Cotton Cluster File Request

Name: 
Santosh Kumar D
Email Address: 
santoshkumar.dodda@bioseed.com
Email Address: 
santoshkumar.dodda@bioseed.com
Organization: 
Bioseed Research India
Acknowledgement: 
0
Acknowledgement4: 
0

Material and Methods

DNA was extracted from Gossypium turneri (accession D10-3) using CTAB techniques (Kidwell and Osborn 1992). DNA concentration was measured by a Qubit Fluorometer (ThermoFisher, Inc.). The sequencing library was constructed according to PacBio recommendations at the BYU DNA Sequencing Center (DNASC). Fragments >18 kb were selected for sequencing via BluePippen (Sage Science, LLC). Prior to sequencing, the size distribution of fragments in the libraries was evaluated using a Fragment Analyzer (Advanced Analytical Technologie... [more]

Resource Titles: 
Assembly
Gene Predictions
Downloads
Functional Analysis
Homology
Markers
Transcript Alignments
Resource Blocks: 

The Gossypium turneri NSF(BYU) D10-3 Genome v1.0 assembly files are available in FASTA and GFF3 formats.

Chromosome (FASTA file) Gossypium_turneri_NSF-v1.0.fasta.gz

 

The Gossypium turneri NSF(BYU) D10-3 genome v1.0.a2 gene prediction files are available in FASTA and GFF3 formats.

Transcript sequences (FASTA file) Gossypium_turneri_NSF-v1.0.transcripts.fasta.gz
CDS sequences (FASTA file) Gossypium_turneri_NSF-v1.0.CDs.fasta.gz
Gene sequences  (FASTA file) Gossypium_turneri_NSF-v1.0.genes.fasta.gz
Protein sequences  (FASTA file) Gossypium_turneri_NSF-v1.0.proteins.fasta.gz
Genes (GFF3 file) Gossypium_turneri_NSF-v1.0.genes.gff3.gz

 

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 annotation files for the Gossypium turneri D10-3 Genome v1.0 are available for download below. The Gossypium turneri NSF D10-3 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 D10_NSF-v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan D10_NSF-v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways D10_NSF-v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs D10_NSF-v1.0_KEGG-pathways.xlsx.gz

 

Homology of the Gossypium turneri NSF 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

Gossypium turneri NSF v1.0 proteins with NCBI nr homologs (EXCEL file) D10_NSF-v1.0_vs_nr.xlsx.gz
Gossypium turneri NSF v1.0 proteins with NCBI nr (FASTA file) D10_NSF-v1.0_vs_nr_hit.fasta.gz
Gossypium turneri NSF v1.0 proteins without NCBI nr (FASTA file) D10_NSF-v1.0_vs_nr_noHit.fasta.gz
Gossypium turneri NSF v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) D10_NSF-v1.0_vs_tair.xlsx.gz
Gossypium turneri NSF v1.0 proteins with arabidopsis (Araport11) (FASTA file) D10_NSF-v1.0_vs_tair_hit.fasta.gz
Gossypium turneri NSF v1.0 proteins without arabidopsis (Araport11) (FASTA file) D10_NSF-v1.0_vs_tair_noHit.fasta.gz
Gossypium turneri NSF v1.0 proteins with SwissProt homologs (EXCEL file) D10_NSF-v1.0_vs_swissprot.xlsx.gz
Gossypium turneri NSF v1.0 proteins with SwissProt (FASTA file) D10_NSF-v1.0_vs_swissprot_hit.fasta.gz
Gossypium turneri NSF v1.0 proteins without SwissProt (FASTA file) D10_NSF-v1.0_vs_swissprot_noHit.fasta.gz
Gossypium turneri NSF v1.0 proteins with TrEMBL homologs (EXCEL file) D10_NSF-v1.0_vs_trembl.xlsx.gz
Gossypium turneri NSF v1.0 proteins with TrEMBL (FASTA file) D10_NSF-v1.0_vs_trembl_hit.fasta.gz
Gossypium turneri NSF v1.0 proteins without TrEMBL (FASTA file) D10_NSF-v1.0_vs_trembl_noHit.fasta.gz

 

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 turneri 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.turneri_D10_NSF-v1.0_SNP
CottonGen InDel markers mapped to genome G.turneri_D10_NSF-v1.0_InDel
CottonGen RFLP markers mapped to genome G.turneri_D10_NSF-v1.0_RFLP
CottonGen SSR markers mapped to genome G.turneri_D10_NSF-v1.0_SSR

 

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. turneri 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.turneri_D10_NSF-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.turneri_D10_NSF-v1.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.turneri_D10_NSF-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.turneri_D10_NSF-v1.0_g.raimondii_cottongen_reftransV1

NCBI cotton sequences updated (7/9/19)

On Mar 14, 2019 and  56,299 genes, 212,530 mRNA, and 212,489 proteins from  NCBI were uploaded to CottonGen. They are available through the 'Search Genes and Transcripts' (dataset=NCBI Cotton Data) and 'Search Sequences' (type=region). 

