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High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico

1
Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
2
Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Sinaloa 81101, Mexico
3
Laboratory of Plant Breeding and Biometry, Agricultural University of Athens, 75 Iera Odos, Athens 11855, Greece
4
Instituto 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, Spain
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Viruses 2019, 11(7), 594; https://doi.org/10.3390/v11070594
Received: 26 March 2019 / Revised: 28 May 2019 / Accepted: 17 June 2019 / Published: 29 June 2019
(This article belongs to the Special Issue Plant Virus Ecology and Biodiversity)
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Abstract

Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae 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 de novo 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. View Full-Text
Keywords: geminivirus; high-throughput sequencing; non-cultivated plants; viral biodiversity; agro-ecological interface geminivirus; high-throughput sequencing; non-cultivated plants; viral biodiversity; agro-ecological interface
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary materials

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    Link: https://www.dropbox.com/sh/ha6pkzls9217dhf/AAADNUa0TfYj3EZ8bb315cSga?dl=0.
    Description: Supplementary Materials: Contigs used for the metagenomic analysis. FastA S2: file with total contigs generated by SPADES of the library from Baja California. FastA S3: file with all contigs generated by SPADES of the library from Sonora. FastA S4: file with all contigs generated by SPADES of the library from Sinaloa. FastA S5: file with all contigs generated by SPADES of the library from Colima-Nayarit. FastA S6: file with all contigs generated by SPADES of the library from Coahuila-Durango.
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Rodríguez-Negrete, E.A.; Morales-Aguilar, J.J.; Domínguez-Duran, G.; Torres-Devora, G.; Camacho-Beltrán, E.; Leyva-López, N.E.; Voloudakis, A.E.; Bejarano, E.R.; Méndez-Lozano, J. High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico. Viruses 2019, 11, 594.

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