Gossypium darwinii (AD5) genome HGS_v1.1
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Overview
Please Note: This genome assembly is made available through a "Reserved Analyses" restriction. Please see the Restrictions on Dataset Usage for further details.
About the assembly The WGS assembly of Gossypium darwinii (AD5) v1.1 was isolated from isolate=1808015.09 with 80.57x of the genome coverage. The data was submitted by HGS (HudsonAlpha Genome Sequencing Center) and stored under NCBI BioProject PRJNA516409.
Gossypium darwinii genome v1.1 data is made available before scientific publication according to the Ft. Lauderdale Accord. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by principal investigators of a comprehensive genome analysis without the consent of project's investigators listed in Contacts below. ("Reserved Analyses"). "Reserved analyses" include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome- scale comparisons with other species. The embargo on publication of Reserved Analyses by researchers outside of the Gossypium barbadense Genome Sequencing Project is expected to extend until the publication of the results of the sequencing project is accepted. Studies of any type on the reserved data sets that are not in direct competition with those planned by the principle investigators may also be undertaken after an agreement with project's principle investigators. The assembly and sequence data should not be redistributed or repackaged without permission from the project's principle investigators. We request that potential users of this sequence assembly contact the individuals listed under Contacts with their plans to ensure that proposed usage of sequence data are not considered Reserved Analyses. Contacts Principal Investigators: Assembly
The chromosomes (pseudomolecules) for Gossypium darwinii genome. These files belong to the HGS Assembly v1.1 (NCBI BioProject PRJNA516409)
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 Annotation
Functional annotation files for the Gossypium darwinii HGS Genome v1.1 are available for download below. The Gossypium darwinii HGS 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 G. darwinii genome. These files belong to the HGS-AD5 Assembly v1.1 (NCBI BioProject PRJNA516409)
Homology
Homology of the Gossypium darwinii HGS Genome v1.1 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 darwinii 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.
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. darwinii 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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