High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico
Plant DNA viruses of the genus <i>Begomovirus</i> have been documented as the most genetically diverse in the family <i>Geminiviridae</i> and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize n...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/11/7/594 |
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| author | Edgar Antonio Rodríguez-Negrete Juan José Morales-Aguilar Gustavo Domínguez-Duran Gadiela Torres-Devora Erika Camacho-Beltrán Norma Elena Leyva-López Andreas E. Voloudakis Eduardo R. Bejarano Jesús Méndez-Lozano |
| author_facet | Edgar Antonio Rodríguez-Negrete Juan José Morales-Aguilar Gustavo Domínguez-Duran Gadiela Torres-Devora Erika Camacho-Beltrán Norma Elena Leyva-López Andreas E. Voloudakis Eduardo R. Bejarano Jesús Méndez-Lozano |
| author_sort | Edgar Antonio Rodríguez-Negrete |
| collection | DOAJ |
| description | Plant DNA viruses of the genus <i>Begomovirus</i> have been documented as the most genetically diverse in the family <i>Geminiviridae</i> and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012−2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent <i>de novo</i> assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions. |
| first_indexed | 2024-12-14T19:24:05Z |
| format | Article |
| id | doaj.art-3b98ff8678644b6588cae750fc95eb35 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-12-14T19:24:05Z |
| publishDate | 2019-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-3b98ff8678644b6588cae750fc95eb352022-12-21T22:50:14ZengMDPI AGViruses1999-49152019-06-0111759410.3390/v11070594v11070594High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific MexicoEdgar Antonio Rodríguez-Negrete0Juan José Morales-Aguilar1Gustavo Domínguez-Duran2Gadiela Torres-Devora3Erika Camacho-Beltrán4Norma Elena Leyva-López5Andreas E. Voloudakis6Eduardo R. Bejarano7Jesús Méndez-Lozano8Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoInstituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoInstituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoInstituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoInstituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoInstituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoLaboratory of Plant Breeding and Biometry, Agricultural University of Athens, 75 Iera Odos, Athens 11855, GreeceInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Campus Teatinos, 29071 Málaga, SpainInstituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, MexicoPlant DNA viruses of the genus <i>Begomovirus</i> have been documented as the most genetically diverse in the family <i>Geminiviridae</i> and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012−2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent <i>de novo</i> assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.https://www.mdpi.com/1999-4915/11/7/594geminivirushigh-throughput sequencingnon-cultivated plantsviral biodiversityagro-ecological interface |
| spellingShingle | Edgar Antonio Rodríguez-Negrete Juan José Morales-Aguilar Gustavo Domínguez-Duran Gadiela Torres-Devora Erika Camacho-Beltrán Norma Elena Leyva-López Andreas E. Voloudakis Eduardo R. Bejarano Jesús Méndez-Lozano High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico Viruses geminivirus high-throughput sequencing non-cultivated plants viral biodiversity agro-ecological interface |
| title | High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico |
| title_full | High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico |
| title_fullStr | High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico |
| title_full_unstemmed | High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico |
| title_short | High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico |
| title_sort | high throughput sequencing reveals differential begomovirus species diversity in non cultivated plants in northern pacific mexico |
| topic | geminivirus high-throughput sequencing non-cultivated plants viral biodiversity agro-ecological interface |
| url | https://www.mdpi.com/1999-4915/11/7/594 |
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