Gossypium raimondii (D5) 'D5-8' genome ISU_v1

Overview
Analysis NameGossypium raimondii (D5) 'D5-8' genome ISU_v1
MethodAbySS & Chromosomer (v. 2.0.1 & v August 2017) (v. 2.0.1 & v August 2017)
Source (v1)
Date performed2021-02-17

Materials and Methods

DNA was extracted from leaves of D5-8. Samples obtained from Iowa State University, Ames, IA were prepared at the USDA-ARS GBRU core facility using Accel-NGS 2S PCR-Free (Product number 20024 with adapter set 26396, Swift Biosciences, Ann Arbor,MI, USA). Library sizes were validated on the Agilent TapeStation 2200 High Sensitivity D1000 Assay (Part No. 5067-5584, Agilent Technologies, Santa Clara, CA, USA) and assayed for concentration prior to equimolar pooling by a KAPA Library Quantification Kit (Product number KK4854, Kapa Biosystems, Inc., Wilmington, MA, USA) on a qPCR instrument (LightCycler 96, Roche Applied Science, Indianapolis, IN, USA). Each pool was clustered onboard an Illumina HiSeq2500 DNA sequencer with a HiSeq PE (pairedend) Rapid v2 flowcell clustering kit (Product number PE-402- 4002, Illumina, San Diego, CA, USA) and sequenced as 2 x 100 bp with the HiSeq Rapid SBS Kit v2 (Product number FC- 402-4021, Illumina, San Diego, CA, USA). Reads were trimmed and filtered with Trimmomatic v0.32 (Bolger et al. 2014) with the following options: 1) sequence adapter removal, 2) removal of leading and/or trailing bases when the quality score (Q) <28, 3) removal of bases after average Q < 28 (8 nt window) or single base quality <10, and 4) removal of reads <85 nt. Detailed parameters can be found at https://github.com/IGBB/D_Cottons_USDA, last accessed December 18, 2018.

About the assembly

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 NCBI PRJNA488266.

Summary of the Updated Assembly Numbers
Total sequence length 615,032,910
Total ungapped length 534,567,798
Gaps between scaffolds 0
Number of scaffolds 94,517
Scaffold N50 46,774,767
Scaffold L50 7
Number of contigs 894,248
Contig N50 1,101
Contig L50 106,943
Total number of chromosomes and plasmids 13
Number of component sequences (WGS or clone) 94,517

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
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/D5_ISU_v1&loc=
Analysis Typewhole_genome
Assembly

The Gossypium raimondii D5 ISU Genome v1.0 assembly file is available in FASTA format.

Downloads

Chromosomes (FASTA file) Gossypium_raimondii_D5_ISU_v1.0.fasta.gz

 

Functional Analysis

Functional annotation files for the Gossypium raimondii ISU Genome v1.0 are available for download below. The Gossypium raimondii ISU 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 D5_ISU_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan D5_ISU_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways D5_ISU_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs D5_ISU_v1_KEGG-pathways.xlsx.gz

 

Gene Predictions

The Gossypium raimondii D5 ISU v1.0 genome gene prediction files are available in FASTA and GFF3 formats.

Downloads

Protein sequences  (FASTA file) Gossypium_raimondii_D5_ISU_v1.0.proteins.fasta.gz
CDS  (FASTA file) Gossypium_raimondii_D5_ISU_v1.0.cds.fasta.gz
RNA sequences  (FASTA file) Gossypium_raimondii_D5_ISU_v1.0.rnas.fasta.gz

 

Homology

Homology of the Gossypium raimondii 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.raimondii ISU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) D5_ISU_v1_vs_nr.xlsx.gz
G.raimondii ISU Genome v1.0 proteins with NCBI nr (FASTA file) D5_ISU_v1_vs_nr_hit.fasta.gz
G.raimondii ISU Genome v1.0 proteins without NCBI nr (FASTA file) D5_ISU_v1_vs_nr_noHit.fasta.gz
G.raimondii ISU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) D5_ISU_v1_vs_tair.xlsx.gz
G.raimondii ISU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) D5_ISU_v1_vs_tair_hit.fasta.gz
G.raimondii ISU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) D5_ISU_v1_vs_tair_noHit.fasta.gz
G.raimondii ISU Genome v1.0 proteins with SwissProt homologs (EXCEL file) D5_ISU_v1_vs_swissprot.xlsx.gz
G.raimondii ISU Genome v1.0 proteins with SwissProt (FASTA file) D5_ISU_v1_vs_swissprot_hit.fasta.gz
G.raimondii ISU Genome v1.0 proteins without SwissProt (FASTA file) D5_ISU_v1_vs_swissprot_noHit.fasta.gz
G.raimondii ISU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) D5_ISU_v1_vs_trembl.xlsx.gz
G.raimondii ISU Genome v1.0 proteins with TrEMBL (FASTA file) D5_ISU_v1_vs_trembl_hit.fasta.gz
G.raimondii ISU Genome v1.0 proteins without TrEMBL (FASTA file) D5_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 Gossypium raimondii ISU me 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.raimondii_ISU-D5_SNP
CottonGen RFLP markers mapped to genome G.raimondii_ISU-D5_RFLP
CottonGen SSR markers mapped to genome G.raimondii_ISU-D5_SSR
CottonGen InDel markers mapped to genome G.raimondii_ISU-D5_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 G. raimondii 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.raimondii_ISU-D5_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.raimondii_ISU-D5_G.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.raimondii_ISU-D5_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.raimondii_ISU-D5_g.raimondii_cottongen_reftransV1