Gossypium stocksii (E1) genome NSF_v1

Overview
Analysis NameGossypium stocksii (E1) genome NSF_v1
MethodPacBio, Hi-C,Bionano
Source (v1)
Date performed2021-08-07

We report a high-quality de novo genome assembly for G. stocksii (E1). This genome was initially assembled using 58x coverage of PacBio reads, yielding a draft assembly of 316 contigs with N50=17.8 Mb. HiC and Bionano reads were used to order and orient contigs into a final assembly consisting of 13 chromosomes (average length =110 Mb) and containing only 5.7 kb (<0.001%) gap sequence within the chromosomal scaffolds. The assembly has a total length of 1424 Mb, ~93% of the estimated 1359 Mb genome (Hendrix and Stewart 2005).

 

 Assembly Summary G. stocksii
 Coverage (raw) ~58x
 Assembly Length** 1424 Mb
 Total Scaffold Number 13
 Average Contig Length*** 17.54 Mb
 Total Length of Ns 5700
 Scaffold N50 115.60 Mb
 Scaffold N75 106.4 Mb

 ** G. anomalum is 1359 Mb (Hendrix and Stewart, 2005)

 

Publication

Corrinne E Grover, Daojun Yuan, Mark A Arick, II, Emma R Miller, Guanjing Hu, Daniel G Peterson, Jonathan F Wendel, Joshua A Udall, The Gossypium stocksii genome as a novel resource for cotton improvement, G3 Genes|Genomes|Genetics, Volume 11, Issue 7, July 2021, jkab125, https://doi.org/10.1093/g3journal/jkab125

Properties
Additional information about this analysis:
Property NameValue
JBrowse URLhttps://www.cottongen.org/jbrowse/index.html?data=data/E1_NSF_v1&loc=
Analysis Typewhole_genome
Assembly

The chromosomes (pseudomolecules) and scaffolds for Gossypium stocksii '(E1)' genome. This file belongs to the NSF G. stocksii Assembly v1.0

Chromosomes & scaffolds (FASTA format) G.stocksii_NSF_E1.fa.gz
Genes

The predicted gene model, their alignments and proteins for Gossypium stocksii '(E1)' genome. These files belong to the NSF G. stocksii Assembly v1.0

Predicted gene models with exons (GFF3 format) G.stocksii_NSF_E1.gff3.gz
Coding sequences, CDS (FASTA format) G.stocksii_NSF_E1.cds.fa.gz
Protein sequences (FASTA format) G.stocksii_NSF_E1.pep.fa.gz