Gossypium davidsonii (D3d-8) genome CRI_v1
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Overview
About the assembly The Gossypium davidsonii 'D3d-8' was obtained from the National Wild Cotton Nursery China and its DNA was extracted from 180 young leave collected from greenhouse in Sanya, China. We assembled the genomes of G. thurberi and G. davidsonii using data from both the nanopore long-read and the Hi-C short-read technologies. We produced 114.3 Gb and 108.3 Gb clean reads, respectively, for G. thurberi (~ 146×) and G. davidsonii (~ 135×) using the Nanopore platform (publication: Additional file 1: Table S1-S2). After correction using the Illumina short reads, we generated a G. thurberi genome of 779.6 Mb with a contig N50 of 24.7 Mb; the corresponding values for G. davidsonii were 801.2 Mb and 26.8 Mb (publication: Table 1 and Additional file 1: Table S3); the sequence continuities are significantly improved for both species as compared with other recently reported genome assemblies. Table 1. Summary of Nanopore sequencing clean data in G. thurberi and G.davidsoni
Publication Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium davidsonii '(D3d-8)' genome. These files belong to the CRI Assembly v1.0
Functional Analysis
Functional annotation files for the Gossypium davidsonii CRI Genome v1.0 are available for download below. The Gossypium davidsonii CRI 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 davidsonii '(D3d-8)' genome. These files belong to the CRI Assembly v1.0
Homology
Homology of the Gossypium davidsonii CRI 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
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 davidsonii CRI D3d-8 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. davidsonii 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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