Gossypium hirsutum (AD1) TM1 genome CRI Assembly v1 & Annotation a1

Overview
Analysis NameGossypium hirsutum (AD1) TM1 genome CRI Assembly v1 & Annotation a1
MethodCanu v. 1.5
SourceG. hirsutum (AD1) TM1 genome CRI assembly
Date performed2019-08-28

About the assembly

The TM-1 assembly was conducted using a Canu-based pipeline (Koren, S. et al. 2017) with the following procedures: longer seed reads were selected with the settings genomeSize = 600000000 and corOutCoverage = 35; raw reads overlapping was detected through a high sensitive overlapper MHAP (mhap-2.1.2, option corMhapSensitivity = low/normal/high), and an error correction was performed through Falcon sense method (option correctedErrorRate = 0.025); error-corrected reads were trimmed of unsupported bases and hairpin adapters in order to reach their longest supporting range with the default parameters, and then the draft assembly was generated using the top 80% longest trimmed reads. The raw Illumina reads were filtered as mentioned in the Illumina sequencing section. Finally, the clean reads from the same sequencing individuals were integrated to correct the SNPs and InDels in the draft assemblies using Pilon v1.22 (Walker, B. J. et al., 2014) with the parameters -mindepth 10 –changes –threads 4 –fix bases.

Summary of the Assembly  
Total sequence length 2,287,866,413
Total ungapped length 2,287,799,113
Gaps between scaffolds 0
Number of scaffolds 599
Scaffold N50 96,727,820
Scaffold L50 11
Number of contigs 1,272
Contig N50 4,760,671
Contig L50 141
Total number of chromosomes and plasmids 26
Number of component sequences (WGS or clone) 599

Publication

Yang, et al., Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nature Communicationsvolume 10, Article number: 2989 (2019). 

Assembly

The chromosomes (pseudomolecules) for G. hrisutum TM-1 genome. These files belong to the CRI Assembly v1

Chromosomes (FASTA format) G.hirsutum_CRI-TM1_assembly_v1.fa.gz
Genes

The predicted gene model, their alignments and proteins for G. hirsutum 'TM-1' genome. These files belong to the CRI Assembly v1 & Annotation a1.0

Predicted gene models with exons (GFF3 format) G.hirsutum_CRI-TM1_v1_a1.0_genemodels.gz
Coding sequences, CDS (FASTA format) G.hirsutum_CRI-TM1_v1_a1.0_cds.gz  
Protein sequences (FASTA format) G.hirsutum_CRI-TM1_v1_a1.0_pep.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.

Homology

Homology of the Gossypium hirsutum CRI-TM1 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 (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

G.hirsutum CRI-TM1 Genome v1.0 proteins with NCBI nr homologs (EXCEL file) AD1_CRI_TM1-v1.0_vs_nr.xlsx.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with NCBI nr (FASTA file) AD1_CRI_TM1-v1.0_vs_nr_hit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins without NCBI nr (FASTA file) AD1_CRI_TM1-v1.0_vs_nr_noHit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) AD1_CRI_TM1-v1.0_vs_tair.xlsx.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) AD1_CRI_TM1-v1.0_vs_tair_hit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) AD1_CRI_TM1-v1.0_vs_tair_noHit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with SwissProt homologs (EXCEL file) AD1_CRI_TM1-v1.0_vs_swissprot.xlsx.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with SwissProt (FASTA file) AD1_CRI_TM1-v1.0_vs_swissprot_hit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins without SwissProt (FASTA file) AD1_CRI_TM1-v1.0_vs_swissprot_noHit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with TrEMBL homologs (EXCEL file) AD1_CRI_TM1-v1.0_vs_trembl.xlsx.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins with TrEMBL (FASTA file) AD1_CRI_TM1-v1.0_vs_trembl_hit.fasta.gz
G.hirsutum CRI-TM1 Genome v1.0 proteins without TrEMBL (FASTA file) AD1_CRI_TM1-v1.0_vs_trembl_noHit.fasta.gz

 

Functional Analysis

Functional annotation files for the Gossypium hirsutum CRI-TM1 Genome v1.0 are available for download below. The Gossypium hirsutum CRI-TM1 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 AD1_CRI_TM1-v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan AD1_CRI_TM1-v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways AD1_CRI_TM1-v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs AD1_CRI_TM1-v1.0_KEGG-pathways.xlsx.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 hirsutum 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.hirsutum_CRI_TM1-v1.0_SNP
CottonGen InDel markers mapped to genome G.hirsutum_CRI_TM1-v1.0_InDel
CottonGen RFLP markers mapped to genome G.hirsutum_CRI_TM1-v1.0_RFLP
CottonGen SSR markers mapped to genome G.hirsutum_CRI_TM1-v1.0_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. hirsutum 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. hirsutum_CRI-TM1-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G. hirsutum_CRI-TM1-v1.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G. hirsutum_CRI-TM1-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G. hirsutum_CRI-TM1-v1.0_g.raimondii_cottongen_reftransV1