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A Lineage of Begomoviruses Encode Rep and AC4 Proteins of Enigmatic Ancestry: Hints on the Evolution of Geminiviruses in the New World

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División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
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Centro de Investigación Científica de Yucatán, A.C., Mérida 97000, Yucatán, México
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CONACYT–CIIDZA–Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., México
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CONACyT-Universidad de Colima, Laboratorio de Agrobiotecnología, Carretera Los Limones-Loma de Juarez (s/n), Tecnoparque CLQ Colima 28629, Colima, México
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Facultad de Ciencias Forestales, Universidad Juárez del Estado de Durango, Río Papaloapan Esquina con Blvd Durango (s/n), Col. Valle del Sur. 34120, Durango, Dgo, México
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Viruses 2019, 11(7), 644; https://doi.org/10.3390/v11070644
Received: 20 June 2019 / Revised: 9 July 2019 / Accepted: 10 July 2019 / Published: 13 July 2019
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
The begomoviruses (BGVs) are plant pathogens that evolved in the Old World during the Cretaceous and arrived to the New World (NW) in the Cenozoic era. A subgroup of NW BGVs, the “Squash leaf curl virus (SLCV) lineage” (S-Lin), includes viruses with unique characteristics. To get clues on the evolutionary origin of this lineage, a search for divergent members was undertaken. Four novel BGVs were characterized, including one that is basal to the group. Comparative analyses led to discover a ~670 bp genome module that is nearly exclusive of this lineage, encompassing the replication origin, the AC4 gene, and 480 bp of the Rep gene. A similar DNA module was found in two curtoviruses, hence suggesting that the S-Lin ancestor acquired its distinctive genomic segment by recombination with a curtovirus. This hypothesis was definitely disproved by an in-depth sequence analysis. The search for homologs of S-Lin Rep uncover the common origin of Rep proteins encoded by diverse Geminiviridae genera and viral “fossils” integrated at plant genomes. In contrast, no homolog of S-Lin Rep was found in public databases. Consequently, it was concluded that the SLCV clade ancestor evolved by a recombination event between a primitive NW BGV and a virus from a hitherto unknown lineage. View Full-Text
Keywords: geminivirus evolution; replication protein; curtovirus taxonomy; endogenous viral element; replication origin; rolling-circle replication geminivirus evolution; replication protein; curtovirus taxonomy; endogenous viral element; replication origin; rolling-circle replication
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Torres-Herrera, S.I.; Romero-Osorio, A.; Moreno-Valenzuela, O.; Pastor-Palacios, G.; Cardenas-Conejo, Y.; Ramírez-Prado, J.H.; Riego-Ruiz, L.; Minero-García, Y.; Ambriz-Granados, S.; Argüello-Astorga, G.R. A Lineage of Begomoviruses Encode Rep and AC4 Proteins of Enigmatic Ancestry: Hints on the Evolution of Geminiviruses in the New World. Viruses 2019, 11, 644.

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