Whole-genome sequence of the planarian Dugesia japonica combining Illumina and PacBio data

被引：11

作者：

Tian, Qingnan ^{[1
]}

Guo, Qi ^{[1
]}

Guo, Yanan ^{[1
]}

Luo, Longhai ^{[3
]}

Kristiansen, Karsten ^{[4
]}

Han, Zujing ^{[3
]}

Fang, Huimin ^{[1
]}

Zhang, Shoutao ^{[1
,2
]}

机构：

[1] Zhengzhou Univ, Sch LifeSci, Zhengzhou, Henan, Peoples R China

[2] Henan Key Lab Bioact Macromol, Zhengzhou, Henan, Peoples R China

[3] Beijing IgeneCode Biotech Co Ltd, Beijing, Peoples R China

[4] Univ Copenhagen, Dept Biol, Copenhagen, Denmark

来源：

GENOMICS | 2022年 / 114卷 / 02期

基金：

中国国家自然科学基金;

关键词：

Bioinformatics; Whole genome sequencing; Functional annotation; D; japonica; Planarian; STEM-CELLS; SCHMIDTEA-MEDITERRANEA; GENE; REGENERATION; PREDICTION; NEOBLASTS; ALIGNMENT; TOPHAT;

D O I：

10.1016/j.ygeno.2022.110293

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Advances in stem cell biology have posed the challenges in revealing the mechanistic themes underlying whole tissues and organs formation during regeneration. The planarian Dugesia japonica is an ideal model organism for the study of regeneration and stem cell biology. However, the genome resources for this species are still limited. Here, we combined single-molecule real-time DNA sequencing platform Pacific Biosciences (PacBio) sequencing, Illumina paired-end sequencing and 10x Genomics linked reads data to obtain the whole-genome sequence of the planarian D. japonica. The final assembled D. japonica genome is 1.13G with contig N50 of 248.44 kb, and scaffold N50 of 652.52 kb. Repeat elements account for 64.92% of the genome, and 12,031 protein coding genes were annotated, of which 10,114 genes had at least one functional annotation, representing 84.07% of the total genes. We present a highly contiguous genome assembly of D. japonica. The D. japonica genome assembly, together with gene annotation and transcriptome data provide a valuable resource to investigate molecular mechanism of planarian and stem cell research.

引用

页数：10

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