation v1.0

Overview
Analysis NameGossypium arboreum (A2) genome CRI-Updated Assembly v1.0 & Annotation v1.0
MethodPacBio long-reads and Hi-C
SourceG. arboreum A2 genome CRI-Updated v1.0-a1.0
Date performed2019-02-17

About the assembly

A new assembly of the Gossypium arboreum genome (cultivated diploid cotton Shixiya1) was reported by the Cotton Research Institute of Chinese Academy of Agricultural Sciences (CRI-CAAS).  The reassembled vesrion is on the basis of PacBio long-reads and Hi-C technologies, and the population structure and genomic divergence trends of 243 diploid cotton accessions was analyzed. A number of candidate loci that may facilitate the genetic improvement of cotton lint production were identified.

142.54 Gb of raw PacBio reads (approximately 77.6-fold genome coverage) was generated by using SMRT sequencing technology and these reads were assembled into 8,223 contigs, producing a 1,710 Mb G. arboreum genome with a contig N50 of 1,100 kb; the longest contig in the new assembly was 12.37 Mb.

Summary of the Updated Assembly Numbers N50 (kb) Longest (Mb) Size (Mb) Percentage of assembly
Contigs 8,223 1,100 12.37 1,710 100
Scaffolds n/a n/a n/a n/a n/a
Anchored and oriented 3,720 730 12.37 1,573 92
Gene annotated 40,960 n/a n/a 123 72
Repeat sequences n/a n/a n/a 1,460 85.39

 

Publication

Du et al. Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits. Nature genetics. 2018 May 07.

Assembly

The chromosomes (pseudomolecules) and scaffolds for G. aboreum genome. These files belong to the CRI Updated Assembly v1.0

Chromosomes & scaffolds (FASTA format) G.arboreum_CRI-A2_assembly_v1.0.fasta.gz
Genes

The predicted gene model, their alignments and proteins for G. aboreum genome. These files belong to the CRI Updated Assembly 1.0 & Annotation 1.0

Predicted gene models with exons (GFF3 format) G.arboreum_CRI-A2_v1.0_a1.0_functional.gff.gz
Coding sequences, CDS (FASTA format) G.arboreum_CRI-A2_v1.0_a1.0_cds.fasta.gz
Protein sequences (FASTA format) G.arboreum_CRI-A2_v1.0_a1.0_pep.fasta.gz
Downloads

All 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 do download.  Alternatively, you can use the FTP repository for bulk download.

Homology

Homology of the Gossypium arboreum CRI 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 (TAIR10), UniProtKB/SwissProt (Release 2018-04), and UniProtKB/TrEMBL (Release 2018-04) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

Gossypium arboreum CRI v1.0 proteins with NCBI nr homologs (EXCEL file) A2_CRI_v1.0_vs_nr.xlsx.gz
Gossypium arboreum CRI v1.0 proteins with NCBI nr (FASTA file) A2_CRI_v1.0_vs_nr_hit.fasta.gz
Gossypium arboreum CRI v1.0 proteins without NCBI nr (FASTA file) A2_CRI_v1.0_vs_nr_noHit.fasta.gz
Gossypium arboreum CRI v1.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) A2_CRI_v1.0_vs_tair.xlsx.gz
Gossypium arboreum CRI v1.0 proteins with arabidopsis (TAIR10) (FASTA file) A2_CRI_v1.0_vs_tair_hit.fasta.gz
Gossypium arboreum CRI v1.0 proteins without arabidopsis (TAIR10) (FASTA file) A2_CRI_v1.0_vs_tair_noHit.fasta.gz
Gossypium arboreum CRI v1.0 proteins with SwissProt homologs (EXCEL file) A2_CRI_v1.0_vs_swissprot.xlsx.gz
Gossypium arboreum CRI v1.0 proteins with SwissProt (FASTA file) A2_CRI_v1.0_vs_swissprot_hit.fasta.gz
Gossypium arboreum CRI v1.0 proteins without SwissProt (FASTA file) A2_CRI_v1.0_vs_swissprot_noHit.fasta.gz
Gossypium arboreum CRI v1.0 proteins with TrEMBL homologs (EXCEL file) A2_CRI_v1.0_vs_trembl.xlsx.gz
Gossypium arboreum CRI v1.0 proteins with TrEMBL (FASTA file) A2_CRI_v1.0_vs_trembl_hit.fasta.gz
Gossypium arboreum CRI v1.0 proteins without TrEMBL (FASTA file) A2_CRI_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Gossypium arboreum CRI Genome v1.0 are available for download below. The Gossypium arboreumCRI Genome 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 A2_CRI_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan A2_CRI_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways A2_CRI_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs A2_CRI_v1.0_KEGG-pathways.xlsx.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 are linked to JBrowse.
 
CottonGen SNP markers mapped to genome G.arboreum_A2-CRI_v1.0_SNP
CottonGen InDel markers mapped to genome G.arboreum_A2-CRI_v1.0_InDel
CottonGen RFLP markers mapped to genome G.arboreum_A2-CRI_v1.0_RFLP
CottonGen SSR markers mapped to genome G.arboreum_A2-CRI_v1.0_SSR

 

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.

 

G. arboreum CottonGen RefTrans v1 G.arboreum_CRI_v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.arboreum_CRI_v1.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.arboreum_CRI_v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.arboreum_CRI_v1.0_g.raimondii_cottongen_reftransV1