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.

Host-specific co-evolution likely driven by diet in Buchnera aphidicola

“…Although the detection of Buchnera transcripts in aphid RNA-seq experiments is not uncommon (Liu et al, 2012;Teixeira et al, 2018;Kaech et al, 2021) and has been previously identi ed in D. noxia (Rojas et al, 2020), it is interesting that no further investigations proceeded as to why Buchnera transcripts were found to be present after sequencing of a poly-A RNA selected library. The low level of RNA-seq reads that mapped to the BDn reference genome (roughly between 2% and 5%; Additional File 5) was found to be consistent between sequencing libraries constructed through use of total RNA (Nicholson, et al, 2015) and mRNA capture (this study).…”

A plastidial retrograde signal potentiates biosynthesis of systemic stress response activators

“…The potato aphid ( Macrosiphum euphorbiae ) isolate WU11 (Teixeira et al ., 2018) was maintained on the adapted hosts for over 2.5 y in a growth chamber at 20°C with a 16 h light photoperiod. To infest new Arabidopsis seedlings, the colony was released to the growth chamber with the experimental plants to allow the infestation (Teixeira et al ., 2018).…”

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.…”