Gossypium anomalum (B1) genome NSF_v1
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Overview
We report a high-quality de novo genome assembly for G. anomalum (B1). This genome was initially assembled using 55x coverage of PacBio reads, yielding a draft assembly of 229 contigs with an N50 of 11 Mb. HiC reads (140.5 million) were integrated to the final, contiguous assembly, consisting of 13 chromosomes with an average length of 92 Mb and containing only 20.7 kb (0.002%) gap sequence within the chromosomal scaffolds. The total assembly is composed of 68 contigs (including the 13 chromosomal scaffolds) with a total length of 1193 Mb, ~88% of the estimated 1359 Mb genome (Hendrix and Stewart 2005).
** G. anomalum is 1359 Mb (Hendrix and Stewart, 2005)
Publication Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium anomalum '(B1)' genome. This file belongs to the NSF Assembly v1.0
Functional Analysis
Functional annotation files for the Gossypium anomalum NSF Genome v1.0 are available for download below. The Gossypium anomalum 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 anomalum '(B1)' genome. These files belong to the NSF Assembly v1.0
Homology
Homology of the Gossypium anomalum 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 anomalum 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. anomalum 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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