[DOI] 10.5524/100984
[Title] Supporting data for "A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of Chinese No.1 cotton variety CRI-12"
[Release Date] 2022-01-28
[Citation] Lu, X; Chen, X; Wang, D; Yin, Z; Wang, J; Fu, X; Wang, S; Guo, L; Zhao, L; Cui, R; Dai, M; Rui, C; Fan, Y; Zhang, Y; Sun, L; Malik, W, A; Han, M; Chen, C; Ye, W (2022): Supporting data for "A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of Chinese No.1 cotton variety CRI-12" GigaScience Database. http://dx.doi.org/10.5524/100984
[Data Type] Genomic,Transcriptomic
[Dataset Summary] Gossypium hirsutum L. is the most widely cultivated cotton species, and a high-quality reference genome is necessary for researching the molecular mechanism of agronomic traits in cotton. Here, we adopted the PacBio platform and Hi-C sequencing technologies to assemble a new upland cotton genome of the Chinese No.1 cotton variety CRI-12. We generated a high-quality assembled CRI-12 genome of 2.31 Gb with a contig N50 of 19.65 Mb, which was superior to reported genomes. Comparisons between CRI-12 and other reported genomes revealed 7,966 structural variations (SVs) and 7,378 presence/absence variations (PAVs). The distribution of the haplotypes among A-genome (G. arboreum), D-genome (G. raimondii), and AD-genome (G. hirsutum and G. barbadense) suggested that many haplotypes were lost and recombined in the process of polyploidization. More than half of the haplotypes that correlated with different tolerances were located on chromosome D13, suggesting that this chromosome may be important for wide adaptation. In addition, DNA methylation may provide adaptive advantages in environmental adaptation by whole-genome bisulfite sequencing (WGBS) analysis. This research provides a new reference genome for molecular biology research on Gossypium hirsutum L. and decodes the broad environmental adaptation mechanism in the Chinese No.1 cotton variety CRI-12.
[File Location] https://ftp.cngb.org/pub/gigadb/pub/10.5524/100001_101000/100984/
[File name] - [File Description]
Zhong12.fasta - Gossypium hirsutum genome assembly
readme_100984.txt - None
pasa2.longest.filter.cds - Gossypium hirsutum coding gene nucleotide sequences
pasa2.longest.filter.pep - Gossypium hirsutum coding gene translated sequences
Zhong12.Repeat.gff3 - Gossypium hirsutum repeat annotation
all.cds - Gossypium hirsutum gene family alignments of coding gene nucleotide sequences between Gossypium hirsutum CRI-12 and other cotton species
all.pep - Gossypium hirsutum gene family alignments of coding gene translated sequences between Gossypium hirsutum CRI-12 and other cotton species
pep.nwk - Phylogenetic tree file
mianhua_BUSCO_result.txt - BUSCO results output file - summary
pav.KEGG_pathway_scatterplot.pdf - Figure of Structural Variants analysis of presence/absence variations in terms of KEGG Pathway enrichment (PDF format)
trinity.out.Trinity.fasta - Gossypium hirsutum De novo transcriptome assembly
CRI12_L_1_FRAS210013025-1r.clean.rpkm - Expression levels of total RNA isolated from leaf of Gossypium hirsutum at trefoil stage
CRI12_R_1_FRAS210013040-1r.clean.rpkm - Expression levels of total RNA isolated from root of Gossypium hirsutum at trefoil stage
CRI12_S_1_FRAS210013055-1r.clean.rpkm - Expression levels of total RNA isolated from stem of Gossypium hirsutum at trefoil stage
PAV.csv - Tabular data showing results of Structural Variants analysis of presence/absence variations (CSV format)
pav.GO_pathway_scatterplot.pdf - Figure of Structural Variants analysis of presence/absence variations in terms of GO Pathway enrichment (PDF format)
pav.gene.difgoall.filt.merg.csv - Tabular data showing results of Structural Variants analysis of presence/absence variations in terms of GO Pathway enrichment (CSV format)
pav.GO_pathway_scatterplot.png - Figure of Structural Variants analysis of presence/absence variations in terms of GO Pathway enrichment (PNG format)
pav.gene.difkegg.filt.csv - Tabular data showing results of Structural Variants analysis of presence/absence variations in terms of KEGG Pathway enrichment (CSV format)
pav.KEGG_pathway_scatterplot.png - Figure of Structural Variants analysis of presence/absence variations in terms of KEGG Pathway enrichment (PNG format)
sv.csv - Tabular data showing results of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations (CSV format)
sv.GO_pathway_scatterplot.pdf - Figure of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations in terms of GO Pathway enrichment (PDF format)
pasa2.longest.filter.gff3 - Gossypium hirsutum coding gene annotations
sv.gene.difkegg.filt.csv - Tabular data showing results of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations in terms of KEGG Pathway enrichment (CSV format)
sv.KEGG_pathway_scatterplot.pdf - Figure of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations in terms of KEGG Pathway enrichment (PDF format)
Zhong12.tRNA.gff3 - Gossypium hirsutum non-coding RNA annotations - tRNA
Zhong12.miRNA.gff3 - Gossypium hirsutum non-coding RNA annotations - miRNA
Zhong12.rRNA.gff3 - Gossypium hirsutum non-coding RNA annotations - rRNA
stat.function.stat.csv - Functional annotation - Summary of Functional Annotation
NR.result - Functional annotation - NR result
stat.iprscan.golist - Functional annotation - InterPro GO result
stat.venn.svg - Venn Diagram of Functional Annotation (SVG format)
Swissprot.result - Functional annotation - SwissProt result
KEGG.result - Functional annotation - KEGG result
stat.iprscan.pfamlist - Functional annotation - InterPro pfamlist
stat.iprscan.wego - Functional annotation - InterPro Web Gene Ontology result
IPRSCAN.result - Functional annotation - InterPro result
all.sort.bam - Gossypium hirsutum alignments to Hi-C data
sv.gene.difgoall.filt.merg.csv - Tabular data showing results of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations in terms of GO Pathway enrichment (CSV format)
sv.GO_pathway_scatterplot.png - Figure of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations in terms of GO Pathway enrichment (PNG format)
sv.KEGG_pathway_scatterplot.png - Figure of Structural Variants analysis of deletion variations, insertion variations, copy number variants, and inversion variations in terms of KEGG Pathway enrichment (PNG format)
Zhong12.snRNA.gff3 - Gossypium hirsutum non-coding RNA annotations - snRNA
mianhua_missing_busco_list.tsv - BUSCO results output file - list of missing BUSCOs
mianhua_full_table.tsv - BUSCO full table results output file
[License]
All files and data are distributed under the Creative Commons Attribution-CC0 License unless specifically stated otherwise, see http://gigadb.org/site/term for more details.
[Comments]
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