Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1
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Overview
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.
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
HAU-AD1_v1.0 Downloads
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.
All HAU-AD1.v1.0 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 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
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
HAU-AD1_v1.0 Downloads
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
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.
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.
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.
Links
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