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Overview
Analysis Name | Gossypium hirsutum (AD1) 'HPF17' genome ZJU_v1 |
Method | SMRTLink (v8.0), hifiasm (v0.2.0), Bowtie2 (v2.2.3), HiC-Pro (v2.7.8) |
Source | (v1.0) |
Date performed | 2024-04-02 |
HPF17 is one Hainan Island cotton (HIC) belonging to a wild Gossypium hirsutum (Heterotypic Synonym: Gossypium purpurascens Poir.) and was collected from Yacheng, Sanya, Hainan Province, China. Hainan Island Native Cotton (HIC) has long been grown extensively on Hainan Island, China. We assembled a high-quality genome of one HIC plant, HPF17. The genome size of HPF17 was estimated to be ~2,055 Mb based on K-mer analysis. We produced 130.65 Gb (~57 x genome equivalent) of high-quality PacBio circular consensus sequencing (CCS) reads and assembled the genome using hifiasm. The initial assembly generated 3,394 contigs with an N50 value of 13.20 Mb. Subsequently, we categorized and ordered the contigs to produce chromosome-scale scaffolds using approximately 50-fold coverage of valid unique interacting paired-end data generated through high-throughput chromosome conformation capture (Hi-C) (Table S12). The final assembly included 2,558,691,823 bases and 3,343 scaffolds, resulting in a scaffold N50 value of 88.21 Mb. A total of 2,267,310,418 (88.61 %) bases from the contigs were anchored and oriented onto pseudochromosomes.
Table S12
Summary of Hi-C data from HPF17 genome |
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Read length (bp) |
100 |
Raw paired-end reads |
1,898,199,945 |
Raw bases (bp) |
569,459,983,500 |
Clean paired-end reads |
1,825,566,132 |
Clean paired-end reads rate (%) |
96.17 |
Unique mapped paired-end reads |
599,098,373 |
Dangling end paired-end reads |
11,986,037 |
Dangling end paired-end reads rate (%) |
2 |
Self-circled paired-end reads |
537,109 |
Self-circled paired-end reads rate (%) |
0.09 |
Dumped paired-end reads |
4,543,916 |
Dumped paired-end reads rate (%) |
0.76 |
Interaction paired-end reads |
582,031,311 |
Interaction paired-end reads rate (%) |
97.15 |
Valid paired-end reads |
581,672,933 |
Valid paired-end reads rate (%) |
97.09 |
Publication: Cheng et al., Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton.
Assembly
The chromosomes (pseudomolecules) for Gossypium hirsutum 'HPF17' genome. These files belong to the Gossypium hirsutum (AD1) 'HPF17' genome ZJU_v1.
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 hirsutum HPF17 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.
Publication
Publication
Cheng Y, Huang C, Hu Y, Jin S, Zhang X, Si Z, Zhao T, Chen J, Fang L, Dai F, Yang W, Wang P, Mei G, Guan X, Zhang T. Gossypium purpurascens genome provides insight into the origin and domestication of upland cotton. Journal of advanced research. 2023 Mar 24.
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. hirsutum HPF17 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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