TY - JOUR
T1 - High-throughput sequencing reveals differential begomovirus species diversity in non-cultivated plants in northern-pacific mexico
AU - Rodríguez-Negrete, Edgar Antonio
AU - Morales-Aguilar, Juan José
AU - Domínguez-Duran, Gustavo
AU - Torres-Devora, Gadiela
AU - Camacho-Beltrán, Erika
AU - Leyva-López, Norma Elena
AU - Voloudakis, Andreas E.
AU - Bejarano, Eduardo R.
AU - Méndez-Lozano, Jesús
N1 - Publisher Copyright:
© 2019 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2019/7
Y1 - 2019/7
N2 - 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.
AB - 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.
KW - Agro-ecological interface
KW - Geminivirus
KW - High-throughput sequencing
KW - Non-cultivated plants
KW - Viral biodiversity
UR - http://www.scopus.com/inward/record.url?scp=85069261010&partnerID=8YFLogxK
U2 - 10.3390/v11070594
DO - 10.3390/v11070594
M3 - Artículo
C2 - 31261973
AN - SCOPUS:85069261010
SN - 1999-4915
VL - 11
JO - Viruses
JF - Viruses
IS - 7
M1 - 594
ER -