Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome

BMC Genomics

Feifei Guan¹  Jian Tian¹  Guoshun Xu¹  Yuquan Xu¹  Ningfeng Wu¹  Liwen Zhang¹  Xiaoqing Liu¹  Haitao Yue²  Jin-Qun Huang³  Jieyin Chen³ 

[1] Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, 100081, Beijing, People’s Republic of China;Department of Biology and Biotechnology, Xinjiang University, 666 Shengli Road, 830046, Urumqi, People’s Republic of China;State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, People’s Republic of China;

关键词: Soil DNA;    Metagenome;    PacBio;    Illumina;    Combined assembly;   

DOI  :  10.1186/s12864-021-08260-3

来源: Springer

【 摘 要 】

BackgroundAdvances in DNA sequencing technologies have transformed our capacity to perform life science research, decipher the dynamics of complex soil microbial communities and exploit them for plant disease management. However, soil is a complex conglomerate, which makes functional metagenomics studies very challenging.ResultsMetagenomes were assembled by long-read (PacBio, PB), short-read (Illumina, IL), and mixture of PB and IL (PI) sequencing of soil DNA samples were compared. Ortholog analyses and functional annotation revealed that the PI approach significantly increased the contig length of the metagenomic sequences compared to IL and enlarged the gene pool compared to PB. The PI approach also offered comparable or higher species abundance than either PB or IL alone, and showed significant advantages for studying natural product biosynthetic genes in the soil microbiomes.ConclusionOur results provide an effective strategy for combining long and short-read DNA sequencing data to explore and distill the maximum information out of soil metagenomics.

【 授权许可】

CC BY