数字农科院2.0

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

文献类型： 外文期刊

作者： Xu, Guoshun;Zhang, Liwen;Liu, Xiaoqing;Guan, Feifei;Xu, Yuquan;Yue, Haitao;Huang, Jin-Qun;Chen, Jieyin;Wu, Ningfeng;Tian, Jian

作者机构：

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

期刊名称： BMC GENOMICS

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCIE（2022版）

摘要： Background Advances 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. Results Metagenomes 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. Conclusion Our 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.

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