Virus discovery in all three major lineages of terrestrial arthropods highlights the diversity of single-stranded DNA viruses associated with invertebrates

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Microbiology

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Introduction

Materials and Methods

Sample collection and processing

Detection of CRESS DNA viral genomes and genome completion

CRESS DNA genome sequence analyses

Phylogenetic analyses

Results

CRESS DNA viruses identified in all three major lineages of terrestrial arthropods

Terrestrial arthropods harbor diverse novel CRESS DNA viruses

Terrestrial arthropods harbor a diversity of species representing new members of established CRESS DNA viral groups

Detection of a cyclovirus endogenous element in a non-arthropod invertebrate

Discussion

Most CRESS DNA viral diversity circulates among arthropods and other invertebrates

Related CRESS DNA viruses identified in disparate organisms

Genomic fossil record supports widespread distribution of CRESS DNA viruses among invertebrates

Conclusion

Supplemental Information

Data S1. Alignment used to create approximately maximum likelihood tree shown in Figure 1 in fasta format.

Details regarding sequence acronyms, descriptions, and accession numbers can be found in Data S2.

DOI: 10.7717/peerj.5761/supp-1

Data S2. Excel workbook containing three worksheets with details regarding intrinsically disordered protein profiles, alignment used for analysis shown in Figure 1 and non-CRESS DNA molecules.

Excel workbook containing three worksheets (W#) with the following information: details regarding intrinsically disordered protein (IDP) profiles (W1), detailed information for sequences found in the alignment used to create approximately maximum likelihood tree shown in Figure 1 (Data S1) (W2), and a table listing accession numbers and information regarding non-CRESS DNA molecules detected in terrestrial arthropods (W3).

DOI: 10.7717/peerj.5761/supp-2

Fig. S1. Maximum likelihood phylogenetic tree depicted in Figure 2 showing details regarding the source and accession numbers for all the sequences included in the analysis for the family Genomoviridae.

Branch colors distinguish sequences associated with various types of organisms and environmental sources. Bars on the right indicate clades representing genomovirus genera and unclassified sequences. Rep sequences representing Gemygorvirus (accessions: KF371632, KT862254, KT862238, KT862239, JN704610, KT732790, KT732791, KJ413144, KJ547635), Gemyduguivirus (accessions: JX185428, KY312558, KY230613), and Gemykrogvirus (accessions: KJ547634, MF327559, KJ938717, LK931484) species were merged by clade. Reps representing members from the family Geminiviridae were used as an outgroup. Genomovirus Reps identified in this study are named and highlighted with schematics of terrestrial arthropods from which they were identified, including viruses associated with sierra dome spiders (SdSACV), pimoid spiders (PiSACV), tubeweb spiders (TuwSACV), grasshoppers (GhACV) and termites (TACV). Viruses identified in multiple species of spiders are identified as spider associated circular viruses (SACV). Branches with <70% Shimodaira–Hasegawa (SH)-like support were collapsed. Arthropod silhouettes credit: Shutterstock vector library at https://www.shutterstock.com.

DOI: 10.7717/peerj.5761/supp-3

Additional Information and Declarations

Competing Interests

Mya Breitbart is an Academic Editor for PeerJ.

Author Contributions

Karyna Rosario conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Kaitlin A. Mettel performed the experiments, approved the final draft.

Bayleigh E. Benner performed the experiments, approved the final draft.

Ryan Johnson performed the experiments, approved the final draft.

Catherine Scott contributed reagents/materials/analysis tools, approved the final draft.

Sohath Z. Yusseff-Vanegas contributed reagents/materials/analysis tools, approved the final draft.

Christopher C.M. Baker contributed reagents/materials/analysis tools, approved the final draft.

Deby L. Cassill contributed reagents/materials/analysis tools, approved the final draft.

Caroline Storer contributed reagents/materials/analysis tools, approved the final draft.

Arvind Varsani analyzed the data, prepared figures and/or tables, approved the final draft.

Mya Breitbart conceived and designed the experiments, analyzed the data, prepared figures and/or tables, approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The genomes and replicons described here are accessible via GenBank accession numbers: MG917674 to MG917677 and MH545497 to MH545543.

Funding

This work was funded through NSF Assembling the Tree of Life Program grant DEB-1239976 to Karyna Rosario and Mya Breitbart. Field work for blow fly collections in the Caribbean was funded through NSF grants DEB-1314749 and DEB-1050253 to Ingi Agnarsson and Greta Binford from the University of Vermont and Lewis & Clark College, respectively (Principal Investigators for Sohath Z Yusseff-Vanegas). Fungus-farming termites and ant samples from Africa were collected in the course of fieldwork funded by NSF grant DEB-1355122 to Corina Tarnita and Robert Pringle from Princeton University (Principal Investigators for Christopher CM Baker). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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