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Overview
Analysis Name | Gossypium herbaceum (A1) 'A1a wild' genome HAU_v1 |
Method | Oxford Nanopore; Illumina (Canu v. 1.3) |
Source | (v1) |
Date performed | 2023-09-08 |
About the assembly
Seven new assembly and annotation of seven diploid cotton genomes were reported in Wang, et al. Net. Genet. 2022 Dec. They are: Two of G. herbaceum (A1) genomes (a wild form 'A1a' and an A1 cultivar 'ZhongCao1’), each one of G. anomalum (B1), G. sturtianum (C1), G. stocksii (E1), G. longicalyx (F1) and G. bickii (G1). The seven genomes were assembled by integration of Nanopore long reads (126–161×), Illumina short reads (52–79×) and high-throughput chromosome conformation capture (Hi-C) data. Table 1 is the summary of detailed information in 7 genome assemblies.
Table 1. Summary of detailed information in 7 genome assemblies.
Assembly Metrics (bp) |
G.herbaceum (A1a) |
G.herbaceum (A1) |
G.anomalum (B1) |
G.sturtianum (C1) |
G.stocksii (E1) |
G.longicalyx (F1) |
G.bickii (G1) |
Total length of all contigs |
151,8491,120 |
1,621,008,062 |
1,202,727,438 |
1,903,530,088 |
1,442,088,789 |
1,198,534,575 |
1,606,432,167 |
Number of contigs |
759 |
848 |
162 |
564 |
126 |
148 |
154 |
Contig N50 |
10,515,852 |
11,199,225 |
19,802,926 |
7,671,138 |
28,801,805 |
20,138,000 |
22,888,721 |
Contig N90 |
3,279,696 |
3,426,106 |
4,795,930 |
1,970,427 |
6,479,102 |
5,689,122 |
5,951,034 |
Minimum contig length |
1,618 |
3,584 |
254,410 |
30,321 |
39,072 |
40,977 |
31,914 |
Average contig length |
1,785,825 |
1,910,051 |
3,836,759 |
3,375,053 |
11,445,149 |
8,098,206 |
10,431,377 |
Maximum contig length |
46,901,260 |
44,454,407 |
10,090,100 |
31,024,449 |
64,292,180 |
56,164,400 |
74,215,947 |
Total length of scaffolds |
1,518,510,620 |
1,514,399,279 |
1,202,738,338 |
1,903,576,288 |
1,442,098,089 |
1,198,547,475 |
1,606,445,567 |
Number of scaffolds |
600 |
651 |
53 |
122 |
33 |
19 |
20 |
Scaffold N50 |
123,512,226 |
124,037,455 |
98,351,605 |
156,041,810 |
115,821,386 |
95,944,508 |
132,272,514 |
Scaffold N90 |
94,341,082 |
94,910,960 |
73,514,615 |
110,824,594 |
88,888,218 |
76,618,481 |
97,521,415 |
Minimum scaffold length |
3,584 |
1,618 |
30,275 |
30,321 |
39,072 |
66,792 |
31,914 |
Average scaffold length |
2,530,851 |
2,326,266 |
22,693,176 |
15,603,084 |
43,699,942 |
63,081,446 |
80,322,278 |
Maximum scaffold length |
134,223,852 |
137,970,533 |
107,526,953 |
173,404,516 |
129,798,129 |
110,469,152 |
152,440,763 |
Anchored length |
1,496,892,602 |
1,490,728,467 |
1,197,579,856 |
1,891,333,840 |
1,438,429,494 |
1,197,329,593 |
1,605,310,299 |
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
Assembly
The chromosomes (pseudomolecules) and scaffolds for Gossypium herbaceum (A1) wild genome. This file belongs to the HAU G. herbaceum A1 wild Assembly v1.0.
Chromosomes & scaffolds (FASTA format) |
G.herbaceum_ A1_wild_genome_HAU.fa.gz |
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 herbaceum HAU v1.0 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. herbaceum 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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