Teixeira, M.A., Department of Nematology, University of California, Riverside, CA, United States, Ministry of Agriculture, Livestock and Food Supply, Brasilia, Brazil;

Atamian, H.S., Department of Nematology, University of California, Riverside, CA, United States, Schmid College of Science and Technology, Chapman University, Orange, CA, United States;

Bao, E., Graduate Program in Computer Science and Engineering, University of California, Riverside, CA, United States, School of Software Engineering, Beijing Jiaotong University, Beijing, China;

Chaudhary, R., Department of Nematology, University of California, Riverside, CA, United States, National Institutes of Health, Bethesda, MD, United States; MacWilliams, J., Department of Nematology, University of California, Riverside, CA, United States;

He, J., Department of Nematology, University of California, Riverside, CA, United States; Mantelin, S., Department of Nematology, University of California, Riverside, CA, United States, Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, United Kingdom;

Girke, T., Department of Botany and Plant Sciences, University of California, Riverside, CA, United States, Institute for Integrative Genome Biology, University of California, Riverside, CA, United States;

Kaloshian, I., Department of Nematology, University of California, Riverside, CA, United States, Institute for Integrative Genome Biology, University of California, Riverside, CA, United States, Center for Infectious Disease Vector Research, University of California, Riverside, CA, United States

The potato aphid, Macrosiphum euphorbiae, is an important agricultural pest that causes economic losses to potato and tomato production. To establish the transcriptome for this aphid, RNA-Seq libraries constructed from aphids maintained on tomato plants were used in Illumina sequencing generating 52.6 million 75–105 bp paired-end reads. The reads were assembled using Velvet/Oases software with SEED preprocessing resulting in 22,137 contigs with an N50 value of 2,003bp. After removal of contigs from tomato host origin, 20,254 contigs were annotated using BLASTx searches against the non-redundant protein database from the National Center for Biotechnology Information (NCBI) as well as IntereProS-can. This identified matches for 74% of the potato aphid contigs. The highest ranking hits for over 12,700 contigs were against the related pea aphid, Acyrthosiphon pisum. Gene Ontology (GO) was used to classify the identified M. euphorbiae contigs into biological process, cellular component and molecular function. Among the contigs, sequences of microbial origin were identified. Sixty five contigs were from the aphid bacterial obligate endosymbiont Buchnera aphidicola origin and two contigs had amino acid similarities to viruses. The latter two were named Macrosiphum euphorbiae virus 2 (MeV-2) and Macrosiphum euphorbiae virus 3 (MeV-3). The highest sequence identity to MeV-2 had the Dysaphis plantaginea densovirus, while to MeV-3 is the Hubei sobemo-like virus 49. Characterization of MeV-2 and MeV-3 indicated that both are transmitted vertically from adult aphids to nymphs. MeV-2 peptides were detected in the aphid saliva and only MeV-2 and not MeV-3 nucleic acids were detected inside tomato leaves exposed to virus-infected aphids. However, MeV-2 nucleic acids did not persist in tomato leaf tissues, after clearing the plants from aphids, indicating that MeV-2 is likely an aphid virus. © 2018 Teixeira et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.