Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus
Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De...
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| Format: | Article |
| Language: | English |
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Hanrimwon Publishing Company
2021-12-01
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| Series: | The Plant Pathology Journal |
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| Online Access: | http://www.ppjonline.org/upload/pdf/PPJ-OA-10-2021-0151.pdf |
| _version_ | 1811308512296304640 |
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| author | Zohreh Moradi Mohsen Mehrvar |
| author_facet | Zohreh Moradi Mohsen Mehrvar |
| author_sort | Zohreh Moradi |
| collection | DOAJ |
| description | Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23–99.26% and 98.04–98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96–98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects. |
| first_indexed | 2024-04-13T09:24:37Z |
| format | Article |
| id | doaj.art-95907f7ea652489d85687c9b1e879525 |
| institution | Directory Open Access Journal |
| issn | 1598-2254 2093-9280 |
| language | English |
| last_indexed | 2024-04-13T09:24:37Z |
| publishDate | 2021-12-01 |
| publisher | Hanrimwon Publishing Company |
| record_format | Article |
| series | The Plant Pathology Journal |
| spelling | doaj.art-95907f7ea652489d85687c9b1e8795252022-12-22T02:52:29ZengHanrimwon Publishing CompanyThe Plant Pathology Journal1598-22542093-92802021-12-0137661963110.5423/PPJ.OA.10.2021.01512289Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the VirusZohreh Moradi0Mohsen Mehrvar1 Department of Plant Pathology, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University, P.O. Box 578, Sari, Iran Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, P.O. Box 91779-1163, Mashhad, IranAlfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23–99.26% and 98.04–98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96–98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.http://www.ppjonline.org/upload/pdf/PPJ-OA-10-2021-0151.pdfalfamovirusevolutionary analysislesser periwinklerna-seqwisteria |
| spellingShingle | Zohreh Moradi Mohsen Mehrvar Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus The Plant Pathology Journal alfamovirus evolutionary analysis lesser periwinkle rna-seq wisteria |
| title | Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus |
| title_full | Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus |
| title_fullStr | Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus |
| title_full_unstemmed | Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus |
| title_short | Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of and in Iran: with Implications for the Genetic Structure of the Virus |
| title_sort | whole genome characterization of alfalfa mosaic virus obtained from metagenomic analysis of and in iran with implications for the genetic structure of the virus |
| topic | alfamovirus evolutionary analysis lesser periwinkle rna-seq wisteria |
| url | http://www.ppjonline.org/upload/pdf/PPJ-OA-10-2021-0151.pdf |
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