Sequence analysis of the potato aphid Macrosiphum euphorbiae transcriptome identified two new viruses

Abstract

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 IntereProScan. 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.

Aphid Viruses: A Brief View of a Long History

“…In addition, prior studies indicated that host plants play important roles in horizontal transmission of aphid densoviruses. MpDV could be detected in healthy aphids that placed on leaves far from the infected-aphids infested leaves (12,27,28). Although no evidence indicate that these viruses could replicate in plants, current data suggest that aphid densoviruses may circulate in plants.…”

“…Additionally, partial sequence (2,668 nt) of a new densovirus Macrosiphum euphorbiae virus 2 (MeV-2) was retrieved from the transcriptome data of the potato aphid Macrosiphum euphorbiae. Although sequence alignment indicated that MeV-2 was closely related with DplDV, the detailed molecular characters and classification of this virus are not clear (28).…”

“…Few studies revealed that aphid densoviruses including DplDV, MpDV, and the putative MeV-2 can be transmitted vertically from infected adults to nymphs (12,27,28). Interestingly, although the majority of nymphs produced by infected aphids were tested positively, a proportion of nymphs were still virus free for DplDV and MpDV (12,27).…”

Virome Analysis of Aphid Populations That Infest the Barley Field: The Discovery of Two Novel Groups of Nege/Kita-Like Viruses and Other Novel RNA Viruses

“…Many of these viruses were discovered because of their phenotype alternations of the host aphids (Teixeira et al, 2016). More recently, analyses using next-generation sequencing (NGS) have identified several novel aphid-infecting viruses, including six positive-sense RNA viruses: three flavi-like viruses [Macrosiphum euphorbiae virus 1 (MeV-1); two jingmenviruses, Wuhan aphid virus 1 and 2 (WhAV-1 and -2)] (Shi et al, 2016b;Teixeira et al, 2016), a tetra-like virus (Aphis glycine virus 2), a negelike virus [Aphis glycine virus 3 (ApGlV-3)] (Feng et al, 2017) and a sobemo-like virus (Macrosiphum euphorbiae virus 3) (Teixeira et al, 2018); a negative-sense RNA phlebolike virus (Aphis citricidus bunyavirus) (Zhang et al, 2019); and a DNA densovirus (Macrosiphum euphorbiae virus 2) (Teixeira et al, 2018). Nevertheless, little is known about the viromes of aphid populations, particularly those that infest cereal plants in the field.…”

Genome Size Estimation of Potato Aphid <i>Macrosiphum Euphorbiae</i> using Flow Cytometry

“…The unusual biology of aphids makes them ideal models for the study of several biological processes that are not readily studied in other genetic model systems. In recent years, few studies have generated the genomic and transcriptomic data of aphid species (Czosnek and Ghanim, 2016;Teixeira et al, 2018;Chen et al, 2019) that has created genomic information which is now becoming useful for better understanding of aphid species. Being an important pest of potato with complex biology, M. euphorbiae has been studied at transcriptome level for identification of virus responsive genes and inhabiting plant viruses (Teixeira et al, 2018).…”