What the lough whispers: detecting the viral gene expression signals in microbial metatranscriptomes
Viruses constitute an important part of any biocoenosis, and those of freshwater habitats are not an exception. While several metagenomic studies have explored the structure and functional potential of viral communities in lacustrine ecosystems, no attempt to investigate transcriptional activity of environmental viruses has been made.
We conducted an extensive investigation of viral gene expression in the two largest lakes in Northern Ireland, Lough Neagh (LN) and Lough Erne (LE). To that end, water samples from these lakes were collected and viromes and strand-specific metatranscriptomes were generated. The subsequent assembly of the viromes produced 184,605 contigs for the LN and 116,972 for the LE sample, with the longest contigs being 77 kb. Taxonomic annotation could be assigned to 37.6% of LN and 29.1% of LE contigs, and the majority of the contigs were categorised as derived from the genomes of Caudovirales, although algae- and amoebae- infecting Phycodnaviridae and Mimiviridae were also present.
To study transcriptional activity, metatranscriptomic short reads were mapped onto long viral contigs. Actively transcribed genes were identified, with bacteriophage structural protein genes being the most numerous, although the expression of auxiliary metabolic genes and genes with unknown function was also detected. Gene expression profiles were obtained for viral genomes with the highest levels of transcriptional activity, revealing characteristic expression patterns. We also included in the analysis 2,949 large contigs assembled from viromes obtained in our previous studies of Lough Neagh. Some of these contigs were absent from the LN virome, but found in the corresponding metatranscriptome, which can be explained by the transcription of some of the prophage genes. Finally, antisense transcription of some of the viral genes was detected.
This work is the first to examine sequences of viral origin in microbial metatranscriptomes. It provides a much-needed insight into the nature and extent of transcriptional activity of viruses in natural communities.
We conducted an extensive investigation of viral gene expression in the two largest lakes in Northern Ireland, Lough Neagh (LN) and Lough Erne (LE). To that end, water samples from these lakes were collected and viromes and strand-specific metatranscriptomes were generated. The subsequent assembly of the viromes produced 184,605 contigs for the LN and 116,972 for the LE sample, with the longest contigs being 77 kb. Taxonomic annotation could be assigned to 37.6% of LN and 29.1% of LE contigs, and the majority of the contigs were categorised as derived from the genomes of Caudovirales, although algae- and amoebae- infecting Phycodnaviridae and Mimiviridae were also present.
To study transcriptional activity, metatranscriptomic short reads were mapped onto long viral contigs. Actively transcribed genes were identified, with bacteriophage structural protein genes being the most numerous, although the expression of auxiliary metabolic genes and genes with unknown function was also detected. Gene expression profiles were obtained for viral genomes with the highest levels of transcriptional activity, revealing characteristic expression patterns. We also included in the analysis 2,949 large contigs assembled from viromes obtained in our previous studies of Lough Neagh. Some of these contigs were absent from the LN virome, but found in the corresponding metatranscriptome, which can be explained by the transcription of some of the prophage genes. Finally, antisense transcription of some of the viral genes was detected.
This work is the first to examine sequences of viral origin in microbial metatranscriptomes. It provides a much-needed insight into the nature and extent of transcriptional activity of viruses in natural communities.
Reference:
Posters Day 2-T03-Pos-53
Session:
Posters Covering Ecology, Host population control, Co-Evolutionary dynamics and Subversion/Evasion of Host Defences
Presenters:
Timofey Skvortsov
Session:
Day 2 Posters Covering: Ecology, Host population control, Co-evolutionary dynamics and Subversion/Evasion of host defences
Presentation type:
Poster presentation
Room:
Poster Halls
Date:
Tuesday, 19 July 2016
Time:
12:05 - 15:00