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

Gregorio-Jorge, Josefat; Bernal-Alcocer, Artemiza; Bañuelos-Hernández, Bernardo; Alpuche-Solís, Ángel G.; Hernández‐Zepeda, Cecilia; Moreno‐Valenzuela, Oscar A.; Frías-Treviño, Gustavo; Argüello‐Astorga, Gerardo R.

doi:10.1186/1743-422x-7-275

Cited by 27 publications

(16 citation statements)

References 67 publications

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“…New World BGVs are grouped in several secondary linages or "clades," such as the Squash leaf curl virus (SLCuV) clade, the Abutilon mosaic virus (AbMV) clade and the Brazil clade (Argüello-Astorga et al, 1994;Rojas et al, 2005). Members of the SLCuV clade display distinctive features in their replication origin, AC4 protein and N-terminal domain of their Rep protein (Argüello-Astorga et al, 1994;Gregorio-Jorge et al, 2010;Torres-Herrera et al, 2019). Legumoviruses and sweepoviruses are grouped by the host that they specifically infect.…”

Section: Introductionmentioning

confidence: 99%

First report of begomoviruses infectingCucumis sativusL. in North America and identification of a proposed new begomovirus species

Sanchez-Chavez

Regla-Márquez

Cardenas-Conejo

et al. 2020

PeerJ

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Background Members of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs. Methods To identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses. Results We identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade. Conclusions The findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops.

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Section: Introductionmentioning

confidence: 99%

First report of begomoviruses infectingCucumis sativusL. in North America and identification of a proposed new begomovirus species

Sanchez-Chavez

Regla-Márquez

Cardenas-Conejo

et al. 2020

PeerJ

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“…Leaf samples of a variety of weeds exhibiting symptoms of virosis (e.g., leaf curling, yellowing, mosaics, interveinal chlorosis, growth stunting, and so on) were collected during the summer of 2007 in diverse localities of Yucatán and Morelos, México (See Section 2). The presence of BGVs was tested by PCR using a combination of both “universal” and “lineage-specific” primers designed to improve the detection of either S-Lin members or “typical” NW BGVs [30,34]. Nine out 16 examined samples produced amplicons of the expected size (~1.4 kb) with the pair of primers repSL-2150for/cpYMACrev, specific for detection of S-Lin members.…”

Section: Resultsmentioning

confidence: 99%

“…To increase the quantity of the field sample DNA, the extracts were subjected to rolling circle amplification (RCA) using the TempliPhi kit (GE Healthcare, Chicago, IL, USA). Polymerase chain reaction (PCR)-detection for begomoviruses was performed using Taq DNA Polymerase master mix (New England BioLabs, USA) and paired sets of lineage-specific primers, repSL2150for/cpYMAC-rev [30] and repDGR-for/cpYMAC-rev [34]. The PCR products were cloned in pGem-T Easy vector system (Promega, Madison, WI, USA).…”

Section: Methodsmentioning

confidence: 99%

“…One of these clades, named after the Squash leaf curl virus , encompasses a number of BGV species, which are scattered from Southern USA to Argentina [29,30,31]. Members of the SLCV lineage (S-Lin, for simplicity) display two significant features distinguishing them from other NW BGVs: (a) the Rep-binding sites (iterons) are more numerous and display a unique arrangement in the Ori [23,32], and (b) the N-terminal domain of its Rep protein exhibits low aa sequence identity (<50%) with its putative homologous from other BGV lineages [24,30]. The evolutionary and functional significance of those distinctive characteristics has not been addressed up till now, notwithstanding its evident interest for a better understanding of BGVs’ evolution in the Americas.…”

Section: Introductionmentioning

confidence: 99%

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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

Torres-Herrera

Romero-Osorio

Moreno‐Valenzuela

et al. 2019

Viruses

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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.

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“…The DNA-A was amplified by PCR using two pairs of primers that produce amplicons overlapping along a ~520-bp segment, and that jointly encompass the full A genomic component. The DNA-B was PCR amplified using two sets of degenerate primers, BC1-290rev/BV1-310for and BC1-290for/BV1-470-rev, as previously described [37]; the latter primers are complementary to conserved sequences in the B genomic component of New World BGVs. The amplicons were cloned into pGEM-T Easy Vector (Promega) and analysed in restriction fragment length polymorphism (RFLP) assays using EcoRI and HinfI endonucleases.…”

Section: Methodsmentioning

confidence: 99%

Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes

et al. 2019

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A novel bipartite begomovirus, Blechum interveinal chlorosis virus (BleICV), was characterized at the genome level. Comparative analyses revealed that BleICV coat protein (CP) gene promoter is highly divergent from the equivalent region of other begomoviruses (BGVs), with the single exception of Tomato chino La Paz virus (ToChLPV) with which it shares a 23-bp phylogenetic footprint exhibiting dyad symmetry. Systematic examination of the homologous CP promoter segment of 132 New World BGVs revealed the existence of a quasi-palindromic DNA segment displaying a strongly conserved ACTT-(N7)-AAGT core. The spacer sequence between the palindromic motifs is constant in length, but its sequence is highly variable among viral species, presenting a relaxed consensus (TT)GGKCCCY, which is similar to the Conserved Late Element or CLE (GTGGTCCC), a putative TrAP-responsive element. The homologous CP promoter region of Old World BGVs exhibited a distinct organization, with the putative TATA-box overlapping the left half of the ACTT-N7 composite element. Similar CP promoter sequences, dubbed “TATA-associated composite element” or TACE, were found in viruses belonging to different Geminiviridae genera, hence hinting unsuspected evolutionary relationships among those lineages. To get cues about the TACE function, the regulatory function of the CLE was explored in distinct experimental systems. Transgenic tobacco plants harboring a GUS reporter gene driven by a promoter composed by CLE multimers expressed high beta-glucuronidase activity in absence of viral factors, and that expression was increased by begomovirus infection. On the other hand, the TrAP-responsiveness of a truncated CP promoter of Tomato golden mosaic virus (TGMV) was abolished by site-directed mutation of the only CLE present in it, whereas the artificial addition of one CLE to the -125 truncated promoter strongly enhanced the transactivation level in tobacco protoplasts. These results indicate that the CLE is a TrAP-responsive element, hence providing valuable clues to interpret the recurrent association of the CLE with the TACE. On the basis of the aforesaid direct evidences and the insights afforded by the extensive comparative analysis of BleICV CP promoter, we propose that the TACE might be involved in the TrAP-mediated derepression of CP gene in vascular tissues.

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

Cited by 27 publications

References 67 publications

First report of begomoviruses infectingCucumis sativusL. in North America and identification of a proposed new begomovirus species

First report of begomoviruses infectingCucumis sativusL. in North America and identification of a proposed new begomovirus species

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

Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes

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