Enhanced Apiaceous Potyvirus Phylogeny, Novel Viruses, and New Country and Host Records from Sequencing Apiaceae Samples

Abstract

The family Apiaceae comprises approximately 3700 species of herbaceous plants, including important crops, aromatic herbs and field weeds. Here we report a study of 10 preserved historical or recent virus samples of apiaceous plants collected in the United Kingdom (UK) import interceptions from the Mediterranean region (Egypt, Israel and Cyprus) or during surveys of Australian apiaceous crops. Seven complete new genomic sequences and one partial sequence, of the apiaceous potyviruses apium virus Y (ApVY), carrot thin leaf virus (CaTLV), carrot virus Y (CarVY) and celery mosaic virus (CeMV) were obtained. When these 7 and 16 earlier complete non-recombinant apiaceous potyvirus sequences were subjected to phylogenetic analyses, they split into 2 separate lineages: 1 containing ApVY, CeMV, CarVY and panax virus Y and the other CaTLV, ashitabi mosaic virus and konjac virus Y. Preliminary dating analysis suggested the CarVY population first diverged from CeMV and ApVY in the 17th century and CeMV from ApVY in the 18th century. They also showed the “time to most recent common ancestor” of the sampled populations to be more recent: 1997 CE, 1983 CE and 1958 CE for CarVY, CeMV and ApVY, respectively. In addition, we found a new family record for beet western yellows virus in coriander from Cyprus; a new country record for carrot torradovirus-1 and a tentative novel member of genus Ophiovirus as a co-infection in a carrot sample from Australia; and a novel member of the genus Umbravirus recovered from a sample of herb parsley from Israel.

Expanding the repertoire of the plant infecting ophioviruses

“…The genomes of 14 out of 16 viruses with all RNA segments annotated had three segments, and two monocot-associated ophioviruses had four segments ( Table 1 , Figure 1 ). Three out five of those ophioviruses whose complete genome were assembled, had four RNA segments, which is also a genomic organization of the ophiovirus Mirafiori lettuce big-vein virus (MLBVV) and lettuce ring necrosis virus (LRNV) (Garcia et al, 2017) and the recently reported carrot ophiovirus 1 (Fox et al, 2022). Thus, the most frequent genomic organization found for ophioviruses consists of three RNA segments.…”

“…Nevertheless, to our knowledge, the diversity of ophioviruses appears to be stagnated, with no new ophiovirus species recognized by the ICTV since 2015. Two recent works have described the complete genome of a novel proposed ophiovirus associated to carrot, carrot ophiovirus 1 (CaOV1) (Fox et al, 2022) and other found in pepper, pepper chlorosis-associated virus (PCaV) (Shimomoto et al, 2023). In addition, the segment that encodes the capsid protein (CP) of a putative novel ophiovirus was assembled from transcriptomic data of Dactylorhiza hatagirea (Sidharthan et al, 2021).…”

Comparative-genomic analysis reveals dynamic NLR gene loss and gain across Apiaceae species

“…Apiaceae species are annual or perennial herbs that are widely distributed in temperate regions of the world (Fox et al, 2022). Recently, the genomes of seven species from Apiaceae, including Apioideae and Mackinlayoideae, have been sequenced (https://www.…”

“…plabipd.de/plant_genomes_pa.ep). Apiaceae species have always played an important role in socio-economic and human life, among which Angelica sinensis, Bupleurum chinense, Centella asiatica and O. javanica are medicinal plants (Lu and Li, 2019;Sun et al, 2020;Liu et al, 2022), as well as Apium graveolens, Coriandrum sativum and D. carota are vegetables (Fox et al, 2022). Previous studies have shown that the Ks peak of the paralogous genes in five Apioideae species, including Daucus carota, Oenanthe javanica, A. sinensis, C. sativum and A. graveolens, corresponded to a recent WGD (whole genome duplication) event, possibly specific in Apioideae instead of Mackinlayoideae (Han et al, 2022).…”

“…Previous studies have shown that the Ks peak of the paralogous genes in five Apioideae species, including Daucus carota, Oenanthe javanica, A. sinensis, C. sativum and A. graveolens, corresponded to a recent WGD (whole genome duplication) event, possibly specific in Apioideae instead of Mackinlayoideae (Han et al, 2022). A variety of pathogens are known to be capable of infecting Apiaceae plants and causing economic losses (Fox et al, 2022). However, few studies reported the composition and evolutionary pattern of NLR genes in the Apiaceae family, limiting the discovery of functional NLR genes and their application in production.…”