Gossypium herbaceum (A1) 'Mutema' genome WHU_v1

Overview
Analysis NameGossypium herbaceum (A1) 'Mutema' genome WHU_v1
MethodUltra-depth PacBio long-reads and Hi-C technologies
SourceGherbaceum_A1-0076_WHUv3.0rc.genome.standard
Date performed2020-04-04

About the assembly

The first assembly of Gossypium herbaceum genome (variety africanum 'Mutema', A1-0076) was released from the Institute for Advanced Studies, Wuhan University, Wuhan, China (IAS-WHU). The assembly was generated by ~225 Gb PacBio single-molecule real-time (SMRT) long reads (the N50 of these reads was 13 kb) with 138-fold genome coverage. The assembly captured 1,556 Mb of genome sequences, consisting of 1,781 contigs with the N50 of these contigs reaching up to 1,915 kb. The assemblies were also corrected by using highly accurate Illumina paired-end reads. Finally, 95.69% of total contigs spanning 1,489 Mb were categorized and ordered into 13 chromosome-scale scaffolds using Hi-C data.

Summary of Assembly Gossypium herbaceum Mutema
Total PacBio reads (Gb) 225
Number of total contigs 1,781
N50 of contigs (kb) 1,915
Anchored and oriented contigs (Mb) 1,489
Number of total scaffolds 732
Total assembled genome size (Mb) 1,556
Percentage of anchoring and ordering (%) 95.69
Transposable elements (TEs) proportion (%) 79.71
Number of annotated protein-coding genes 43,952

Publication

Huang, G. et al., Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics. 2020. doi.org/10.1038/s41588-020-0607-4

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/A1_WHU_v1&loc=
Short NameA1_WHU
Assembly

The chromosomes (pseudomolecules) and scaffolds for Gossypium herbaceum (A1) 'Mutema (A1-076)' genome. These files belong to the WHU Assembly v1.0

Chromosomes & scaffolds (FASTA format) Gherbaceum_A1-0076_WHUv3.0rc.genome.standard.fa.gz
Transposable Elements (GFF format) Gherbaceum_A1-0076_WHUv3.0rc.transposableElements.gff.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.

Functional Analysis

Functional annotation files for the Gossypium herbaceum WHU Genome v1.0 are available for download below. The Gossypium herbaceum WHU 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 A1_WHU_v1_a1_genes2GO.xlsx.gz
IPR assignments from InterProScan A1_WHU_v1_a1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways A1_WHU_v1_a1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs A1_WHU_v1_a1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium herbaceum (A1) 'Mutema (A1-076)' genome. These files belong to the WHU Assembly v1.0

Predicted gene models with exons (GFF3 format) Gherbaceum_A1-0076_WHUv3.0rc.gene.standard.gff3.gz
Coding sequences, CDS (FASTA format) Gherbaceum_A1-0076_WHUv3.0rc.gene.cds.standard.fa.gz
Protein sequences (FASTA format) Gherbaceum_A1-0076_WHUv3.0rc.gene.pep.standard.fa.gz
Homology

Homology of the Gossypium herbaceum WHU 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 (Araport11), UniProtKB/SwissProt (Release 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format. 

 

Protein Homologs

G. herbaceum WHU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) A1_WHU_v1_a1_vs_nr.xlsx.gz
G. herbaceum WHU Genome v1.0 proteins with NCBI nr (FASTA file) A1_WHU_v1_a1_vs_nr_hit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins without NCBI nr (FASTA file) A1_WHU_v1_a1_vs_nr_noHit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) A1_WHU_v1_a1_vs_tair.xlsx.gz
G. herbaceum WHU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) A1_WHU_v1_a1_vs_tair_hit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) A1_WHU_v1_a1_vs_tair_noHit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins with SwissProt homologs (EXCEL file) A1_WHU_v1_a1_vs_swissprot.xlsx.gz
G. herbaceum WHU Genome v1.0 proteins with SwissProt (FASTA file) A1_WHU_v1_a1_vs_swissprot_hit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins without SwissProt (FASTA file) A1_WHU_v1_a1_vs_swissprot_noHit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) A1_WHU_v1_a1_vs_trembl.xlsx.gz
G. herbaceum WHU Genome v1.0 proteins with TrEMBL (FASTA file) A1_WHU_v1_a1_vs_trembl_hit.fasta.gz
G. herbaceum WHU Genome v1.0 proteins without TrEMBL (FASTA file) A1_WHU_v1_a1_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 herbaceum 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.herbaceum_WHU-A1_SNP
CottonGen InDel markers mapped to genome G.herbaceum_WHU-A1_InDel
CottonGen RFLP markers mapped to genome G.herbaceum_WHU-A1_RFLP
CottonGen SSR markers mapped to genome G.herbaceum_WHU-A1_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. herbaceum 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.herbaceum_WHU-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.herbaceum_WHU-v1.0_G.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.herbaceum_WHU-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.herbaceum_WHU-v1.0_g.raimondii_cottongen_reftransV1