Gossypium longicalyx (F1) genome NSF_v1

Overview
Analysis NameGossypium longicalyx (F1) genome NSF_v1
MethodChicago Highrise, Hi-C, BioNano
Sourcelongicalyx
Date performed2020-01-30

About the assembly

We report a de novo genome assembly for G. longicalyx germplasm name 'F1-1'. This genome was first assembled from ~144x coverage (raw) of PacBio reads, which alone produced an assembly consisting of 229 contigs with an N50 of 28.8 MB (Table1).  The contigs were scaffolded using a combination of Chicago Highrise, Hi-C, and BioNano to produce a chromosome level assembly consisting of 17 contigs with an average length of 70.4 Mb (containing only 8.4 kb of gap sequence). Thirteen of the chromosomes were assembled into single contigs.  Exact placement sequences were included in NCBI with the assembled chromosomes.  The final genome assembly size was 1190.7 MB, representing over 90% of the estimated genome size (Hendrix and Stewart 2005)

 

 Assembly Summary G. longicalyx
 Coverage (raw) ~144x
 Assembly Length** 1190.67 Mb
 Total Contig Number 17
 Average Contig Length 70.04 Mb
 Total Length of Ns 8488
 Contig N50 95.88 Mb
 Contig N90 76.29 Mb

 ** Genome size for G. longicalyx is 1311 (Hendrix and Stewart, 2005)

Publication

Grover, et al., (2020) The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. G3: Genes, Genomes, Genetics Early online March 2, 2020; https://doi.org/10.1534/g3.120.401050
 

Properties
Additional information about this analysis:
Property NameValue
Short NameF1_NSF
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/F1_NSF_v1.0&loc=
Assembly

The chromosomes (pseudomolecules) and scaffolds for G. longicalyx genome. These files belong to the NSF-F1 Assembly

Chromosomes & scaffolds (FASTA format) G.longicalyx_NSF-F1_assembly.fasta.gz
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 Analysis

Functional annotation files for the Gossypium longicalyx NSF Genome v1.0 are available for download below. The Gossypium longicalyx 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

GO assignments from InterProScan F1_NSF_v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan F1_NSF_v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways F1_NSF_v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs F1_NSF_v1.0_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for G. longicalyx genome. These files belong to the NSF-F1 Assembly v1

Predicted gene models with exons (GFF3 format) G.longicalyx_NSF-F1.gff.gz
Coding sequences, CDS (FASTA format) G.longicalyx_NSF-F1_CDS.fas
Protein sequences (FASTA format) G.longicalyx_NSF-F1_proteins.fas
Homology

Homology of the Gossypium longicalyx NSF 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-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

G. longicalyx NSF Genome v1.0 proteins with NCBI nr homologs (EXCEL file) F1_NSF_v1.0_vs_nr.xlsx.gz
G. longicalyx NSF Genome v1.0 proteins with NCBI nr (FASTA file) F1_NSF_v1.0_vs_nr_hit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins without NCBI nr (FASTA file) F1_NSF_v1.0_vs_nr_noHit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) F1_NSF_v1.0_vs_tair.xlsx.gz
G. longicalyx NSF Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) F1_NSF_v1.0_vs_tair_hit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) F1_NSF_v1.0_vs_tair_noHit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins with SwissProt homologs (EXCEL file) F1_NSF_v1.0_vs_swissprot.xlsx.gz
G. longicalyx NSF Genome v1.0 proteins with SwissProt (FASTA file) F1_NSF_v1.0_vs_swissprot_hit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins without SwissProt (FASTA file) F1_NSF_v1.0_vs_swissprot_noHit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins with TrEMBL homologs (EXCEL file) F1_NSF_v1.0_vs_trembl.xlsx.gz
G. longicalyx NSF Genome v1.0 proteins with TrEMBL (FASTA file) F1_NSF_v1.0_vs_trembl_hit.fasta.gz
G. longicalyx NSF Genome v1.0 proteins without TrEMBL (FASTA file) F1_NSF_v1.0_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 Gossypium longicalyx 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.longicalyx_NSF-F1_SNP
CottonGen InDel markers mapped to genome G.longicalyx_NSF-F1_InDel
CottonGen RFLP markers mapped to genome G.longicalyx_NSF-F1_RFLP
CottonGen SSR markers mapped to genome G.longicalyx_NSF-F1_SSR

 

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. longicalyx 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.longicalyx_NSF-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.longicalyx_NSF-v1.0_G.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.longicalyx_NSF-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.longicalyx_NSF-v1.0_g.raimondii_cottongen_reftransV1