Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain
The genetic variation and population structure of gene N (nucleocapsid) and part of gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated and compared with sequences of EMDV isolates from other countries retrieved from GenBank. Phylogenetic inference of...
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| Format: | article |
| Language: | Inglés |
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MDPI
2024
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| Online Access: | https://hdl.handle.net/20.500.11939/8959 https://www.mdpi.com/2223-7747/13/2/250 |
| _version_ | 1855032885854076928 |
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| author | Alfaro-Fernández, Ana Taengua, Rafael Font-San-Ambrosio, Isabel Sanahuja-Edo, Esmeralda Peiró, Rosa Galipienso, Luis Rubio, Luis |
| author_browse | Alfaro-Fernández, Ana Font-San-Ambrosio, Isabel Galipienso, Luis Peiró, Rosa Rubio, Luis Sanahuja-Edo, Esmeralda Taengua, Rafael |
| author_facet | Alfaro-Fernández, Ana Taengua, Rafael Font-San-Ambrosio, Isabel Sanahuja-Edo, Esmeralda Peiró, Rosa Galipienso, Luis Rubio, Luis |
| author_sort | Alfaro-Fernández, Ana |
| collection | ReDivia |
| description | The genetic variation and population structure of gene N (nucleocapsid) and part of
gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated
and compared with sequences of EMDV isolates from other countries retrieved from GenBank.
Phylogenetic inference of part of gene L showed three main clades, one containing an EMDV isolate
from Australia and the other two containing isolates from Iran and Europe, as well as four subclades.
EMDV isolates from Spain were genetically very similar and grouped in a subclade together with
one isolate from Germany and one from the UK. No new recombination events were detected in
addition to one recombination previously reported, suggesting that recombination is rare for EMDV.
The comparison of synonymous and non-synonymous rates showed that negative selection played
an important role, and only two codons were under positive selection. Genetic differentiation (Fst
test), phylogenetic and nucleotide diversity analyses suggest a unique introduction of EMDV to Spain
and low gene flow with other countries. In contrast, Greece and Italy showed diverse populations
with high gene flow between both. |
| format | article |
| id | ReDivia8959 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | ReDivia89592025-04-25T14:49:39Z Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain Alfaro-Fernández, Ana Taengua, Rafael Font-San-Ambrosio, Isabel Sanahuja-Edo, Esmeralda Peiró, Rosa Galipienso, Luis Rubio, Luis Negative-strand RNA virus Alphanucleorhabdovirus melongenae Nucleotide diversity H20 Plant diseases Phylogeny Recombination Selection Gene flow The genetic variation and population structure of gene N (nucleocapsid) and part of gene L (replicase) from 13 eggplant mottle dwarf virus (EMDV) isolates from Spain were evaluated and compared with sequences of EMDV isolates from other countries retrieved from GenBank. Phylogenetic inference of part of gene L showed three main clades, one containing an EMDV isolate from Australia and the other two containing isolates from Iran and Europe, as well as four subclades. EMDV isolates from Spain were genetically very similar and grouped in a subclade together with one isolate from Germany and one from the UK. No new recombination events were detected in addition to one recombination previously reported, suggesting that recombination is rare for EMDV. The comparison of synonymous and non-synonymous rates showed that negative selection played an important role, and only two codons were under positive selection. Genetic differentiation (Fst test), phylogenetic and nucleotide diversity analyses suggest a unique introduction of EMDV to Spain and low gene flow with other countries. In contrast, Greece and Italy showed diverse populations with high gene flow between both. 2024-08-29T07:39:24Z 2024-08-29T07:39:24Z 2024 article publishedVersion Alfaro-Fernández, A., Taengua, R., Font-San-Ambrosio, I., Sanahuja-Edo, E., Peiró, R., Galipienso, L., & Rubio, L. (2024). Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain. Plants, 13(2), 250. 2223-7747 2223-7747 https://hdl.handle.net/20.500.11939/8959 10.3390/plants13020250 https://www.mdpi.com/2223-7747/13/2/250 en This research was funded by the Spanish Ministerio de Ciencia e Innovación, grant PID2021- 125787OR-C31, co-financed by FEDER Attribution-NonCommercial-NoDerivatives 4.0 Internacional http://creativecommons.org/licenses/by-nc-nd/4.0/ openAccess MDPI electronico |
| spellingShingle | Negative-strand RNA virus Alphanucleorhabdovirus melongenae Nucleotide diversity H20 Plant diseases Phylogeny Recombination Selection Gene flow Alfaro-Fernández, Ana Taengua, Rafael Font-San-Ambrosio, Isabel Sanahuja-Edo, Esmeralda Peiró, Rosa Galipienso, Luis Rubio, Luis Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain |
| title | Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain |
| title_full | Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain |
| title_fullStr | Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain |
| title_full_unstemmed | Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain |
| title_short | Genetic Variation and Evolutionary Analysis of Eggplant Mottled Dwarf Virus Isolates from Spain |
| title_sort | genetic variation and evolutionary analysis of eggplant mottled dwarf virus isolates from spain |
| topic | Negative-strand RNA virus Alphanucleorhabdovirus melongenae Nucleotide diversity H20 Plant diseases Phylogeny Recombination Selection Gene flow |
| url | https://hdl.handle.net/20.500.11939/8959 https://www.mdpi.com/2223-7747/13/2/250 |
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