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

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

doi:10.1186/s12864-021-08260-3

Abstract

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.

Highlights

Advances in DeoxyriboNucleic Acid (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 manage‐ ment
Pacific Biosciences (PacBio), Illumina, and combined sequencing assembly statistics DNA extracted from three soil samples collected from the Ürümqi Glacier No 1 in the Tianshan Mountains at 2200, 2750 and 3700 m altitudes was sequenced using both PB and Secondgeneration / short-read sequencing platforms (IL) platforms
In this study, we used three soil samples collected from three different altitudes to evaluate the performance of three high-throughput DNA sequencing/assembly strategies

Summary

Introduction

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 manage‐ ment. Soil is a complex conglomerate, which makes functional metagenomics studies very challenging. Metagenomics studies have revealed that in soil microbiomes, uncultured species outnumber the culturable by two to three orders of magnitude [1], highlighting the vast potential of high-throughput DNA sequencing to discover novel functional genes and pathways directly from the soil samples. High-throughput, short-read DNA sequencing platforms such as the Illumina are usually referred to as “second-generation” sequencing technologies, are currently employed in metagenomics [4,5,6,7]. Systematic evaluation of the performance of these technologies on the quality of metagenomic sequences is urgently needed

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Conclusion