Gossypium herbaceum (A1) 'Mutema' genome WHU_v1
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Overview
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.
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 Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium herbaceum (A1) 'Mutema (A1-076)' genome. These files belong to the WHU Assembly v1.0
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 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
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
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
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.
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 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.
Links
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