Gossypioides kirkii genome ISU_v3_a3
About the assembly
Gossypioides kirkii germplasm 'JFW-EA'. DNA extracted from mature plant leaves.
Udall et al. (2019) The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front. Plant Sci., 27 November 2019 | https://doi.org/10.3389/fpls.2019.01541
Additional information about this analysis:
All 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.
Functional annotation files for the Gossypioides kirkii ISU Genome v3.0 are available for download below. The Gossypioides kirkii ISU 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).
The Gossypioides kirkii ISU Genome v3.0 gene prediction files are available in FASTA and GFF3 formats.
Homology of the Gossypioides kirkii ISU Genome v3.0 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 2019-01), and UniProtKB/TrEMBL (Release 2019-01) databases. The best hit reports are available for download in Excel format.
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 Gossypioides kirkii 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 were performed by the CottonGen Team of Main Bioinformatics Lab at WSU. The alignment tool 'BLAT' was used to map transcripts to the Gossypioides kirkii genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.