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

Nicolas Bejerman,Philippe Roumagnac,Lev G. Nemchinov

doi:10.3389/fmicb.2020.553109

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.

Highlights

Importance of Alfalfa WorldwideAlfalfa (Medicago sativa L.), known as lucerne, is a major forage crop worldwide cultivated in more than 80 countries, where it is mainly used as silage for grazing livestock (Samarfard et al, 2020)
It is becoming increasingly obvious that in research on alfalfa virology, similar to research on the virology of any other plant species or agricultural crop, high-throughput sequencing (HTS) technologies and their derivatives, such as the exploration of public transcriptomic datasets, are making a major contribution toward the discovery of novel viral genomes, the sequences of emerging pathogens transitioning to new host species and the detection of known viruses
The virome of alfalfa plants from many other geographic locations, other than those described in this review (Western Europe, United States, China, Australia, and Argentina) remains to be characterized

Summary

Introduction

Importance of Alfalfa WorldwideAlfalfa (Medicago sativa L.), known as lucerne, is a major forage crop worldwide cultivated in more than 80 countries, where it is mainly used as silage for grazing livestock (Samarfard et al, 2020). In the United States, it has recently become the third most valuable field crop planted on 22 million acres, with an estimated value of over $9.3 billion (National Alfalfa and Forage Alliance, 2018; Miller, 2019). Alfalfa is the principal forage crop in 15 countries of Southern, Eastern and Western Europe, where it is grown on nearly 2.5 million hectares (Julier et al, 2017). Most of these alfalfa fields (65%) are located in Italy, France, Romania, and Spain (Julier et al, 2017).

Objectives

Findings

Conclusion