Material and Methods

DNA was extracted from G. raimondii (accession D5-4) plants using CTAB techniques (Kidwell and Osborn 1992). DNA concentration was measured by a Qubit Fluorometer (ThermoFisher, Inc.). The sequencing library was constructed according to PacBio recommendations at the BYU DNA Sequencing Center (DNASC). Fragments >18 kb were selected for sequencing via BluePippen (Sage Science, LLC). Prior to sequencing, the size distribution of fragments in the libraries was evaluated using a Fragment Analyzer (Advanced Analytical Technologies, Inc). Eight and eleven PacBio cells were sequenced... [more]

Resource Titles: 
Assembly
Genes
Downloads
Functional Analysis
Homology
Transcript Alignments
Markers
Resource Blocks: 

The chromosomes (de novo) for G. raimondii 'D5-4' genome. These files belong to the NSF-D5 (also called BYU-D5) Assembly v1.0

Chromosomes (FASTA format) G.raimondii_NSF-D5_assembly_v1.fasta.gz
Chromosomes (GFF3 format) G.raimondii_NSF-D5_assembly_v1.gff3

The predicted gene model, their alignments and proteins for G. raimondii 'D5-4' genome. These files belong to the NSF-D5 Assembly v1 & Annotation a1

Transcripts sequences (FASTA format) G.raimondii_NSF-D5_v1_a1_transcripts.gz
Protein sequences (FASTA format) G.raimondii_NSF-D5_v1_a1_proteins.gz

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 annotation files for the Gossypium raimondii NSF Genome v1.0 are available for download below. The Gossypium raimondii NSF 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 D5_NSF-v1.0_genes2GO.xlsx.gz
IPR assignments from InterProScan D5_NSF-v1.0_genes2IPR.xlsx.gz
Proteins mapped to KEGG Pathways D5_NSF-v1.0_KEGG-orthologis.xlsx.gz
Proteins mapped to KEGG Orthologs D5_NSF-v1.0_KEGG-pathways.xlsx.gz

 

Homology of the Gossypium raimondii NSF 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 BYU Genome v1.0 proteins with NCBI nr homologs (EXCEL file) D5_NSF_vs_nr.xlsx.gz
G. raimondii BYU Genome v1.0 proteins with NCBI nr (FASTA file) D5_NSF_vs_nr_hit.fasta.gz
G. raimondii BYU Genome v1.0 proteins without NCBI nr (FASTA file) D5_NSF_vs_nr_noHit.fasta.gz
G. raimondii BYU Genome v1.0 proteins with arabidopsis (Araport11) homologs (EXCEL file) D5_NSF_vs_tair.xlsx.gz
G. raimondii BYU Genome v1.0 proteins with arabidopsis (Araport11) (FASTA file) D5_NSF_vs_tair_hit.fasta.gz
G. raimondii BYU Genome v1.0 proteins without arabidopsis (Araport11) (FASTA file) D5_NSF_vs_tair_noHit.fasta.gz
G. raimondii BYU Genome v1.0 proteins with SwissProt homologs (EXCEL file) D5_NSF_vs_swissprot.xlsx.gz
G. raimondii NSF Genome v1.0 proteins with SwissProt (FASTA file) D5_NSF_vs_swissprot_hit.fasta.gz
G. raimondii BYU Genome v1.0 proteins without SwissProt (FASTA file) D5_NSF_vs_swissprot_noHit.fasta.gz
G. raimondii BYU Genome v1.0 proteins with TrEMBL homologs (EXCEL file) D5_NSF_vs_trembl.xlsx.gz
G. raimondii BYU Genome v1.0 proteins with TrEMBL (FASTA file) D5_NSF_vs_trembl_hit.fasta.gz
G. raimondii BYU Genome v1.0 proteins without TrEMBL (FASTA file) D5_NSF_vs_trembl_noHit.fasta.gz

 

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_NSF-v1.0_g.arboreum_cottongen_reftransV1
G. barbadense CottonGen RefTrans v1 G.raimondii_NSF-v1.0_g.barbadense_cottongen_reftransV1
G. hirsutum CottonGen RefTrans v1 G.raimondii_NSF-v1.0_g.hirsutum_cottongen_reftransV1
G. raimondii CottonGen RefTrans v1 G.raimondii_NSF-v1.0_g.raimondii_cottongen_reftransV1
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 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.raimondii_D5_NSF-v1.0_SNP
CottonGen InDel markers mapped to genome G.raimondii_D5_NSF-v1.0_InDel
CottonGen RFLP markers mapped to genome G.raimondii_D5_NSF-v1.0_RFLP
CottonGen SSR markers mapped to genome G.raimondii_D5_NSF-v1.0_SSR