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

Gossypium turneri (accession D10-3) plants was collected at the Brigham Young University (BYU) greenhouse. DNA was extracted 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 Tech... [more]

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

Leaf tissue of mature G. raimondii (accession D5-4) plants was collected at the Brigham Young University (BYU) greenhouse. DNA was extracted 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... [more]

Resource Titles: 
Assembly
Genes
Downloads
Resource Blocks: 

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

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

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

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

  • Masonbrink RE, Gallagher JP, Jareczek JJ, Renny-Byfield S, Grover CE, Gong L, Wendel JF. CenH3 evolution in diploids and polyploids of three angiosperm genera. BMC Plant Biol. 2014 Dec 30;14:383. doi: 10.1186/s12870-014-0383-3.
BACKGROUND: Centromeric DNA sequences alone are neither necessary nor sufficient for centromere specification. The centromere specific histone, CenH3, evolves rapidly in many species, perhaps as a coevolutionary response to rapidly evolving centromeric DNA. To gain insight into CenH3 evolution, we characterized patterns of nucleotide and protein diversity among diploids and allopolyploids within three diverse angiosperm genera, Brassica, Oryza, ... [more]

Cotton Cluster File Request

Name: 
Dick Fabro
Email Address: 
Via Galvani 138
Email Address: 
Via Galvani 138
Organization: 
Giphy GbR
Acknowledgement: 
0
Acknowledgement4: 
0