Gossypium arboreum (A2) 'SXY1' genome HAU_v2

Overview
Analysis NameGossypium arboreum (A2) 'SXY1' genome HAU_v2
MethodCanu v. 1.3; Oxford Nanopore; Illumina (Canu v. 1.3)
Source (v2)
Date performed2023-01-30

 

Global statistics

Genomic feature Gossypium arboreum 'ShiXiYa-1' HAU.v2 (NCBI: ASM2569848v2)
Total sequence length 1,621,352,140
Total ungapped length 1,621,329,640
Gaps between scaffolds 0
Number of scaffolds 948
Scaffold N50 129,592,444
Scaffold L50 6
Number of contigs 1,173
Contig N50 11,691,474
Contig L50 40
Total number of chromosomes and plasmids 15
Number of component sequences (WGS or clone) 948

 

Publication

Wang, M. et al. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat. Genet. 2022 Dec;54(12):1959-1971. doi: 10.1038/s41588-022-01237-2. Epub 2022 Dec 6.       .

Assembly

The chromosomes (pseudomolecules) and scaffolds for Gossypium arboreum (A2) genome. This file belongs to the HAU G. arboreum 'ShiXiYa-1' Assembly v2.0.

Chromosomes & scaffolds (FASTA format) G.arboreum_HAU.v2.fa.gz
G.arboreum_HAU.v2.fa.gz.md5
Functional Analysis

Functional annotation files for the Gossypium arboreum HAU Genome v2.0 are available for download below. The Gossypium arboreum HAU Genome v2.0 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_HAU_v2_genes2GO.xlsx.gz
IPR assignments from InterProScan A2_HAU_v2_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs A2_HAU_v2_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways A2_HAU_v2_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium arboreum (A2) genome. These files belong to the HAU G. arboreum 'ShiXiYa-1' Assembly v2.0.

Predicted gene models with exons (GFF3 format) G.arboreum_HAU.v2.gff3.gz
G.arboreum_HAU.v2.gff3.gz.md5
Coding sequences, Transcript (FASTA format) G.arboreum_HAU.v2.transcript.fa.gz
G.arboreum_HAU.v2.transcript.fa.gz.md5
Protein sequences (FASTA format) G.arboreum_HAU.v2.pep.fa.gz
G.arboreum_HAU.v2.pep.fa.gz.md5
Homology

Homology of the Gossypium arboreum HAU Genome v2.0 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 2021-09) and 1e-6  for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

G.arboreum HAU Genome v2.0 proteins with NCBI nr homologs (EXCEL file) A2_HAU_v2_vs_nr.xlsx.gz
G.arboreum HAU Genome v2.0 proteins with NCBI nr (FASTA file) A2_HAU_v2_vs_nr_hit.fasta.gz
G.arboreum HAU Genome v2.0 proteins without NCBI nr (FASTA file) A2_HAU_v2_vs_nr_noHit.fasta.gz
G.arboreum HAU Genome v2.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) A2_HAU_v2_vs_tair.xlsx.gz
G.arboreum HAU Genome v2.0 proteins with arabidopsis (Araport11) (FASTA file) A2_HAU_v2_vs_tair_hit.fasta.gz
G.arboreum HAU Genome v2.0 proteins without arabidopsis (Araport11) (FASTA file) A2_HAU_v2_vs_tair_noHit.fasta.gz
G.arboreum HAU Genome v2.0 proteins with SwissProt homologs (EXCEL file) A2_HAU_v2_vs_swissprot.xlsx.gz
G.arboreum HAU Genome v2.0 proteins with SwissProt (FASTA file) A2_HAU_v2_vs_swissprot_hit.fasta.gz
G.arboreum HAU Genome v2.0 proteins without SwissProt (FASTA file) A2_HAU_v2_vs_swissprot_noHit.fasta.gz
G.arboreum HAU Genome v2.0 proteins with TrEMBL homologs (EXCEL file) A2_HAU_v2_vs_trembl.xlsx.gz
G.arboreum HAU Genome v2.0 proteins with TrEMBL (FASTA file) A2_HAU_v2_vs_trembl_hit.fasta.gz
G.arboreum HAU Genome v2.0 proteins without TrEMBL (FASTA file) A2_HAU_v2_vs_trembl_noHit.fasta.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 Gossypium arboreum HAU v2.0 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_HAU_SNP
CottonGen RFLP markers mapped to genome G.arboreum_A2_HAU_RFLP
CottonGen SSR markers mapped to genome G.arboreum_A2_HAU_SSR
CottonGen InDel markers mapped to genome G.arboreum_A2_HAU_InDel

 

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_A2_HAU_g.arboreum_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.arboreum_A2_HAU_g.hirsutum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.arboreum_A2_HAU_g.barbadense_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.arboreum_A2_HAU_g.raimondii_cottongen_reftransV1