Temporal analysis and adaptive evolution of the global population of potato virus M.

Potato virus M (PVM), which is a member of the genus Carlavirus in the family Betaflexviridae, causes critical economic losses of nightshade crops. PVM is transmitted by aphids in a non-persistent manner, by sap inoculation and also transmitted in tubers. Previously, several reports described the genetic structure of PVM. However, the evolutionary rate, timescale, spread and adaptation evolution of the virus have not been examined. In this study, we investigated the phylodynamics of PVM using 145 nucleotide sequences of the coat protein gene and 117 sequences of the cysteine-rich nucleic acid-binding protein (NABP) gene, which were sampled between 1985 and 2013. We found that at least three lineages with isolates that were defined geographically but not by the original host were clustered. The evolutionary rate of the NABP (1.06 × 10-2) was faster than that of the CP (4.12 × 10-3). The time to the most recent common ancestors (TMRCAs) is similar between CP (CIs 31-110) and NABP (CIs 28-33) genes. Based on CP and NABP genes, PVM migrated from China to Canada, Iran, India and European countries, and it circulated within China. Our study is the first attempt to evaluate the evolutionary rates, timescales and migration dynamics of PVM.

Complete Genome Sequences of Seven Peanut Stunt Virus Strains from Japan.

We present the complete genomic RNA sequences of seven isolates of Peanut stunt virus discovered in diseased legume plants in various regions in Japan. These sequences and the published viral sequences were compared with respect to nucleotide percentages. Their phylogenetic analysis showed that all the isolates belong to subgroup IA.

Effects of infection by Turnip mosaic virus on the population growth of generalist and specialist aphid vectors on turnip plants.

Recent studies have revealed that relationships between plant pathogens and their vectors differ depending on species, strains and associated host plants. Turnip mosaic virus (TuMV) is one of the most important plant viruses worldwide and is transmitted by at least 89 aphid species in a non-persistent manner. TuMV is fundamentally divided into six phylogenetic groups; among which Asian-BR, basal-BR and world-B groups are known to occur in Japan. In Kyushu Japan, basal-BR has invaded approximately 2000 and immediately replaced the predominant world-B virus group. To clarify the relationships between TuMV and vector aphids, we examined the effects of the TuMV phylogenetic group on the population growth of aphid vectors in turnip plants. The population growth of a generalist aphid, Myzus persicae, was not significantly different between non-infected and TuMV-infected treatments. The population growth of a specialist aphid, Lipaphis erysimi, was higher in TuMV-infected plants than non-infected ones. Similar results were obtained in experiments using world-B and basal-BR groups of TuMV. Therefore, we conclude that L. erysimi is more mutualistic with TuMV than M. persicae, and differences in TuMV phylogenetic groups do not affect the growth of aphid vectors on turnip plants.

First Genome Sequence of Shallot Latent Carlavirus from Allium macrostemon Bunge.

A wild Japanese garlic plant (Allium macrostemon Bunge, wild onion) with leaves showing chlorotic stripes was collected in Saitama Prefecture, Japan. Genome sequencing showed that it was infected with shallot latent carlavirus. The genomic sequence of this virus is reported for the first time from wild onion.

The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus.

Plant viruses have important global impacts on crops, and identifying their centre and date of emergence is important for planning control measures. Turnip mosaic virus (TuMV) is a member of the genus Potyvirus in the family Potyviridae and is a major worldwide pathogen of brassica crops. For two decades, we have collected TuMV isolates, mostly from brassicas, in Turkey and neighbouring countries. This region is thought to be the centre of emergence of this virus. We determined the genomic sequences of 179 of these isolates and used these to estimate the timescale of the spread of this virus. Our Bayesian coalescent analyses used synonymous sites from a total of 417 novel and published whole-genome sequences. We conclude that TuMV probably originated from a virus of wild orchids in Germany and, while adapting to wild and domestic brassicas, spread via Southern Europe to Asia Minor no more than 700 years ago. The population of basal-B group TuMVs in Asia Minor is older than all other populations of this virus, including a newly discovered population in Iran. The timescale of the spread of TuMV correlates well with the establishment of agriculture in these countries.

The phylogenetics of the global population of potato virus Y and its necrogenic recombinants.

Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5' terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3' terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.

Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus.

There is no attempt to evaluate evolutionary rates, timescales and diversities of viruses collected from mixedly infected hosts in nature. Plants of the genus Narcissus are a monocotyledon and are susceptible to several viruses. In this study, narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected in Japan, and these were investigated for potyvirus infections using potyvirus-specific primers. Individual narcissus plants were found frequently to be mixedly infected with different potyviruses, different isolates and quasispecies of same virus. The viruses were potyviruses and a macluravirus in the family Potyviridae, namely Narcissus late season yellows virus (NLSYV), Narcissus yellow stripe virus (NYSV), Narcissus degeneration virus (NDV), Cyrtanthus elatus virus A (CyEVA) and Narcissus latent virus (NLV). Genetic diversities of coat protein coding region of different virus species were different; NYSV and CyEVA were most diverse whereas NDV was least. Evolutionary rates of all five narcissus viruses were 1.33-7.15×10-3nt/site/year and were similar. The most recent common ancestors (TMRCAs) varied between virus species; NYSV and CyEVA were the oldest whereas NDV was the youngest. Thus, the oldness of TMRCAs of the viruses correlated well with the greatness of nucleotide diversities.

