Gossypium hirsutum (AD1) Genome HAU Assembly v1.0 & Annotation a1.0

Overview
Analysis NameGossypium hirsutum (AD1) Genome HAU Assembly v1.0 & Annotation a1.0
MethodIrys Solve (BioNano) (v3.2)
SourceIllumina paired-end, BioNano and PacBio
Date performed2018-10-30

3/16/19 Announcement from authors about updated HAU-AD1_v1.0:

It is found that the genome sequence HAU-AD1 v1.0 contains some missing SNPs and InDels (which were from the PacBio reads) were not fully corrected in previous sequence polishing analysis. To improve the base quality, another Illumina dataset covering 60X of genome was used to correct these SNPs and InDels. Consequently, ~500 genes that affected by the InDels have been re-annotated. The updated genome (named as HAU-AD1_v1.1) does not have any changes of sequence structure, and should represent a high-quality reference genome for TM-1. 

 

About the Assembly v1.0

Single-molecule real-time sequencing technology (PacBio RSII) was applied to assemble de novo the genome sequence of G. hirsutum accession TM-1, generated 194.01 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 v1.0 Summary G. hirsutum  
 Total length of contigs 2,281,853,441  
 Total length of assemblies 2,347,017,486 
 Estimated gap size, bp 65,164,045
 Percentage of anchoring, bp 98.94% 
 Percentage of anchoring and ordering, bp 96.16% 
 Number of contigsa 4,746
 Contig L50, bp 1,891,906
 Number of scaffoldsb 2,190
 Scaffold L50, bp 97,738,592
 GC content 34.3%
 Percentage of repeat sequences 69.86% 
 Number of genes 70,199 
 Number of transcripts 115,835
 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 hirsutum HAU Genome v1.1 and v1.0 assembly files are available in FASTA and GFF3 formats.

HAU-AD1_v1.1 Downloads

Chromosome (FASTA file) Gossypium_hirsutum_HAU_v1.1.fasta.gz
Chromosome Repeat Annotation (GFF3 file) Gossypium_hirsutum_HAU_v1.1.repeat.annotation.gff3.gz

 

HAU-AD1_v1.0 Downloads

Chromosome (FASTA file) Gossypium_hirsutum_HAU_v1.0.fasta.gz
Chromosome Repeat Annotation (GFF3 file) Gossypium_hirsutum_HAU_v1.0.repeat.annotation.gff3.gz

 

Gene Predictions

The Gossypium hirsutum HAU genome v1.1 and v1.0 gene prediction files are available in FASTA and GFF3 formats.

HAU-AD1_v1.1 Downloads

Transcript sequences (FASTA file) Gossypium_hirsutum_HAU_v1.1.transcripts.fasta.gz
CDS sequences (FASTA file) Gossypium_hirsutum_HAU_v1.1.CDs.fasta.gz
Protein sequences  (FASTA file) Gossypium_hirsutum_HAU_v1.1.proteins.fasta.gz
Genes (GFF3 file) Gossypium_hirsutum_HAU_v1.1.genes.gff3.gz

 

HAU-AD1_v1.0 Downloads

Transcript sequences (FASTA file) Gossypium_hirsutum_HAU_v1.0.transcripts.fasta.gz
CDS sequences (FASTA file) Gossypium_hirsutum_HAU_v1.0.CDs.fasta.gz
Protein sequences  (FASTA file) Gossypium_hirsutum_HAU_v1.0.proteins.fasta.gz
Genes (GFF3 file) Gossypium_hirsutum_HAU_v1.0.genes.gff3.gz

 

Downloads

03/16/19:  Announcement from authors about HAU-AD1_v1.1

It is found that the genome sequence HAU-AD1 v1.0 contains some missing SNPs and InDels (which were from the PacBio reads) were not fully corrected in previous sequence polishing analysis. To improve the base quality, another Illumina dataset covering 60X of genome was used to correct these SNPs and InDels. Consequently, ~500 genes that affected by the InDels have been re-annotated. The updated genome (named as HAU-AD1 v1.1) does not have any changes of sequence structure, and should represent a high-quality reference genome for TM-1.  To download the HAU-AD1 v1.1 data, go to this link FTP repository HAU-AD1_v1.1

 

All HAU-AD1.v1.0 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.

Homology

Homology of the Gossypium hirsutum 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 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 hirsutum HAU v1.0 proteins with NCBI nr homologs (EXCEL file) AD1_HAU_v1.0_vs_nr.xlsx.gz
Gossypium hirsutum HAU v1.0 proteins with NCBI nr (FASTA file) AD1_HAU_v1.0_vs_nr_hit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins without NCBI nr (FASTA file) AD1_HAU_v1.0_vs_nr_noHit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) AD1_HAU_v1.0_vs_tair.xlsx.gz
Gossypium hirsutum HAU v1.0 proteins with arabidopsis (TAIR10) (FASTA file) AD1_HAU_v1.0_vs_tair_hit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins without arabidopsis (TAIR10) (FASTA file) AD1_HAU_v1.0_vs_tair_noHit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins with SwissProt homologs (EXCEL file) AD1_HAU_v1.0_vs_swissprot.xlsx.gz
Gossypium hirsutum HAU v1.0 proteins with SwissProt (FASTA file) AD1_HAU_v1.0_vs_swissprot_hit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins without SwissProt (FASTA file) AD1_HAU_v1.0_vs_swissprot_noHit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins with TrEMBL homologs (EXCEL file) AD1_HAU_v1.0_vs_trembl.xlsx.gz
Gossypium hirsutum HAU v1.0 proteins with TrEMBL (FASTA file) AD1_HAU_v1.0_vs_trembl_hit.fasta.gz
Gossypium hirsutum HAU v1.0 proteins without TrEMBL (FASTA file) AD1_HAU_v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Gossypium hirsutum HAU Genome v1.0 are available for download below. The Gossypium hirsutum HAU 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 AD1_HAU_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan AD1_HAU_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways AD1_HAU_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs AD1_HAU_v1.0_KEGG-pathways.xlsx.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. hirsutum HAU v1.0 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.hirsutum_HAU_v1.0_SNP-InDel
CottonGen RFLP markers mapped to genome G.hirsutum_HAU_v1.0_RFLP
CottonGen SSR markers mapped to genome G.hirsutum_HAU_v1.0_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. hirsutum HAU v1.0 genome. Only alignments with a percent identity of 90% were retained.
 
Arabidopsis thaliana TAIR10 G.hirsutum_HAU_v1.0_arabidopsis_proteins.gff3.gz
UniProtKB SwissProt cotton proteins G.hirsutum_HAU_v1.0_sptr_proteins.gff3.gz
UniProtKB TrEMBL cotton proteins G.hirsutum_HAU_v1.0_trembl_proteins.gff3.gz
NCBI nr cotton proteins G.hirsutum_HAU_v1.0_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. hirsutum 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.hirsutum_HAU_v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.hirsutum_HAU_v1.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.hirsutum_HAU_v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.hirsutum_HAU_v1.0_g.raimondii_cottongen_reftransV1