Kokia drynarioides genome ISU_v1

Overview
Analysis NameKokia drynarioides genome ISU_v1
Methodnanopore, Hi-C, Canu v2.1, yahs v1.1, ragtag v2.1.0
Source (v1)
Date performed2024-05-08

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.

Fresh leaf tissue was harvested from K. cookei (WAI 16c69) and K. kauaiensis (WAI 19s9) growing at Waimea Valley (arboretum and botanical garden in Haleiwa, HI, USA), and K. drynarioides growing in the Iowa State University greenhouse. All samples were sequenced with nanopore and hi-c.

K. drynarioides was assembled using Canu v2.1. K. cookei and K. kauaiensis were assembled using hifiasm v0.18.5-r499.  The contigs for each sample were scaffolded using yahs v1.1 with their respective hi-c reads. The scaffolds were oriented and arranged into chromosome using ragtag v2.1.0 and the G. kirkii genome. Each chromosome was validated and edited if necessary using the hic contact maps.

The genomes were masked for repeats using RepeatMasker v4.1.5 using a species-specific repeat database created with RepeatModeler2 v2.0.5 and annotated using BRAKER3 (v1.0.4.1) with the OrthoDB v11 Viridiplantae protein database.

Assembly

The Kokia drynarioides ISU Genome v1.0 assembly file is available in FASTA format.

Chromosomes and unplaced scaffolds (FASTA file) Kokia_drynarioides.fasta.gz

 

Functional Analysis

Functional annotation files for the Kokia drynarioides Genome v1.0 are available for download below. The K. drynarioides 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

GO assignments from InterProScan Kokia_drynarioides_ISU_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan Kokia_drynarioides_ISU_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Orthologs Kokia_drynarioides_ISU_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Pathways Kokia_drynarioides_ISU_v1_KEGG-pathways.xlsx.gz
Genes

The Kokia drynarioides ISU Genome v1.0 gene prediction files are in GFF*, GTF, and FASTA formats.
*CottonGen Team converted based on the original GTF format.

Genes (GFF file)* Kokia_drynarioides.gff.gz
CDS sequences (FASTA file) Kokia_drynarioides.cds.fasta.gz
Protein sequences (FASTA file) Kokia_drynarioides.pep.fa.gz
Genes (GTF file) Kokia_drynarioides.gtf.gz

 

Homology

Homology of the Kokia drynarioides 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

K. drynarioides Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) Kdrynarioides_ISU_v1_vs_tair.xlsx.gz
K. drynarioides Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) Kdrynarioides_ISU_v1_vs_tair_hit.fasta.gz
K. drynarioides Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) Kdrynarioides_ISU_v1_vs_tair_noHit.fasta.gz
K. drynarioides Genome v1.0 proteins with SwissProt homologs (EXCEL file) Kdrynarioides_ISU_v1_vs_swissprot.xlsx.gz
K. drynarioides Genome v1.0 proteins with SwissProt (FASTA file) Kdrynarioides_ISU_v1_vs_swissprot_hit.fasta.gz
K. drynarioides Genome v1.0 proteins without SwissProt (FASTA file) Kdrynarioides_ISU_v1_vs_swissprot_noHit.fasta.gz
K. drynarioides Genome v1.0 proteins with TrEMBL homologs (EXCEL file) Kdrynarioides_ISU_v1_vs_trembl.xlsx.gz
K. drynarioides Genome v1.0 proteins with TrEMBL (FASTA file) Kdrynarioides_ISU_v1_vs_trembl_hit.fasta.gz
K. drynarioides Genome v1.0 proteins without TrEMBL (FASTA file) Kdrynarioides_ISU_v1_vs_trembl_noHit.fasta.gz
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 drynarioides 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. Markers available in CottonGen are linked to JBrowse.
 
CottonGen SNP markers mapped to genome Kodry_SNP
CottonGen RFLP markers mapped to genome Kodry_RFLP
CottonGen SSR markers mapped to genome Kodry_SSR
CottonGen InDel markers mapped to genome Kodry_InDel
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 drynarioides genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3.
G. arboreum CottonGen RefTrans v1 Kodry_g.arboreum_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 Kodry_g.hirsutum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 Kodry_g.barbadense_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 Kodry_g.raimondii_cottongen_reftransV1