Gossypium herbaceum (A1) 'Wagad' genome USDA_v1

Overview
Analysis NameGossypium herbaceum (A1) 'Wagad' genome USDA_v1
Methodn/a
SourceA1.wagad.fasta
Date performed2022-05-04

About the assembly

Here we report a genome assembly of Gossypium herbaceum (variety 'Wagad', A1-0135, PI 630010) that complements the existing genome assemblies and diversity studies (Huang et al. 2020). Our data provide a foundation for understanding the transition from wild to domesticated G. herbaceum, thereby providing an additional perspective on the commonalities of domestication in multiple cotton species.

PacBio CCS reads were assembled using Hifiasm, a fast haplotype-resolved de novo genome assembler for PacBio HiFi sequence reads (Cheng et al. 2021). The contigs were aligned to previously assembled genomes of G. herbaceum and G. arboreum (Huang et al. 2020) using minimap2 (Li 2018) and visualized by dotPlotly (https://github.com/tpoorten/dotPlotly). Multiple contigs aligning to the same contig were manually scaffolded (or concatenated) to create the final chromosomes. The final chromosomes were labeled and again aligned to the previously published A-genome using minimap2 and visualized by dotPlotly.

Hi-C libraries were constructed by Phase Genomics (Seattle, WA) from seedling tissue grown at Brigham Young University Greenhouses (different tissue source than sequenced by PacBio above). Short-read sequencing (Illumina, San Diego, CA; 150PE) of the libraries was performed by PhaseGenomics. The Hi-C data was mapped to the assembled genome sequence using bwa mem (with the -5SP option for HiC data, Li and Durbin 2009). The Hi-C interactions were used as evidence for contig proximity and in scaffolding contig sequences. Matlock (https://github.com/phasegenomics/matlock) was used in conjunction with the mapped reads to identify linkages between different genomic regions in the bam file. Juicebox (Robinson et al. 2018) was used to visualize the linkages along the pseudomolecules. All inversions were identified in alignments created by minimap2 (Li 2018).

 

Publication: Ramaraj T, et al. (2022) The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. bioRxiv. https://doi.org/10.1101/2022.06.07.494775 

Assembly

The chromosomes (pseudomolecules) and scaffolds for Gossypium herbaceum (A1) 'Wagad (A1-135)' genome. These files belong to the USDA Assembly v1.0

Chromosomes & scaffolds (FASTA format) Gherbaceum_A1.wagad.fasta.gz
Functional Analysis

Functional annotation files for the Gossypium herbaceum Wagad Genome USDA v1.0 are available for download below. The Gossypium herbaceum USDA 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 A1_USDA_Wagad_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan A1_USDA_Wagad_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs A1_USDA_Wagad_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways A1_USDA_Wagad_v1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium herbaceum (A1) 'Wagad (A1-135)' genome. These files belong to the USDA Assembly v1.0

Predicted gene models with exons (GFF3 format) Gherbaceum_A1.gff3.gz
Coding sequences, CDS (FASTA format) Gherbaceum_A1.transcripts.fa.gz
Protein sequences (FASTA format) Gherbaceum_A1.proteins.fa.gz
Homology

Homology of the Gossypium herbaceum USDA 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.herbaceum USDA Genome v1.0 proteins with NCBI nr homologs (EXCEL file) A1_USDA_Wagad_v1_vs_nr.xlsx.gz
G.herbaceum USDA Genome v1.0 proteins with NCBI nr (FASTA file) A1_USDA_Wagad_v1_vs_nr_hit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins without NCBI nr (FASTA file) A1_USDA_Wagad_v1_vs_nr_noHit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) A1_USDA_Wagad_v1_vs_tair.xlsx.gz
G.herbaceum USDA Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) A1_USDA_Wagad_v1_vs_tair_hit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) A1_USDA_Wagad_v1_vs_tair_noHit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins with SwissProt homologs (EXCEL file) A1_USDA_Wagad_v1_vs_swissprot.xlsx.gz
G.herbaceum USDA Genome v1.0 proteins with SwissProt (FASTA file) A1_USDA_Wagad_v1_vs_swissprot_hit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins without SwissProt (FASTA file) A1_USDA_Wagad_v1_vs_swissprot_noHit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins with TrEMBL homologs (EXCEL file) A1_USDA_Wagad_v1_vs_trembl.xlsx.gz
G.herbaceum USDA Genome v1.0 proteins with TrEMBL (FASTA file) A1_USDA_Wagad_v1_vs_trembl_hit.fasta.gz
G.herbaceum USDA Genome v1.0 proteins without TrEMBL (FASTA file) A1_USDA_Wagad_v1_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 USDA 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_A1_USDA_SNP
CottonGen RFLP markers mapped to genome G.herbaceum_A1_USDA_RFLP
CottonGen SSR markers mapped to genome G.herbaceum_A1_USDA_SSR
CottonGen InDel markers mapped to genome G.herbaceum_A1_USDA_InDel

 

Publication

 

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_A1_USDA_g.arboreum_cottongen_refTransV1
G. hirsutun CottonGen RefTrans v1 G.herbaceum_A1_USDA_g.hirsutum_cottongen_refTransV1
G. barbadense CottonGen RefTrans v1 G.herbaceum_A1_USDA_g.barbadense_cottongen_refTransV1
G. raimondii CottonGen RefTrans v1 G.herbaceum_A1_USDA_g.raimondii_cottongen_refTransV1