Gossypium stocksii (E1) genome NSF_v1
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Overview
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).
** 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 Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium stocksii '(E1)' genome. This file belongs to the NSF G. stocksii Assembly v1.0
Functional Analysis
Functional annotation files for the Gossypium stocksii NSF Genome v1.0 are available for download below. The Gossypium stocksii NSF 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
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
Homology
Homology of the Gossypium stocksii 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 2021-09) and 1e-6 for the Arabidoposis proteins (Araport11), UniProtKB/SwissProt (Release 2021-09), and UniProtKB/TrEMBL (Release 2021-09) databases. The best hit reports are available for download in Excel format.
Protein Homologs
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 stocksii NSF 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.
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. stocksii genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
Links
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