Discovery and Diagnosis of a New Sobemovirus Infecting Cyperus esculentus Showing Leaf Yellow Mosaic and Dwarfism Using Small-RNA High Throughput Sequencing

Abstract

C. esculentus is a profitable crop in Valencia, Spain, but the emergence of a disease causing of leaf yellow mosaic, dwarfism, and a drastic decrease in tuber production has become a problem. The small-RNA high-throughput sequencing (HTS) of a diseased C. esculentus plant identified only one virus, which could be the causal agent of this disease. The amino-acid comparison with viral sequences from GenBank and phylogenetic analyses indicated that this was a new species of genus Sobemovirus, and the name Xufa yellow dwarf virus was proposed. Completion with Sanger sequencing yielded a contig of 3072 nt corresponding to about 75% of the typical genome of sobemoviruses, including ORFs 2a (polyprotein-containing protease, VPG, and other proteins), 2b (RNA-dependent RNA polymerase), and 3 (coat protein). The nucleotide sequence was used to develop fast and accurate methods for the detection and quantification of xufa yellow dwarf virus (XYDV) based on reverse transcription (RT) and DNA amplification. XYDV was detected in leaves and tubers and showed a high incidence in the field in both symptomatic (almost 100%) and asymptomatic (70%) plants, but its accumulation was much higher in symptomatic plants. The relevance of these results for disease control was discussed.

Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany

“…Examples are Wuhan insect virus 23, Forsythia suspensa yan-like virus, Flumine sobemo-like virus 39, Xufa yellow dwarf virus, Wuhan house centipede virus 6, Poaceae Liege sobemovirus, signal crayfish associated tombus-like virus 2, Changjiang tombus-like virus 2, Sanxia tombus-like virus 2, or Beihai tombus-like virus 13. These unclassified viruses were from environmental samples from coastal water [25], wastewater [39], soil [26], and sediment [47], as well as tissue samples of plants [48,54] and invertebrate animals [55] collected in various parts of the world. Most astonishing is the global occurrence of many (very) similar viruses in quite diverse environments.…”

Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods– 3′ RACE and RNA-Seq

“…Sobemovirus infections can lead to a wide range of symptoms in plants, including chlorotic mottling, stunting, leaf deformation, mosaic patterns, malformation, blistering, sterility, and even plant death in severe cases [5][6][7][8]. However, it is important to note that, in certain instances, Sobemovirus infections may proceed asymptomatically with no visible signs of disease [9]. These viruses cause diseases in economically important agricultural plants.…”