Gossypioides kirkii genome ISU Assembly v3.0 & Annotation v3.0

Genome Overview
Analysis NameGossypioides kirkii genome ISU Assembly v3.0 & Annotation v3.0
MethodPacBio, HiC, Bionano
SourceGossypioides kirkii ISU v3.0-a3.0
Date performed2019-02-28

About the assembly

Gossypioides kirkii germplasm 'JFW-EA'. DNA extracted from mature plant leaves.

 

 Assembly Metrics
 Genome features Contig level Pseudomolecule level (Hi-C) Chr. level (Bionano)
 Assembly size (Mb) 544 538 354
 Number of features (gaps) 389 (0) 12 (277) 1079 (3721)
 Longest scaffold length (Mb) 31.1  60.3 16.7
 N50 (Mb) (ave. # contigs/chr.) 9.9 (17)  43.0 (17) 0.3

 

Publication

 

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data%2FGossypioides_kirkii&loc=
Functional Analysis

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).

Downloads

GO assignments from InterProScan Gossypioides_kirkii_genes2GO.xlsx.gz
IPR assignments from InterProScan Gossypioides_kirkii_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways Gossypioides_kirkii_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs Gossypioides_kirkii_KEGG-pathways.xlsx.gz

 

Homology

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. 

 

Protein Homologs

Gossypioides kirkii ISU v3.0 proteins with NCBI nr homologs (EXCEL file) Gossypioides_kirkii_vs_nr.xlsx.gz
Gossypioides kirkii ISU v3.0 proteins with NCBI nr (FASTA file) Gossypioides_kirkii_vs_nr_hit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins without NCBI nr (FASTA file) Gossypioides_kirkii_vs_nr_noHit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins with arabidopsis (TAIR10) homologs (EXCEL file) Gossypioides_kirkii_vs_tair.xlsx.gz
Gossypioides kirkii ISU v3.0 proteins with arabidopsis (TAIR10) (FASTA file) Gossypioides_kirkii_vs_tair_hit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins without arabidopsis (TAIR10) (FASTA file) Gossypioides_kirkii_vs_tair_noHit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins with SwissProt homologs (EXCEL file) Gossypioides_kirkii_vs_swissprot.xlsx.gz
Gossypioides kirkii ISU v3.0 proteins with SwissProt (FASTA file) Gossypioides_kirkii_vs_swissprot_hit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins without SwissProt (FASTA file) Gossypioides_kirkii_vs_swissprot_noHit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins with TrEMBL homologs (EXCEL file) Gossypioides_kirkii_vs_trembl.xlsx.gz
Gossypioides kirkii ISU v3.0 proteins with TrEMBL (FASTA file) Gossypioides_kirkii_vs_trembl_hit.fasta.gz
Gossypioides kirkii ISU v3.0 proteins without TrEMBL (FASTA file) Gossypioides_kirkii_vs_trembl_noHit.fasta.gz

 

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 Gossypioides kirkii genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.

 

G. arboreum CottonGen RefTrans v1 G.kirkii_ISU_v3.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.kirkii_ISU_v3.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.kirkii_ISU_v3.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.kirkii_ISU_v3.0_g.raimondii_cottongen_reftransV1
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 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.
CottonGen SNP markers mapped to genome G.kirkii_ISU_v3.0_SNP
CottonGen InDel markers mapped to genome G.kirkii_ISU_v3.0_InDel
CottonGen RFLP markers mapped to genome G.kirkii_ISU_v3.0_RFLP
CottonGen SSR markers mapped to genome G.kirkii_ISU_v3.0_SSR

 

Downloads

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.

Assembly

The Gossypioides kirkii ISU Genome v3.0 assembly files are available in FASTA and GFF3 formats.

Chromosome (FASTA file) Gossypioides_kirkii_ISU-v3.0.fasta.gz

 

Genes

The Gossypioides kirkii ISU Genome v3.0 gene prediction files are available in FASTA and GFF3 formats.

CDS sequences (FASTA file) Gossypioides_kirkii_ISU-v3.0.CDs.fasta.gz
Protein sequences  (FASTA file) Gossypioides_kirkii_ISU-v3.0.proteins.fasta.gz
Genes (GFF3 file) Gossypioides_kirkii_ISU-v3.0.genes.gff3.gz