Gossypium mustelinum (AD4) genome JGI_v1.1

Overview
Analysis NameGossypium mustelinum (AD4) genome JGI_v1.1
MethodPacBio Sequel, Mecat v. 1.0
SourceGossypium_mustelinum_v1.1
Date performed2019-09-19

Please Note: This genome assembly is made available through a "Reserved Analyses" restriction. Please see the Restrictions on Dataset Usage for further details.

 

About the assembly

The WGS assembly of Gossypium mustelinum (AD4) v1.1 was isolated from '1408120.09' with 94.12x of the genome coverage.  The data was submitted by JGI (US DOE Joint Genome Institute) and stored under NCBI BioProject PRJNA525892.

 

Summary of the Assembly  
Total sequence length 2,315,094,184
Total ungapped length 2,297,344,504
Gaps between scaffolds 1,763
Number of scaffolds 2,146
Scaffold N50 2,312,865
Scaffold L50 272
Number of contigs 2,146
Contig N50 272
Contig L50 2,146
Total number of chromosomes and plasmids 26
Number of component sequences (WGS or clone) 2,146

 

Publication: Chen et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement Nat Genet 20 April 2020.

 

Restrictions on Dataset Usage

Gossypium mustelinum genome v1.1 data is made available before scientific publication according to the Ft. Lauderdale Accord. By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data on a whole genome or chromosome scale prior to publication by principal investigators of a comprehensive genome analysis without the consent of project's investigators listed in Contacts below. ("Reserved Analyses"). "Reserved analyses" include the identification of complete (whole genome) sets of genomic features such as genes, gene families, regulatory elements, repeat structures, GC content, or any other genome feature, and whole-genome- or chromosome- scale comparisons with other species. The embargo on publication of Reserved Analyses by researchers outside of the Gossypium barbadense Genome Sequencing Project is expected to extend until the publication of the results of the sequencing project is accepted. Studies of any type on the reserved data sets that are not in direct competition with those planned by the principle investigators may also be undertaken after an agreement with project's principle investigators. The assembly and sequence data should not be redistributed or repackaged without permission from the project's principle investigators.

We request that potential users of this sequence assembly contact the individuals listed under Contacts with their plans to ensure that proposed usage of sequence data are not considered Reserved Analyses.

Contacts

Principal Investigators:
Z. Jeffrey Chen (University of Texas at Austin) (email: zjchen@austin.utexas.edu)
Jane Grimwood (HudsonAlpha Institute for Biotechnology) (email: jgrimwood@hudsonalpha.org)

Properties
Additional information about this analysis:
Property NameValue
Short NameAD4_JGI
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/Gm_JGI-AD4_v1.1&loc=
Assembly

The chromosomes (pseudomolecules) for Gossypium mustelinum genome. These files belong to the JGI Assembly v1.1 (NCBI BioProject PRJNA525892)

Chromosomes (FASTA format) G.mustelinum_JGI-AD4_assembly_v1.1.fa.gz
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.

Functional Analysis

Functional annotation files for the Gossypium mustelinum JGI Genome v1.1 are available for download below. The Gossypium mustelinum Genome v1.1 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 AD4_JGI-v1.1_genes2GO.xlsx.gz
IPR assignments from InterProScan AD4_JGI-v1.1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways AD4_JGI-v1.1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs AD4_JGI-v1.1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for G. mustelinum genome. These files belong to the JGI-AD4 Assembly v1.1 (NCBI BioProject PRJNA525892)

Predicted gene models with exons (GFF3 format) G.mustelinum_JGI-AD4_v1.1_protein_gff.gz
Protein sequences (FASTA format) G.mustelinum_JGI-AD4_v1.1_protein.fasta.gz
Homology

Homology of the Gossypium mustelinum JGI Genome v1.1 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

Gossypium mustelinum JGI Genome v1.1 proteins with NCBI nr homologs (EXCEL file) AD4_JGI-v1.1_vs_nr.xlsx.gz
Gossypium mustelinum JGI Genome v1.1 proteins with NCBI nr (FASTA file) AD4_JGI-v1.1_vs_nr_hit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins without NCBI nr (FASTA file) AD4_JGI-v1.1_vs_nr_noHit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins with arabidopsis (Araport11) homologs (EXCEL file) AD4_JGI-v1.1_vs_tair.xlsx.gz
Gossypium mustelinum JGI Genome v1.1 proteins with arabidopsis (Araport11) (FASTA file) AD4_JGI-v1.1_vs_tair_hit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins without arabidopsis (Araport11) (FASTA file) AD4_JGI-v1.1_vs_tair_noHit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins with SwissProt homologs (EXCEL file) AD4_JGI-v1.1_vs_swissprot.xlsx.gz
Gossypium mustelinum JGI Genome v1.1 proteins with SwissProt (FASTA file) AD4_JGI-v1.1_vs_swissprot_hit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins without SwissProt (FASTA file) AD4_JGI-v1.1_vs_swissprot_noHit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins with TrEMBL homologs (EXCEL file) AD4_JGI-v1.1_vs_trembl.xlsx.gz
Gossypium mustelinum JGI Genome v1.1 proteins with TrEMBL (FASTA file) AD4_JGI-v1.1_vs_trembl_hit.fasta.gz
Gossypium mustelinum JGI Genome v1.1 proteins without TrEMBL (FASTA file) AD4_JGI-v1.1_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 mustelinum 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.mustelinum_JGI-AD4_v1.1.0_SNP
CottonGen InDel markers mapped to genome G.mustelinum_JGI-AD4_v1.1.0_InDel
CottonGen RFLP markers mapped to genome G.mustelinum_JGI-AD4_v1.1.0_RFLP
CottonGen SSR markers mapped to genome G.mustelinum_JGI-AD4_v1.1.0_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. mustelinum 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. mustelinum_CRI-TM1-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G. mustelinum_CRI-TM1-v1.0_g.barbadense_cottongen_reftransV1
G. mustelinum CottonGen RefTrans v1 G. mustelinum_CRI-TM1-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G. mustelinum_CRI-TM1-v1.0_g.raimondii_cottongen_reftransV1