Kokia kauaiensis 'WAI 19s9' genome ISU_v1
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Overview
About the assembly Kokia is an endangered flowering plant genus endemic to these islands, encompassing three extant and one extinct species. Recent studies provided evidence of unexpected genetic diversity within Kokia. Here, we provide high quality genome assemblies for all three extant Kokia species, including an improved genome for K. drynarioides. All three Kokia genomes contain 12 chromosomes exhibiting high synteny within and between Kokia and the sister taxon Gossypioides kirkii.
Assembly
The Kokia kauaiensis ISU Genome v1.0 assembly file is available in FASTA format.
Functional Analysis
Functional annotation files for the Kokia kauaiensis WAI 19s9 Genome v1.0 are available for download below. The K. kauaiensis WAI 19s9 Genome v1.0 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 Kokia kauaiensis ISU Genome v1.0 gene prediction files are available in GFF*, GTF, and fasta format.
Homology
Homology of the Kokia kauaiensis WAI 19s9 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-6 for the Arabidoposis proteins (Araport11, 2022-09), UniProtKB/SwissProt (Release 2024-03), and UniProtKB/TrEMBL (Release 2024-03) 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 Kokia kauaiensis WAI 19s9 v1.0 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 Kokia kauaiensis WAI 19s9 genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3.
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