Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1

Overview
Analysis NameGossypium barbadense (AD2) '3-79' genome HAU_v2_a1
MethodIrys Solve (BioNano) (v3.2)
SourceIllumina paired-end, PacBio and BioNano
Date performed2018-10-30

About the Assembly

Single-molecule real-time sequencing technology (PacBio RSII) was applied to assemble de novo the genome sequence of G. barbadense accession 3–79, generated 210.98 Gb of genome sequence with an estimated depth of coverage of at least 80× for the genome.  Illumina paired-end data was used to correct low-quality nucleotides and insertions/deletions (InDels) from the PacBio sequencing. These polished contigs were processed for a hybrid assembly by using high-resolution optical mapping (BioNano Genomics Irys) data from the same accessions. To construct chromosome-scale scaffolds, we used high-throughput chromosome conformation capture (Hi-C) data from each accession to categorize and order these assemblies obtained by optical mapping.

 

 Assembly Summary G. barbadense  
 Total length of contigs 2,222,525,789  
 Total length of assemblies 2,266,656,771  
 Estimated gap size, bp 44,130,982  
 Percentage of anchoring, bp 97.68%  
 Percentage of anchoring and ordering, bp 96.35%  
 Number of contigsa 4,930  
 Contig L50, bp 2,151,565  
 Number of scaffoldsb 3,032  
 Scaffold L50, bp 92,880,876  
 GC content 34.2%  
 Percentage of repeat sequences 69.83%  
 Number of genes 71,297  
 Number of transcripts 109,778  
 aHi-C + BioNano corrected contigs.  
 bHi-C-assembled genome sequences.  

 

Publication

Wang et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature genetics. 2018 Dec 03

Assembly

The Gossypium barbadense HAU Genome v2.0 assembly files are available in FASTA and GFF3 formats.

Downloads

Chromosome (FASTA file) Gossypium_barbadense_HAU_v2.0.fasta.gz
Gossypium_barbadense_HAU_v2.0.fasta.gz.md5
Chromosome Repeat Annotation (GFF3 file) Gossypium_barbadense_HAU_v2.0.repeat.annotation.gff3.gz

 

Downloads

All annotation files are available for download by selecting the desired data type in the left-hand side bar.  Each data type page will provide a description of the available files and links do download.

Functional Analysis

Functional annotation files for the Gossypium barbadense HAU Genome v2.0 are available for download below. The Gossypium barbadenseTexas 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 AD2_HAU_v2.0_genes2GO.xlsx.gz
IPR assignments from InterProScan AD2_HAU_v2.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs AD2_HAU_v2.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways AD2_HAU_v2.0_KEGG-pathways.xlsx.gz

 

Gene Predictions

The Gossypium hirsutum HAU genome v2.0 gene prediction files are available in FASTA and GFF3 formats.

Downloads

Transcript sequences (FASTA file) Gossypium_barbadense_HAU_v2.0.transcripts.fasta.gz
CDS sequences (FASTA file) Gossypium_barbadense_HAU_v2.0.CDs.fasta.gz
Protein sequences  (FASTA file) Gossypium_barbadense_HAU_v2.0.proteins.fasta.gz
Genes (GFF3 file) Gossypium_barbadense_HAU_v2.0.genes.gff3.gz

 

Homology

Homology of the Gossypium barbadenseHAU 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 barbadense HAU v2.0 proteins with NCBI nr homologs (EXCEL file) AD2_HAU_v2.0_vs_nr.xlsx.gz
Gossypium barbadense HAU v2.0 proteins with NCBI nr (FASTA file) AD2_HAU_v2.0_vs_nr_hit.fasta.gz
Gossypium barbadense HAU v2.0 proteins without NCBI nr (FASTA file) AD2_HAU_v2.0_vs_nr_noHit.fasta.gz
Gossypium barbadense HAU v2.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) AD2_HAU_v2.0_vs_tair.xlsx.gz
Gossypium barbadense HAU v2.0 proteins with arabidopsis (TAIR10) (FASTA file) AD2_HAU_v2.0_vs_tair_hit.fasta.gz
Gossypium barbadense HAU v2.0 proteins without arabidopsis (TAIR10) (FASTA file) AD2_HAU_v2.0_vs_tair_noHit.fasta.gz
Gossypium barbadense HAU v2.0 proteins with SwissProt homologs (EXCEL file) AD2_HAU_v2.0_vs_swissprot.xlsx.gz
Gossypium barbadense HAU v2.0 proteins with SwissProt (FASTA file) AD2_HAU_v2.0_vs_swissprot_hit.fasta.gz
Gossypium barbadense HAU v2.0 proteins without SwissProt (FASTA file) AD2_HAU_v2.0_vs_swissprot_noHit.fasta.gz
Gossypium barbadense HAU v2.0 proteins with TrEMBL homologs (EXCEL file) AD2_HAU_v2.0_vs_trembl.xlsx.gz
Gossypium barbadense HAU v2.0 proteins with TrEMBL (FASTA file) AD2_HAU_v2.0_vs_trembl_hit.fasta.gz
Gossypium barbadense HAU v2.0 proteins without TrEMBL (FASTA file) AD2_HAU_v2.0_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 G. barbadense HAU v2.0 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-InDel markers mapped to genome G.barbadense_HAU_v2.0_SNP-InDel
CottonGen RFLP markers mapped to genome G.barbadense_HAU_v2.0_RFLP
CottonGen SSR markers mapped to genome G.barbadense_HAU_v2.0_SSR
Protein Alignments
Protein alignments available below were performed by the CottonGen Team of the Main Bioinformatics Lab at WSU.  The alignment tool 'exonerate' was used to map protein sequences onto the G. barbadense HAU v2.0 genome. Only alignments with a percent identity of 90% were retained.
 
Arabidopsis thaliana TAIR10 G.barbadense_HAU_v2.0_arabidopsis_proteins.gff3.gz
UniProtKB SwissProt cotton proteins G.barbadense_HAU_v2.0_sptr_proteins.gff3.gz
UniProtKB TrEMBL cotton proteins G.barbadense_HAU_v2.0_trembl_proteins.gff3.gz
NCBI nr cotton proteins G.barbadense_HAU_v2.0_gbnr_proteins.gff3.gz

 

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. barbadense 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.barbadense_HAU_v2.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.barbadense_HAU_v2.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.barbadense_HAU_v2.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.barbadense_HAU_v2.0_g.raimondii_cottongen_reftransV1