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Overview
Global statistics
| Genomic feature |
Gossypium arboreum 'GPD5lz' HAU.v1 (NCBI: ASM2569854v1) |
| Total sequence length |
751,041,726 |
| Total ungapped length |
751,033,826 |
| Gaps between scaffolds |
0 |
| Number of scaffolds |
289 |
| Scaffold N50 |
57,716,579 |
| Scaffold L50 |
7 |
| Number of contigs |
368 |
| Contig N50 |
17,043,680 |
| Contig L50 |
18 |
| Total number of chromosomes and plasmids |
65 |
| Number of component sequences (WGS or clone) |
268 |
Publication
Wang, M. et al. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat. Genet. 2022 Dec;54(12):1959-1971. doi: 10.1038/s41588-022-01237-2. Epub 2022 Dec 6. .
Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium raimondii (D5) genome. This file belongs to the HAU G. raimondii 'GPD5lz' Assembly v1.0.
Genes
The predicted gene model, their alignments and proteins for Gossypium raimondii (D5) genome. These files belong to the HAU G. raimondii 'GPD5lz' Assembly v1.0.
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 raimondii HAU 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.
Publication
Wang M, Li J, Qi Z, Long Y, Pei L, Huang X, Grover CE, Du X, Xia C, Wang P, Liu Z, You J, Tian X, Ma Y, Wang R, Chen X, He X, Fang DD, Sun Y, Tu L, Jin S, Zhu L, Wendel JF, Zhang X. Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium. Nat Genet. 2022 Dec;54(12):1959-1971. doi: 10.1038/s41588-022-01237-2. Epub 2022 Dec 6. PMID: 36474047.
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. raimondii genome assembly. Alignments with an alignment length of 97% and 90% identify were preserved. The available files are in GFF3 format.
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