Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan

Abstract

Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour-joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the values 2.02535, 0.01468, and 0.71862 of Tajima's D, Fu, & Li’s F* and D* respectively, demonstrating that the CMV population is under balancing selection.

Incidence and genetic diversity of cucurbit viruses in the Spanish Mediterranean area

“…Traditionally, cucurbit crops have always been infected by isolates classified within IA and II groups, or even with reassorting isolates (IA‐II‐II), whereas IB isolates, which are more prevalent in Asia (Jacquemond, 2012), were found infecting plants of other families. Nevertheless, in recent years different isolates whose CP genes were classified within Group IB (Ahsan et al., 2020; Xanthis et al., 2015), or even isolates with the three RNA segments that make up the virus genome clustered within that group (IB‐IB‐IB) (Nagendran et al., 2018), have been found infecting cucurbits in Bulgaria, Greece, Mexico, Pakistan and India. However, these kinds of isolates have not been detected infecting cucurbits in other surveys recently carried out in Europe (Desbiez et al., 2020; Valachas et al., 2021).…”

Genetic diversity of cucumber green mottle mosaic virus (CGMMV) infecting cucurbits

“…Traditional production technology adopted by the farmers, conducive environment as well as lack of awareness about virus disease epidemiology, poor management practices and use of uncertified seeds may result in higher incidence of viral diseases ( Ali et al, 2004; Ahsan et al, 2020; Ashfaq et al, 2008; Ahsan et al, 2023 , Ashfaq et al, 2021b ). About 59 viruses from different taxonomic groups are known to infect cucurbits resulting in high yield losses with difficult to manage ( Lecoq and Desbiez, 2012 , Crespo et al, 2017 Ahmed et al, 2021 ).…”