High-Throughput Sequencing for Deciphering the Virome of Alfalfa (Medicago sativa L.)

Abstract

Alfalfa ( Medicago sativa L.), also known as lucerne, is a major forage crop worldwide. In the United States, it has recently become the third most valuable field crop, with an estimated value of over $9.3 billion. Alfalfa is naturally infected by many different pathogens, including viruses, obligate parasites that reproduce only inside living host cells. Traditionally, viral infections of alfalfa have been considered by breeders, growers, producers and researchers to be diseases of limited importance, although they are widespread in all major cultivation areas. However, over the past few years, due to the rapid development of high-throughput sequencing (HTS), viral metagenomics, bioinformatics tools for interpreting massive amounts of HTS data and the increasing accessibility of public data repositories for transcriptomic discoveries, several emerging viruses of alfalfa with the potential to cause serious yield losses have been described. They include alfalfa leaf curl virus (family Geminiviridae ), alfalfa dwarf virus (family Rhabdoviridae ), alfalfa enamovirus 1 (family Luteoviridae ), alfalfa virus S (family Alphaflexiviridae ) and others. These discoveries have called into question the assumed low economic impact of viral diseases in alfalfa and further suggested their possible contribution to the severity of complex infections involving multiple pathogens. In this review, we will focus on viruses of alfalfa recently described in different laboratories on the basis of the above research methodologies.

Characterisation of the Viral Community Associated with the Alfalfa Weevil (Hypera postica) and Its Host Plant, Alfalfa (Medicago sativa)

“…Eight of these contigs correspond to six virus species infecting alfalfa that have already been reported [ 37 ]. Their genomes share high levels of genome identity with their closest relatives (98.2% to 100% n t identity).…”

“…Their genomes share high levels of genome identity with their closest relatives (98.2% to 100% n t identity). These viruses likely represent new isolates belonging to six plant virus species ( Supplementary Table S4, Supplementary Figures S3–S6 ), namely, Alfalfa mosaic virus ( Bromoviridae , Alfamovirus genus), Medicago sativa amalgavirus 1 ( Amalgaviridae , Amalgavirus ), Medicago sativa alphapartitiviruses 1 and 2 ( Partitiviridae , Alphapartitivirus ), Bean leafroll virus ( Luteoviridae , Luteovirus ) and Alfalfa virus F ( Tymoviridae , Marafivirus ) [ 37 ].…”

Illuminating the Plant Rhabdovirus Landscape through Metatranscriptomics Data

“…The scientific interest of the submitters of transcriptome datasets is often limited to a narrow objective within their specific field of study, which leaves a large amount of potentially valuable data not analyzed [ 7 ]. In such transcriptome datasets, viral sequences may be hidden in plain sight; thus, their analysis has become a valuable tool for the discovery of novel viral sequences [ 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 ].…”

Illuminating the plant rhabdovirus landscape through metatranscriptomics data

“…The scientific interest of the submitters of transcriptome datasets is often limited to a narrow objective within their specific field of study, which leaves a large amount of potentially valuable data not analyzed (Bejerman et al, 2020b). In such transcriptome datasets, viral sequences may be hidden in plain sight, thus their analysis has become a valuable tool for the discovery of novel viral sequences (Debat and Bejerman, 2019; Goh et al, 2020; Jiang et al, 2019; Kim et al, 2018; Lauber et al, 2019; Longdon et al, 2015; Mushegian et al, 2016; Nibert et al, 2018: Sidharthan and Baranwal, 2021).…”