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Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments


Metatranscriptomics, a subset of metagenomics, provides valuable information about the whole gene expression profiling of complex microbial communities of an ecosystem. Metagenomic studies mainly focus on the genomic content and identification of microbes present within a community, while metatranscriptomics provides the diversity of the active genes within such community, their expression profile and how these levels change due to change in environmental conditions. Metatranscriptomics has been applied to different types of environments, from the study of human microbiomes, to those found in plants, animals, within soils and in aquatic systems. Metatranscriptomics, based on the utilization of mRNA isolated from environmental samples, is a suitable approach to mine the eukaryotic gene pool for genes of biotechnological relevance. Also, it is imperative to develop different bioinformatic pipelines to analyse the data obtained from metatranscriptomic analysis. In the present review, we summarise the metatranscriptomics applied to soil environments to study the functional diversity, and discuss approaches for isolating the genes involved in organic matter degradation and providing tolerance to toxic metals, role of metatranscriptomics in microbiome research, various bioinformatics pipelines used in data analysis and technical challenges for gaining biologically meaningful insight of this approach.

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Modified from Bragalini et al. (2014)

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Adapted from Lehembre et al. (2013) and Ziller et al. (2017)

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Authors are thankful to Council of Scientific and Industrial Research, Govt. of India for sponsoring a research project on “Novel gene pool from copper polluted soil ecosystem using metatranscriptomic approach” under file No. 38(1425)/16/EMR-II.

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Correspondence to M. Sudhakara Reddy.

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Mukherjee, A., Reddy, M.S. Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech 10, 71 (2020).

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  • Metatranscriptomics
  • Eukaryotic genes
  • Toxic metal tolerance
  • Functional diversity
  • Microbiomes
  • Metagenomes