Gossypium thurberi (D1-5) genome CRI_v1

Overview
Analysis NameGossypium thurberi (D1-5) genome CRI_v1
MethodCanu v1.5; BUSCO v3.0.2b; Hi-C; LACHESIS
Source (CRI-CAAS, China. Directly submitted)
Date performed2021-07-02

About the assembly

The Gossypium thurberi 'D1-5' was obtained from the National Wild Cotton Nursery China and its DNA was extracted from 180 young leave collected from greenhouse in Sanya, China.

We assembled the genomes of G. thurberi and G. davidsonii using data from both the nanopore long-read and the Hi-C short-read technologies. We produced 114.3 Gb and 108.3 Gb clean reads, respectively, for G. thurberi (~ 146×) and G. davidsonii (~ 135×) using the Nanopore platform (publication: Additional file 1: Table S1-S2). After correction using the Illumina short reads, we generated a G. thurberi genome of 779.6 Mb with a contig N50 of 24.7 Mb; the corresponding values for G. davidsonii were 801.2 Mb and 26.8 Mb (publication: Table 1 and Additional file 1: Table S3); the sequence continuities are significantly improved for both species as compared with other recently reported genome assemblies.  

Table 1. Summary of Nanopore sequencing clean data in G. thurberi and G.davidsoni

Species Gossypium thurberi 'D1-5'

Gossypium davidsonii 'D3-d-8'

Sequence Number 3,575,506 3,237,739
Total Length 114,287,348,957 108,304,182,926
Contig N50 42,915 43,855
Contig N90 18,985 20,294
Average Length 31,963 33,450
Max Length 431,233 409,570
Mean Quality 8.33 8.35

Publication

Yang Z, Ge X, Li W, Jin Y, Liu L, Hu W, Liu F, Chen Y, Peng S, Li F. Cotton D genome assemblies built with long-read data unveil mechanisms of centromere evolution and stress tolerance divergence. BMC biology. 2021 Jun 03; 19(1):115.

Properties
Additional information about this analysis:
Property NameValue
Analysis Typewhole_genome
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/D1_CRI_v1&loc=
Assembly

The chromosomes (pseudomolecules) and scaffolds for Gossypium thurberi '(D1-5)' genome. These files belong to the CRI Assembly v1.0

Chromosomes & scaffolds (FASTA format) G.thurberi_ICR_D1-5.genomic.fa.gz
Functional Analysis

Functional annotation files for the Gossypium thurberi CRI Genome v1.0 are available for download below. The Gossypium thurberi CRI 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 D1_CRI_v1_genes2GO.xlsx.gz
IPR assignments from InterProScan D1_CRI_v1_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways D1_CRI_v1_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs D1_CRI_v1_KEGG-pathways.xlsx.gz

 

Genes

The predicted gene model, their alignments and proteins for Gossypium thurberi '(D1-5)' genome. These files belong to the CRI Assembly v1.0

Predicted gene models with exons (GFF3 format) G.thurberi_ICR_D1-5.gff3.gz
Coding sequences, CDS (FASTA format) G.thurberi_ICR_D1-5.cds.fa.gz
Protein sequences (FASTA format) G.thurberi_ICR_D1-5.pep.fa.gz
Homology

Homology of the Gossypium thurberi CRI 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 CRI Genome v1.0 proteins with NCBI nr homologs (EXCEL file) D1_CRI_v1_vs_nr.xlsx.gz
G. thurberi CRI Genome v1.0 proteins with NCBI nr (FASTA file) D1_CRI_v1_vs_nr_hit.fasta.gz
G. thurberi CRI Genome v1.0 proteins without NCBI nr (FASTA file) D1_CRI_v1_vs_nr_noHit.fasta.gz
G. thurberi CRI Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) D1_CRI_v1_vs_tair.xlsx.gz
G. thurberi CRI Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) D1_CRI_v1_vs_tair_hit.fasta.gz
G. thurberi CRI Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) D1_CRI_v1_vs_tair_noHit.fasta.gz
G. thurberi CRI Genome v1.0 proteins with SwissProt homologs (EXCEL file) D1_CRI_v1_vs_swissprot.xlsx.gz
G. thurberi CRI Genome v1.0 proteins with SwissProt (FASTA file) D1_CRI_v1_vs_swissprot_hit.fasta.gz
G. thurberi CRI Genome v1.0 proteins without SwissProt (FASTA file) D1_CRI_v1_vs_swissprot_noHit.fasta.gz
G. thurberi CRI Genome v1.0 proteins with TrEMBL homologs (EXCEL file) D1_CRI_v1_vs_trembl.xlsx.gz
G. thurberi CRI Genome v1.0 proteins with TrEMBL (FASTA file) D1_CRI_v1_vs_trembl_hit.fasta.gz
G. thurberi CRI Genome v1.0 proteins without TrEMBL (FASTA file) D1_CRI_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 thurberi CRI 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.thurberi_CRI_D1-5_SNP
CottonGen RFLP markers mapped to genome G.thurberi_CRI_D1-5_RFLP
CottonGen SSR markers mapped to genome G.thurberi_CRI_D1-5_SSR
CottonGen InDel markers mapped to genome G.thurberi_CRI_D1-5_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. 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.thurberi_CRI-D1_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.thurberi_CRI-D1_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.thurberi_CRI-D1_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.thurberi_CRI-D1_g.raimondii_cottongen_reftransV1