Genetic structure of populations of sugarcane streak mosaic virus in China: Comparison with the populations in India.

Sugarcane streak mosaic virus (SCSMV) causes mosaic and streak symptoms on sugarcane and sorghum crops, and has a broad host range. SCSMV is a member of the genus Poacevirus in the family Potyviridae.Ten SCSMV isolates were collected from sugarcane plants showing mosaic and streaking in Southern China from 2009-2011. Sequence-based phylogenetic and population genetic analyses were conducted using four partial genomic sequences covering the full genomes. These analyses were used to estimate the subpopulation differentiation and divergence within the Chinese virus population, and were compared with isolates from India. SCSMV-infected sugarcane plants in the field commonly harbor virus quasispecies (mutant cloud), and often have mixed infections with the same virus isolates. Inter- and intra-lineage recombination sites were identified in the protein 1, helper-component proteinase, coat protein and 3' non-coding regions of the Chinese isolates. All the Chinese non-recombinant isolates fell into at least nine lineages, and many clustered with Indian isolates. However, estimates of genetic differentiation and gene flow indicated that the SCSMV populations in China and India are genetically independent. Our genetic study of a poacevirus population in South Asia regions indicates the importance of the evolutionary-based design to control viruses.

Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome.

Cucumber mosaic virus (CMV) is a damaging pathogen of over 200 mono- and dicotyledonous crop species worldwide. It has the broadest known host range of any virus, but the timescale of its evolution is unknown. To investigate the evolutionary history of this virus, we obtained the genomic sequences of 40 CMV isolates from brassicas sampled in Iran, Turkey and Japan, and combined them with published sequences. Our synonymous ('silent') site analyses revealed that the present CMV population is the progeny of a single ancestor existing 1550-2600 years ago, but that the population mostly radiated 295-545 years ago. We found that the major CMV lineages are not phylogeographically confined, but that recombination and reassortment is restricted to local populations and that no reassortant lineage is more than 251 years old. Our results highlight the different evolutionary patterns seen among viral pathogens of brassica crops across the world.

Phylodynamic evidence of the migration of turnip mosaic potyvirus from Europe to Australia and New Zealand.

Turnip mosaic virus (TuMV) is a potyvirus that is transmitted by aphids and infects a wide range of plant species. We investigated the evolution of this pathogen by collecting 32 isolates of TuMV, mostly from Brassicaceae plants, in Australia and New Zealand. We performed a variety of sequence-based phylogenetic and population genetic analyses of the complete genomic sequences and of three non-recombinogenic regions of those sequences. The substitution rates, divergence times and phylogeographical patterns of the virus populations were estimated. Six inter- and seven intralineage recombination-type patterns were found in the genomes of the Australian and New Zealand isolates, and all were novel. Only one recombination-type pattern has been found in both countries. The Australian and New Zealand populations were genetically different, and were different from the European and Asian populations. Our Bayesian coalescent analyses, based on a combination of novel and published sequence data from three non-recombinogenic protein-encoding regions, showed that TuMV probably started to migrate from Europe to Australia and New Zealand more than 80 years ago, and that distinct populations arose as a result of evolutionary drivers such as recombination. The basal-B2 subpopulation in Australia and New Zealand seems to be older than those of the world-B2 and -B3 populations. To our knowledge, our study presents the first population genetic analysis of TuMV in Australia and New Zealand. We have shown that the time of migration of TuMV correlates well with the establishment of agriculture and migration of Europeans to these countries.

The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus.

Cauliflower mosaic virus (CaMV) is a plant pararetrovirus with a double-stranded DNA genome. It is the type member of the genus Caulimovirus in the family Caulimoviridae. CaMV is transmitted by sap inoculation and in nature by aphids in a semi-persistent manner. To investigate the patterns and timescale of CaMV migration and evolution, we sequenced and analyzed the genomes of 67 isolates of CaMV collected mostly in Greece, Iran, Turkey, and Japan together with nine published sequences. We identified the open-reading frames (ORFs) in the genomes and inferred their phylogeny. After removing recombinant sequences, we estimated the substitution rates, divergence times, and phylogeographic patterns of the virus populations. We found that recombination has been a common feature of CaMV evolution, and that ORFs I-V have a different evolutionary history from ORF VI. The ORFs have evolved at rates between 1.71 and 5.81×10(-4) substitutions/site/year, similar to those of viruses with RNA or ssDNA genomes. We found four geographically confined lineages. CaMV probably spread from a single population to other parts of the world around 400-500 years ago, and is now widely distributed among Eurasian countries. Our results revealed evidence of frequent gene flow between populations in Turkey and those of its neighboring countries, with similar patterns observed for Japan and the USA. Our study represents the first report on the spatial and temporal spread of a plant pararetrovirus.

Molecular variability of sugarcane streak mosaic virus in China based on an analysis of the P1 and CP protein coding regions.

Sequences of the protein 1 (P1) and coat protein (CP) coding regions of 22 sugarcane streak mosaic virus (SCSMV) isolates were determined. Phylogenetic analysis showed that SCSMV had at least three major lineages, and the lineages seemed to reflect geographical origin. The sudden expansions of the Chinese and Indian subpopulations were supported by calculations showing deviations from the neutral equilibrium model for the individual lineages with an overall lack of nucleotide diversity. Our study shows that Chinese and Indian SCSMV isolates are part of a distinct population, and the subpopulations probably reflect founder effects.