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. 2020;35(3):ME20016.
doi: 10.1264/jsme2.ME20016.

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom

Yuto Chiba  1   2 , Yuji Tomaru  3 , Hiromori Shimabukuro  3 , Kei Kimura  4 , Miho Hirai  5 , Yoshihiro Takaki  5 , Daisuke Hagiwara  1   6 , Takuro Nunoura  7 , Syun-Ichi Urayama  1   6   7
Affiliations

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom

Yuto Chiba et al. Microbes Environ. 2020.

Abstract

Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.

Keywords: RNA virus; algae; dsRNA.

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Figures

Fig. 1.
Fig. 1.
dsRNA-positive marine macroalgae used in the present study. (A) They were identified by morphology and SSU rRNA sequences reconstructed from total RNA-seq data. (B) Agarose gel electrophoresis of the total nucleic acids (T) and dsRNA (ds) of marine macroalgae samples 1–3. Arrowheads indicate dsRNA bands. Nucleic acids were stained with ethidium bromide.
Fig. 2.
Fig. 2.
Genome organization and phylogenetic position of RNA viruses identified from a brown algae sample. (A) Predicted ORFs and identified domains: Met, viral methyltransferase superfamily; Hel, viral helicase 1 superfamily; RdRp, RdRP_2 superfamily. (B) Maximum-likelihood tree of RdRp amino acid sequences from representative members of the Hepe-Virga clade (Shi et al., 2016) and three RNA viral sequences obtained in the present study. Open and closed circles represent bootstrap values of 50–90% and ≥90%, respectively. The best-fitting substitution model was [LG+I+G+F]. A virus identified from surface seawater (Urayama et al., 2018) is marked in blue. Brown circles indicate previously established RNA virus families or order. The scale bar represents the number of amino acid substitutions per site. (C) Enlarged view of the phylogenetic tree of Endornaviridae in Fig. 2B. Viruses identified from plants are marked in green. Orange and gray indicate oomycete endornavirus and fungal endornavirus, respectively.
Fig. 3.
Fig. 3.
Genome organization and phylogenetic position of RNA viruses identified from diatom and red algae samples. (A, B) Predicted ORFs and identified domains: Coat, Totivirus_coat superfamily; RdRp, RdRP_4 superfamily. (C) Maximum-likelihood tree of RdRp amino acid sequences from representative members of the family Totiviridae, two RNA viral sequences obtained in the present study, and their relatives. Open and closed circles represent bootstrap values of 50–90% and ≥90%, respectively. The best-fitting substitution model was [LG+I+G+F]. Viruses identified from red algae (Lachnit et al., 2015) are marked in blue. Brown circles indicate previously established RNA virus genera. The scale bar represents the number of amino acid substitutions per site.
Fig. 4.
Fig. 4.
Classification of 98 representative contigs based on taxonomic information on their top hit virus.
Fig. 5.
Fig. 5.
Plot of amino acid % identity for each centroid encoding RdRp to a known viral sequence.
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