Gossypium arboreum (A2) 'SXY1' genome HAU_v1

Overview


Analysis Name	Gossypium arboreum (A2) 'SXY1' genome HAU_v1
Method	llumina and PacBio
Source	(v1)
Date performed	2021-08-08

About the assembly

In this study, we applied Oxford Nanopore sequencing technology to assemble G. rotundifolium (K₂*) 'K201', G. arboreum (A₂) 'SXY1', and G. raimondii (D₅) 'D502' genomes. G. arboreum and G. raimondii genomes have been de novo assembled previously using Illumina and PacBio reads, but both genomes have a number of sequence gaps and require an improvement in assembly contiguity. We generated a total of 304 Gb, 212 Gb, 125 Gb Nanopore sequencing data with a genome coverage 124×, 131×, 167× for K₂*, A₂ and D₅, respectively. We assembled 3,593, 1,173 and 366 contigs for G. rotundifolium, G. arboreum and G. raimondii with a contig length of 2.44 Gb, 1.62 Gb and 0.75 Gb, respectively (Table 1). These initial contigs were polished using Illumina paired-end reads with a genome coverage of 108×, 118×, 132× for K₂*, A₂ and D₅. The contig N50 is 5.33 Mb, 11.69 Mb and 17.04 Mb for K₂*, A₂ and D₅, respectively. The maximum contig has a length of 32.72 Mb, 58.57 Mb and 43.74 Mb. After polishing contig using Illumina reads, we used high-through chromosome conformation capture (Hi-C) data to order and orient contigs, aimed at constructing pseudo chromosomes of each species. In the Hi-C assisted assembly, 2,559, 485 and 201 contigs were placed on the 13 chromosomes of K₂*, A₂ and D₅ genomes, occupying over 99% of genome length.

*Should be K₁₂

Table 1. Summary of genome assemblies and annotations of G. rotundifolium, G. arboreum and G.raimondii.

Genomic feature	G. rotundifolium 'Grot K201'	*G. arboreum* 'Shixiya1'	G. raimondii 'Grai D502'
Total length of contigs, bp	2,444,364,209	1,621,008,062	750,197,587
Total length of scaffolds, bp	2,444,484,509	1,621,030,562	750,205,487
Total length of gaps, bp	120,300	22,500	7,900
Percentage of anchoring	99.28%	99.47%	99.57%
Percentage of anchoring and ordering	93.16%	98.84%	99.01%
Number of contigs	3,593	1,173	366
Number of scaffolds	2,390	948	287
Contig N50, bp	5,326,689	11,691,474	17,043,680
Contig N90, bp	621,066	2,910,421	3,537,560
Scaffold N50, bp	177,839,665	129,592,444	57,716,579
Scaffold N90, bp	115,394,628	93,157,762	49,929,625
Maximun contig length, bp	32,728,186	58,575,076	43,739,617
Maximum scaffold length, bp	205,722,655	143,367,608	63,188,200
GC content	36.38%	35.16%	33.23%
Percentage of repeat sequences	80.92%	68.05%	57.04%
GC content	36.38%	35.16%	33.23%
Number of genes	41,590	41,778	40,820

Supplementary Table 4. Comparing A2 genome with previously published genome version.

Genomic feature	HAU_A₂	WHU_A₂	CRI_A₂
Total assemblied size, bp	1,621,008,062	1,636,985,834	1,710,104,083
Number of total scaffolds	948	1,269	4,516
Total length of gaps, bp	22,500	116,300	3,730,000
Contig N50, bp	11,691,474	1,832,000	1,100,000
Scaffold N50, bp	129,592,444	118,841,821	113,035,596
Scaffold N90, bp	93,157,762	87,096,684	162,124
Percentage of anchoring and ordering	98.84%	92.19%	85.94%
Number of genes	41,778	43,278	40,960

Publication

Wang, M. et al. Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton. Mol Biol Evol. 2021 May 11:msab128. doi: 10.1093/molbev/msab128.

Publication

Wang M, et al. Comparative genome analyses highlight transposon-mediated genome expansion and the evolutionary architecture of 3D genomic folding in cotton. Molecular biology and evolution. 2021 May 11.

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Gossypium arboreum (A2) 'SXY1' genome HAU_v1