Gossypium raimondii (D5) 'GPD5lz' genome HAU_v1

Overview
Analysis NameGossypium raimondii (D5) 'GPD5lz' genome HAU_v1
MethodCanu ( v1.3)
SourceOxford Nanopore; Illumina ASM2569854 v1
Date performed2023-02-01

 

Global statistics

Genomic feature Gossypium arboreum 'GPD5lz' HAU.v1 (NCBI: ASM2569854v1)
Total sequence length 751,041,726
Total ungapped length 751,033,826
Gaps between scaffolds 0
Number of scaffolds 289
Scaffold N50 57,716,579
Scaffold L50 7
Number of contigs 368
Contig N50 17,043,680
Contig L50 18
Total number of chromosomes and plasmids 65
Number of component sequences (WGS or clone) 268

 

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 raimondii (D5) genome. This file belongs to the HAU G. raimondii 'GPD5lz' Assembly v1.0.

Chromosomes & scaffolds (FASTA format) G.raimondii_HAU.D5lz.fa.gz
G.raimondii_HAU.D5lz.fa.gz.md5
Functional Analysis

Functional annotation files for the Gossypium raimondii GPD5lz HAU Genome v1.0 are available for download below. The Gossypium raimondii GPD5lz HAU Genome v1.0 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 D5_GPD5lz_v1.0genes2GO.xlsx.gz
IPR assignments from InterProScan D5_GPD5lz_v1.0genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs D5_GPD5lz_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways D5_GPD5lz_v1.0_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium raimondii (D5) genome. These files belong to the HAU G. raimondii 'GPD5lz' Assembly v1.0.

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

Homology of the Gossypium raimondii GPD5lz HAU 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 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.raimondii GPD5lz HAU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) D5_GPD5lz_v1.0vs_nr.xlsx.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with NCBI nr (FASTA file) D5_GPD5lz_v1.0vs_nr_hit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins without NCBI nr (FASTA file) D5_GPD5lz_v1.0vs_nr_noHit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) D5_GPD5lz_v1.0vs_tair.xlsx.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) D5_GPD5lz_v1.0vs_tair_hit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) D5_GPD5lz_v1.0vs_tair_noHit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with SwissProt homologs (EXCEL file) D5_GPD5lz_v1.0vs_swissprot.xlsx.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with SwissProt (FASTA file) D5_GPD5lz_v1.0vs_swissprot_hit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins without SwissProt (FASTA file) D5_GPD5lz_v1.0vs_swissprot_noHit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) D5_GPD5lz_v1.0vs_trembl.xlsx.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins with TrEMBL (FASTA file) D5_GPD5lz_v1.0vs_trembl_hit.fasta.gz
G.raimondii GPD5lz HAU Genome v1.0 proteins without TrEMBL (FASTA file) D5_GPD5lz_v1.0vs_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 raimondii HAU me 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.raimondii_D5_lz_HAU_SNP
CottonGen RFLP markers mapped to genome G.raimondii_D5_lz_HAU_RFLP
CottonGen SSR markers mapped to genome G.raimondii_D5_lz_HAU_SSR
CottonGen InDel markers mapped to genome G.raimondii_D5_lz_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. raimondii 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.raimondii_D5_lz_HAU_g.arboreum_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.raimondii_D5_lz_HAU_g.hirsutum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.raimondii_D5_lz_HAU_g.barbadense_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.raimondii_D5_lz_HAU_g.raimondii_cottongen_reftransV1