Assembly of Pepino Genome Based on PacBio's Third-generation Sequencing Technology

doi:10.13560/j.cnki.biotech.bull.1985.2022-0344

Abstract

Abstract:

Pepino（Solanum muricatum）has a variety of biological activities such as antioxidation,antitumor activity,antidiabetic activity. To enrich genomic information and evolutionary development of Solanaceae crops,we obtained the whole genome sequencing information of pepino,which lays the foundation for pepino-related molecular studies. Illumina HiSeq sequencing platform was used to construct a small fragment library for pepino characterization and evaluation while using plant tissues of pepino as experimental material. Then third-generation sequencing technology PacBio's sequencing technology and Hi-C technology were used to construct a whole genome database of the pepino. Different bioinformatics methods were to study assembling the obtained pepino genomes,function annotating and evolutionary analysis. The results showed that a total of 54.11 Gb of Illumina HiSeq data were acquired. First,55.08 Gb of PacBio data were obtained with an average reads length of 14 179 bp. The obtained chromosome conformation capture（Hi-C）was 143 Gb and total length contig sequemce of the assembled genome was 1.16 Gb,with a scaffold N50 of 22.63 Mb,chromosomes with a total of 1.12 Gb length of sequence that can be mapped to 12 chromosomes,accounting for 97.16% of the total genome sequence,respectively. Among the sequences,the length of sequences for which the order and orientation could be determined was 1.08 Gb,96.11% of the total length genes were localized chromosomal sequences. Based on the estimated genome size（1.25 Gb）,the 64.22% repeat sequences were predicted,including 41 571 genes and 99.06% of which could be annotated to NR,GO,KEGG and other databases. Noncoding RNAs included 4 360 tRNAs,5 677 rRNAs,154 miRNAs,and a total of 449 pseudogenes were identified. The evolutionary time between pepino and potato was at approximately 12.82 MYA.

Key words: pepino, genome, PacBio third generation sequencing technology, gene annotation

SI Cheng, ZHONG Qi-wen, YANG Shi-peng. Assembly of Pepino Genome Based on PacBio's Third-generation Sequencing Technology[J]. Biotechnology Bulletin, 2022, 38(9): 180-190.

Figures/Tables 14

References 49

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项目Item	总长度Total length/bp	总数量Total number	最大长度Max length/bp	N50长度N50-length/bp	N90长度N90-length/bp
Contig	1 141 353 553	1 952 498	125 830	2 049	165
Scaffold	1 169 596 440	1 679 956	191 961	3 185	199

项目Item	总长度Total length/bp	总数量Total number	最大长度Max length/bp	N50长度N50-length/bp	N90长度N90-length/bp
Contig	1 141 353 553	1 952 498	125 830	2 049	165
Scaffold	1 169 596 440	1 679 956	191 961	3 185	199

项目Item	基因组信息Genome information
总数TotalNum	1 566
最小长度MinLen	1 000
Scaffold的数量ScfNum	1 566
Scaffold的长度ScfLen/bp	1 156 096 017
Scaffold N50长度ScfN50/bp	87 253 278
Scaffold N90长度ScfN90/bp	74 267 810
最长的scaffold ScfMax/bp	111 830 586
Scaffold数目mScfNum	0
Scaffold的长度mScfLen	0
Contig数目CtgNum	1 813
Ctg长度CtgLen/bp	1 156 071 317
Contig N50的长度CtgN50/bp	22 628 432
Contig N90的长度CtgN90/bp	596 645
最长的contig CtgMax/bp	83 851 337
GC含量GC/%	35.83
Contig数目GapNum	247
Gap长度GapLen/bp	24 700
最大的gap MaxGap	100

项目Item	基因组信息Genome information
总数TotalNum	1 566
最小长度MinLen	1 000
Scaffold的数量ScfNum	1 566
Scaffold的长度ScfLen/bp	1 156 096 017
Scaffold N50长度ScfN50/bp	87 253 278
Scaffold N90长度ScfN90/bp	74 267 810
最长的scaffold ScfMax/bp	111 830 586
Scaffold数目mScfNum	0
Scaffold的长度mScfLen	0
Contig数目CtgNum	1 813
Ctg长度CtgLen/bp	1 156 071 317
Contig N50的长度CtgN50/bp	22 628 432
Contig N90的长度CtgN90/bp	596 645
最长的contig CtgMax/bp	83 851 337
GC含量GC/%	35.83
Contig数目GapNum	247
Gap长度GapLen/bp	24 700
最大的gap MaxGap	100

方法 Method	软件 Software	物种 Species	基因数目 Gene number
Ab initio	Augustus		26 025
	SNAP		47 891
Homology-based	GeMoMa	拟南芥A. thaliana	26 652
		辣椒C. annuum	37 150
		番茄S. lycopersicum	32 312
		潘那利番茄 S. pennellii	33 755
		马铃薯S. tuberosum	51 586
RNAseq	GeneMarkS-T		19 020
	PASA		12 454
Integration	EVM		41 571