Gossypium thurberi (D1-35) genome ISU_v1

Overview
Analysis NameGossypium thurberi (D1-35) genome ISU_v1
MethodIllumina HiSeq; ABySS v2.0.1; Chromosomer v201708 (ABySS v2.0.1; Chromosomer v201708)
Source (Gothu_v1)
Date performed2019-04-19

About the assembly

DNA was extracted from leaves D1-35. Trimmed data were independently assembled for each species via ABySS v2.0.1 (Simpson et al. 2009), using every 5th kmer value from 40 through 100. A single assembly with the highest E-size (Salzberg et al. 2012) was selected for each species and subsequently annotated with MAKER v2.31.6 (Holt and Yandell 2011) using evidence from: 1) the NCBI G. raimondii EST database (Udall et al. 2006), 2) G. raimondii reference genome predicted proteins, as hosted by CottonGen.org (Paterson et al. 2012), and 3) three ab initio gene prediction programs, that is Genemark v4.30 (Borodovsky et al. 2003), SNAP v2013-11-29 (Korf 2004), and Augustus v3.0.3 (Stanke et al. 2006). Both the SNAP and Augustus models were trained using BUSCO v2.0 (Simão et al. 2015). Chromosomer version 0.1.3 (Tamazian et al. 2016), a reference-assisted scaffolder, was used to scaffold the selected assemblies against the gold standard G. raimondii genome. MAKER v2.31.6 (Holt and Yandell 2011) was used to transfer the previous annotations to the Chromosomer-based scaffolds by rerunning MAKER and using the transcripts from the original annotation as evidence. Assemblies are also available under PRJNA488266.

Summary of the Updated Assembly Numbers
Total sequence length 582,006,748
Total ungapped length 556,095,772
Gaps between scaffolds 0
Number of scaffolds 15,297
Scaffold N50 40,416,325
Scaffold L50 7
Number of contigs 277,903
Contig N50 6,033
Contig L50 26,257
Total number of chromosomes and plasmids 13
Number of component sequences (WGS or clone) 15,297

 

Publication

Grover, et al. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biol Evol. 2019 Jan 1;11(1):53-71.

 

Properties
Additional information about this analysis:
Property NameValue
Short NameD1_ISU
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/D1_thurberi_v1.0&loc=
Analysis Typewhole_genome
Assembly

The chromosomes (pseudomolecules) and scaffolds for G. thurberi (D1). These files belong to the ISU Assembly v1.0

Chromosomes & scaffolds (FASTA format) G.thurberi_ISU-ncbi_13_chroms.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 thurberi ISU Genome v1.0 are available for download below. The Gossypium thurberi 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 D1_ISU_v1_a1_genes2GO.xlsx.gz
IPR assignments from InterProScan D1_ISU_v1_a1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways D1_ISU_v1_a1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs D1_ISU_v1_a1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for G. thurberi genome. These files belong to the ISU Assembly 1.0

Predicted gene models with exons (GFF3 format) G.thurberi_ISU-D1_v1_predicted_genes.gff.gz
Coding sequences, CDS (FASTA format) G.thurberi_ISU-D1_v1_transcripts.fasta.gz
Protein sequences (FASTA format) G.thurberi_ISU-D1_v1_protein.fasta.gz
Homology

Homology of the Gossypium thurberi ISU 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. thurberi ISU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) D1_ISU_v1_a1_vs_nr.xlsx.gz
G. thurberi ISU Genome v1.0 proteins with NCBI nr (FASTA file) D1_ISU_v1_a1_vs_nr_hit.fasta.gz
G. thurberi ISU Genome v1.0 proteins without NCBI nr (FASTA file) D1_ISU_v1_a1_vs_nr_noHit.fasta.gz
G. thurberi ISU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) D1_ISU_v1_a1_vs_tair.xlsx.gz
G. thurberi ISU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) D1_ISU_v1_a1_vs_tair_hit.fasta.gz
G. thurberi ISU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) D1_ISU_v1_a1_vs_tair_noHit.fasta.gz
G. thurberi ISU Genome v1.0 proteins with SwissProt homologs (EXCEL file) D1_ISU_v1_a1_vs_swissprot.xlsx.gz
G. thurberi ISU Genome v1.0 proteins with SwissProt (FASTA file) D1_ISU_v1_a1_vs_swissprot_hit.fasta.gz
G. thurberi ISU Genome v1.0 proteins without SwissProt (FASTA file) D1_ISU_v1_a1_vs_swissprot_noHit.fasta.gz
G. thurberi ISU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) D1_ISU_v1_a1_vs_trembl.xlsx.gz
G. thurberi ISU Genome v1.0 proteins with TrEMBL (FASTA file) D1_ISU_v1_a1_vs_trembl_hit.fasta.gz
G. thurberi ISU Genome v1.0 proteins without TrEMBL (FASTA file) D1_ISU_v1_a1_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 thurberi 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.thruberi_ISU-D1_SNP
CottonGen InDel markers mapped to genome G.thruberi_ISU-D1_InDel
CottonGen RFLP markers mapped to genome G.thruberi_ISU-D1_RFLP
CottonGen SSR markers mapped to genome G.thruberi_ISU-D1_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. thurberi 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.thruberi_HGS-v1.1_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.thruberi_HGS-v1.1_G.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.thruberi_HGS-v1.1_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.thruberi_HGS-v1.1_g.raimondii_cottongen_reftransV1