Genetic diversity and evolutionary analyses of potyviruses infecting narcissus in Iran

Abstract

Potyviruses are among the most important pathogens of dicotyledonous and monocotyledonous ornamentals and crop plants. In this study, leaf samples were collected from symptomatic narcissus plants and weeds in Fars and Tehran provinces of Iran. Enzyme-linked immunosorbent assay using broad-spectrum potyvirus antibodies gave a positive reaction with 38 out of 61 narcissus samples tested (62.3%); the results were confirmed by reverse-transcription polymerase chain reaction using universal NIb primers, and for thirty samples, by sequencing and phylogenetic studies. The results suggested the infection of almost all positive samples with narcissus yellow stripe virus (NYSV); only one sample seemed to be infected with narcissus late season yellows virus (NLSYV). The 3'-end of the genome of the NLSYV isolate and six NYSV isolates, encompassing the complete coat protein gene, was amplified and sequenced using species-specific and universal potyvirus primers. Sequence analysis indicated the presence of NLSYV and NYSV, not previously identified from Western Asia. No evidence of recombination was found in Iranian isolates. Based on phylogenetic analyses, isolates of NLSYV and NYSV clustered into five and three phylogroups, respectively, where all the Iranian isolates fell into distinct subpopulations in groups NLSYV-I and NYSV-II. Multiple sequence alignments showed some phylogroup-specific amino acid substitutions for both viruses. Phylogroup IV and II populations had higher nucleotide diversities as compared with other populations of NLSYV and NYSV, respectively. Our findings revealed the presence of negative selection in the populations of both viruses. Almost no statistically significant gene flow was found between populations of these viruses.

Supplementary information: The online version contains supplementary material available at 10.1007/s42161-021-00985-0.

Keywords: Evolutionary analyses; Iran; Narcissus viruses; Potyvirus; West Asia.

Fig. 1

Phylogenetic network tree of the coat protein (cp) gene of narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV) isolates. The tree was rooted with sequences of turnip mosaic virus (TuMV), scallion mosaic virus (SCaMV) and wild onion symptomless virus (WoSV). NLSYV and NYSV isolates from this study are shown in blue and red, respectively. Detailed information of isolates used to construct the tree is listed in Tables S3 and S5. Latin numbers refer to phylogenetic groups which are shown in Fig. 2. Scale bar is 0.1 substitutions/site

Fig. 2

A maximum-likelihood (ML) phylogenetic tree of coat protein (cp) gene sequences of narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV) isolates. Bootstrap values higher than 50 are shown at each node. The tree was rooted with sequences of turnip mosaic virus (TuMV), scallion mosaic virus (SCaMV) and wild onion symptomless virus (WoSV). NLSYV and NYSV isolates from this study are shown in blue and red, respectively. Scale bar is 0.1 substitutions/site

Fig. 3

Nucleotide pairwise identity color matrix of coat protein (cp) gene sequences of narcissus late season yellows virus (NLSYV) and narcissus yellow stripe virus (NYSV) isolates calculated by SDT 1.2 program (Muhire et al. 2013). Corresponding regions of turnip mosaic virus (TuMV), scallion mosaic virus (SCaMV) and wild onion symptomless virus (WoSV) were included for comparison. NLSYV and NYSV isolates from this study are shown in blue and red, respectively

Fig. 4

Plot representing significant signals of natural selection acting on individual codon sites within: (a) narcissus late season yellows virus (NLSYV) coat protein (CP) region, (b) NLSYV partial nuclear inclusion b protein (NIb) region, and (c) narcissus yellow stripe virus (NYSV) CP region. The Abs (Absolut) dN-dS values are plotted for negative (black) and positive (red, blue and green) selection signals. Sites at which episodic diversifying selection was detected using mixed effects model evolution (MEME) method are represented by blue bars, sites at which pervasive diversifying selection was detected using fixed effects likelihood (FEL) and random effect likelihood (REL) methods are shown in green, and those detected to be under both pervasive and episodic selection are shown in red. Codon 1 is the beginning of each cistron and codons 274, 211 and 267 are the termination of NLSYV CP, NLSYV NIb and NYSV CP, respectively