Analysis of a new strain of <it>Euphorbia mosaic virus </it>with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region

• Main Authors: Argüello-Astorga Gerardo R, Frías-Treviño Gustavo, Moreno-Valenzuela Oscar, Hernández-Zepeda Cecilia, Alpuche-Solís Ángel G, Bañuelos-Hernández Bernardo, Bernal-Alcocer Artemiza, Gregorio-Jorge Josefat
• Format: Article
• Language: English
• Published: BMC 2010-10-01
• Series: Virology Journal
• Online Access: http://www.virologyj.com/content/7/1/275

<p>Abstract</p> <p>Background</p> <p><it>Euphorbia mosaic virus </it>(EuMV) is a member of the SLCV clade, a lineage of New World begomoviruses that display distinctive features in their replication-associated protein (Rep) and virion-strand replication origin. The first entirely characterized EuMV isolate is native from Yucatan Peninsula, Mexico; subsequently, EuMV was detected in weeds and pepper plants from another region of Mexico, and partial DNA-A sequences revealed significant differences in their putative replication specificity determinants with respect to EuMV-YP. This study was aimed to investigate the replication compatibility between two EuMV isolates from the same country.</p> <p>Results</p> <p>A new isolate of EuMV was obtained from pepper plants collected at Jalisco, Mexico. Full-length clones of both genomic components of EuMV-Jal were biolistically inoculated into plants of three different species, which developed symptoms indistinguishable from those induced by EuMV-YP. Pseudorecombination experiments with EuMV-Jal and EuMV-YP genomic components demonstrated that these viruses do not form infectious reassortants in <it>Nicotiana benthamiana</it>, presumably because of Rep-iteron incompatibility. Sequence analysis of the EuMV-Jal DNA-B intergenic region (IR) led to the unexpected discovery of a 35-nt-long sequence that is identical to a segment of the <it>rep </it>gene in the cognate viral DNA-A. Similar short <it>rep </it>sequences ranging from 35- to 51-nt in length were identified in all EuMV isolates and in three distinct viruses from South America related to EuMV. These short <it>rep </it>sequences in the DNA-B IR are positioned downstream to a ~160-nt non-coding domain highly similar to the CP promoter of begomoviruses belonging to the SLCV clade.</p> <p>Conclusions</p> <p>EuMV strains are not compatible in replication, indicating that this begomovirus species probably is not a replicating lineage in nature. The genomic analysis of EuMV-Jal led to the discovery of a subgroup of SLCV clade viruses that contain in the non-coding region of their DNA-B component, short <it>rep </it>gene sequences located downstream to a <it>CP</it>-promoter-like domain. This assemblage of DNA-A-related sequences within the DNA-B IR is reminiscent of polyomavirus microRNAs and could be involved in the posttranscriptional regulation of the cognate viral <it>rep </it>gene, an intriguing possibility that should be experimentally explored</p>