Characterization of a new apple luteovirus identified by high-throughput sequencing

Abstract

Background‘Rapid Apple Decline’ (RAD) is a newly emerging problem of young, dwarf apple trees in the Northeastern USA. The affected trees show trunk necrosis, cracking and canker before collapse in summer. In this study, we discovered and characterized a new luteovirus from apple trees in RAD-affected orchards using high-throughput sequencing (HTS) technology and subsequent Sanger sequencing.MethodsIllumina NextSeq sequencing was applied to total RNAs prepared from three diseased apple trees. Sequence reads were de novo assembled, and contigs were annotated by BLASTx. RT-PCR and 5′/3’ RACE sequencing were used to obtain the complete genome of a new virus. RT-PCR was used to detect the virus.ResultsThree common apple viruses and a new luteovirus were identified from the diseased trees by HTS and RT-PCR. Sequence analyses of the complete genome of the new virus show that it is a new species of the genus Luteovirus in the family Luteoviridae. The virus is graft transmissible and detected by RT-PCR in apple trees in a couple of orchards.ConclusionsA new luteovirus and/or three known viruses were found to be associated with RAD. Molecular characterization of the new luteovirus provides important information for further investigation of its distribution and etiological role.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-0998-3) contains supplementary material, which is available to authorized users.

A bushel of viruses: Identification of seventeen novel putative viruses by RNA-seq in six apple trees

“…Like the more common viruses, the presence of AhVd and these four viruses in both healthy and declining plants indicates that if they do play a role in the disease, they are not responsible for the disease alone, but may be part of a larger group of factors that contribute to this disease. In addition ALV1, which has been detected in both symptomatic and asymptomatic trees in the eastern United States [2], was not observed in any of the six trees examined here.…”

“…Apple decline, in which the afflicted trees exhibit dieback along the branches and eventual death, has been observed in certain scion/rootstock combinations, including Honeycrisp and Honeycrisp variants on G.935 rootstock, in Washington state. A similar disease is affecting apple trees in the eastern United States and Canada, specifically Fuji, Gala, Golden Delicious, and Crimson Crisp on M9 rootstock and Gala on M26 rootstock [1][2][3]. In the eastern US, the affected trees exhibit symptoms of dieback on the branches, often with the presence of cankers at the graft union and necrosis moving up the graft union into the scion tissue [1,3].…”

“…Identifying a cause or causes of this disease has been difficult. In Pennsylvania, Apple luteovirus 1 (ALV1) has been observed in some, but not all, declining plants, as were Apple chlorotic leafspot virus (ACLSV), Apple stem grooving virus (ASGV), and Apple stem pitting virus (ASPV) [2]. These viruses were also observed in asymptomatic trees, making it unlikely that they are the sole cause of this disease [2].…”

“…In Pennsylvania, Apple luteovirus 1 (ALV1) has been observed in some, but not all, declining plants, as were Apple chlorotic leafspot virus (ACLSV), Apple stem grooving virus (ASGV), and Apple stem pitting virus (ASPV) [2]. These viruses were also observed in asymptomatic trees, making it unlikely that they are the sole cause of this disease [2]. A recent study of declining trees in the eastern United States examined weather conditions, soil conditions, common viruses, and the microbial rhizosphere population [4].…”

“…Recently, NGS has been used to identify two viruses associated with apple rubbery wood disease [15] and one associated with citrus concave gum disease [16]. ALV1 was also discovered by NGS [2].…”