Abstract
BackgroundMetagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species. This approach, however, cannot be used to identify active functional genes under actual environmental conditions. Metatranscriptomics, which is similar in approach to metagenomics except that it utilizes RNA samples, is a powerful tool for the transcriptomic study of environmental samples. Unlike metagenomic studies, metatranscriptomic studies have not been popular to date due to problems with reliability, repeatability, redundancy and cost performance. Here, we propose a normalized metatranscriptomic method that is suitable for the collection of genes from samples as a platform for comparative transcriptomics.ResultsWe constructed two libraries, one non-normalized and the other normalized library, from samples of marine microorganisms taken during daylight hours from Hiroshima bay in Japan. We sequenced 0.6M reads for each sample on a Roche GS FLX, and obtained 0.2M genes after quality control and assembly. A comparison of the two libraries showed that the number of unique genes was larger in the normalized library than in the non-normalized library. Functional analysis of genes revealed that a small number of gene groups, ribosomal RNA genes and chloroplast genes, were dominant in both libraries. Taxonomic distribution analysis of the libraries suggests that Stramenopiles form a major taxon that includes diatoms. The normalization technique thus increases unique genes, functional categories of genes, and taxonomic richness.ConclusionsNormalization of the marine metatranscriptome could be useful in increasing the number of genes collected, and in reducing redundancies among highly expressed genes. Gene collection through the normalization method was effective in providing a foundation for comparative transcriptomic analysis.
Highlights
Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species
Gene collection through the normalization method was effective in providing a foundation for comparative transcriptomic analysis
We considered that comprehensive gene collection, even in the absence of information regarding expression frequency, would be useful in gaining a better understanding of active functional genes in samples, and would contribute to database construction and microarray design for the cost-effective monitoring of changes in gene expression in various samples
Summary
Metagenomic studies, accelerated by the evolution of sequencing technologies and the rapid development of genomic analysis methods, can reveal genetic diversity and biodiversity in various samples including those of uncultured or unknown species This approach, cannot be used to identify active functional genes under actual environmental conditions. May 2011, more than 470 research articles related to metagenomic studies were identified using a PubMed title search under keywords “metagenome” or “metagenomics.” Most of these studies were published within the last 5 years, indicating that this field of research has grown rapidly This rapid growth was driven by recent developments in next-generation sequencers and high-throughput methods for genomic analysis [4,5]. A metagenomic approach has been applied to many samples, such as seawater, soil, internal organs of animal species and so on, and has revealed the species and genetic diversity in various environmental samples [6]
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