Abstract
BackgroundMetatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition of the metatranscriptomic sequences will enable us to refine the annotations of the metagenomes, and to study the gene activities and their regulation in complex microbial communities and their dynamics.ResultsIn this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences. By incorporating several features of metatranscriptomic sequencing, including strand-specificity, short intergenic regions, and putative antisense transcripts into a Hidden Markov Model, TranGeneScan can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript.ConclusionWe tested TransGeneScan on a mock metatranscriptomic data set containing three known bacterial genomes. The results showed that TranGeneScan performs better than metagenomic gene finders (MetaGeneMark and FragGeneScan) on predicting protein coding genes in assembled transcripts, and achieves comparable or even higher accuracy than gene finders for microbial genomes (Glimmer and GeneMark). These results imply, with the assistance of metatranscriptomic sequencing, we can obtain a broad and precise picture about the genes (and their functions) in a microbial community.AvailabilityTransGeneScan is available as open-source software on SourceForge at https://sourceforge.net/projects/transgenescan/.
Highlights
Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community
The results showed that TranGeneScan performs much more accurately than metagenomic gene finders on metatranscriptomic sequences, and achieves comparable or even higher accuracy than gene finders for microbial genomes
The reads were mapped to the three reference genomes by using BWA [31], and a total of 5,278,699, 2,439,476 and 1,113,601 reads can be mapped to the genomes of E. coli, P. marinus and R. sphaeroides, respectively
Summary
Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. While metagenomic sequencing revealed important functional properties encoded in microbial communities, characterization of these properties requires direct analysis of the active component of the metagenome, through meta-omic techniques such as metatranscriptomics or metaproteomics. Bacteria have low inventories of short-lived mRNAs so that fluctuations in their mRNAs pools provide a highly sensitive bioassay for environmental signals (e.g., the concentrations of dissolved organic carbon [11] and pollutant concentrations [12]) that are relevant to microbes [13], and the collective interaction among microbial organisms in response to the changes of their environment ( e.g., the health condition of the host of human microbiome [14]). HMP II, the second phase of the Human Microbiome Project (HMP) plans to generate coherent meta-omic (metagenomic, metatranscriptomic and metaproteomic) datasets acquired from the same cohorts of healthy human subjects and patients with certain diseases (including diabetes, Crohn’s disease and ulcerative colitis)
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