Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes

Kalia S I Bistolas; Lars G Rudstam; Ian Hewson

doi:10.7717/peerj.3810

Gene expression of benthic amphipods (genus: Diporeia) in relation to a circular ssDNA virus across two Laurentian Great Lakes

PeerJ. 2017 Sep 26:5:e3810. doi: 10.7717/peerj.3810. eCollection 2017.

Authors

Kalia S I Bistolas¹, Lars G Rudstam², Ian Hewson¹

Affiliations

¹ Department of Microbiology, Cornell University, Ithaca, NY, USA.
² Department of Natural Resources and the Cornell Biological Field Station, Cornell University, Bridgeport, NY, USA.

Abstract

Circular rep-encoding ssDNA (CRESS-DNA) viruses are common constituents of invertebrate viral consortia. Despite their ubiquity and sequence diversity, the effects of CRESS-DNA viruses on invertebrate biology and ecology remain largely unknown. This study assessed the relationship between the transcriptional profile of benthic amphipods of genus Diporeia and the presence of the CRESS-DNA virus, LM29173, in the Laurentian Great Lakes to provide potential insight into the influence of these viruses on invertebrate gene expression. Twelve transcriptomes derived from Diporeia were compared, representing organisms from two amphipod haplotype clades (Great Lakes Michigan and Superior, defined by COI barcode sequencing) with varying viral loads (up to 3 × 10⁶ genome copies organism^-1). Read recruitment to de novo assembled transcripts revealed 2,208 significantly over or underexpressed contigs in transcriptomes with above average LM29173 load. Of these contigs, 31.5% were assigned a putative function. The greatest proportion of annotated, differentially expressed transcripts were associated with functions including: (1) replication, recombination, and repair, (2) cell structure/biogenesis, and (3) post-translational modification, protein turnover, and chaperones. Contigs putatively associated with innate immunity displayed no consistent pattern of expression, though several transcripts were significantly overexpressed in amphipods with high viral load. Quantitation (RT-qPCR) of target transcripts, non-muscular myosin heavy chain, β-actin, and ubiquitin-conjugating enzyme E2, corroborated transcriptome analysis and indicated that Lake Michigan and Lake Superior amphipods with high LM29173 load exhibit lake-specific trends in gene expression. While this investigation provides the first comparative survey of the transcriptional profile of invertebrates of variable CRESS-DNA viral load, additional inquiry is required to define the scope of host-specific responses to potential infection.

Keywords: CRESS-DNA; Diporeia; Laurentian Great Lakes; Transcriptomics; ssDNA virus.

Grants and funding

This research is supported by the National Science Foundation (NSF-135696 and DGE-1144153) with additional support from the U.S. Environmental Protection Agency, Cooperative Agreement GL 00E01184-0 to Cornell University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.