A method for constructing draft environmental microbial genomes

Abstract

The invention discloses a method for constructing an environmental microbial genome draft based on micro-cell whole genome sequencing. The method comprises the steps of conducting nucleic acid isolation and amplification on multiple environmental microorganism micro metagenome samples, constructing a high-pass sequencing library, conducting filtration, de novo assembly and open reading frame prediction on sequencing data, conducting sequence classification with the algorithm based on a Hidden Markov model, and obtaining the microbial genome draft. According to the method, the number of times of parallel tests is adjusted according to the complexity of an environment sample microflora, so that the optimal analysis result is obtained. The method can be applied to research of microflorae of various environments such as soil, air, water and human bodies.

Description

technical field [0001] The invention relates to an improved metagenomic library construction method and a metagenomic bioinformatics analysis process method, belonging to the technical fields of next-generation sequencing technology, metagenomics, data statistics, and biological information analysis, and in particular to sequence assembly classification without reference genomes , and the drafting of environmental microbial genomes. Background technique [0002] Microorganisms are the most abundant and numerous forms of life in nature, including viruses, bacteria, archaea, fungi, single-celled algae, and protozoa. Microorganisms are closely related to human activities and play an important role in the fields of environmental protection, energy, food processing, and medical care. Using modern molecular biology techniques, more than 3,000 microbial genomes have been constructed (NCBI), but there are still more microorganisms that are still unknown, especially extreme environm...

AI Technical Summary

Problems solved by technology

However, the core problem still unsolved by metagenomics is that people cannot directly analyze and assemble the genome sequence information of different individual microorganisms from the sequence information obtained by metagenomic sequencing.

Although researchers have used different experimental methods and analysis strategies to reconstruct the whole genome of environmental microorganisms, and achieved certain results [Wang Y, Leung H C M, Yiu S M, et al. MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample[J].Bioinformatics,2012,28(18):i356-i362; Nielsen H B,Almeida M,Juncker A S,etal.Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes[J].Nature biotechnology,2014,32(8):822-828; Rinke C, Schwientek P,Sczyrba A, et al.Insights into thephylogeny and coding potential of microbial dark matter[J].Nature,2013,499 (7459):431-437; Chitsaz H, Yee-Greenbaum J L, Tesler G, et al.Efficient de novoassembly of single-cell bacterial genomes from short-read data sets[J].Naturebiotechnology,2011,29(10): 915-921.], but the genome information of a large number of microbial species in the metagenomics is still incomplete, and it is impossible to explain the interaction between species and species, species and environment from the species level

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