Enrique Moriones

Geminivirus strain demarcation and nomenclature

Geminivirus taxonomy and nomenclature is growing in complexity with the number of genomic sequences deposited in sequence databases. Taxonomic and nomenclatural updates are published at regular intervals (Fauquet et al. in Arch Virol 145:1743–1761, 2000, Arch Virol 148:405–421, 2003). A system to standardize virus names, and corresponding guidelines, has been proposed (Fauquet et al. in Arch Virol 145:1743–1761, 2000). This system is now followed by a large number of geminivirologists in the world, making geminivirus nomenclature more transparent and useful. In 2003, due to difficulties inherent in species identification, the ICTV Geminiviridae Study Group proposed new species demarcation criteria, the most important of which being an 89% nucleotide (nt) identity threshold between full-length DNA-A component nucleotide sequences for begomovirus species. This threshold has been utilised since with general satisfaction. More recently, an article has been published to clarify the terminology used to describe virus entities below the species level [5]. The present publication is proposing demarcation criteria and guidelines to classify and name geminiviruses below the species level. Using the Clustal V algorithm (DNAStar MegAlign software), the distribution of pairwise sequence comparisons, for pairs of sequences below the species taxonomic level, identified two peaks: one at 85–94% nt identity that is proposed to correspond to “strain” comparisons and one at 92–100% identity that corresponds to “variant” comparisons. Guidelines for descriptors for each of these levels are proposed to standardize nomenclature under the species level. In this publication we review the status of geminivirus species and strain demarcation as well as providing updated isolate descriptors for a total of 672 begomovirus isolates. As a consequence, we have revised the status of some virus isolates to classify them as “strains”, whereas several others previously classified as “strains” have been upgraded to “species”. In all other respects, the classification system has remained robust, and we therefore propose to continue using it. An updated list of all geminivirus isolates and a phylogenetic tree with one representative isolate per species are provided.

Tomato yellow leaf curl virus, an emerging virus complex causing epidemics worldwide.

Tomato yellow leaf curl (TYLC) is one of the most devastating viral diseases of cultivated tomato (Lycopersicon esculentum) in tropical and subtropical regions worldwide, and losses of up to 100% are frequent. In many regions, TYLC is the main limiting factor in tomato production. The causal agents are a group of geminivirus species belonging to the genus Begomovirus of the family Geminiviridae, all of them named Tomato yellow leaf curl virus (TYLCV) (sensu lato). There has been almost 40 years of research on TYLCV epidemics and intensive research programmes have been conducted to find solutions to the severe problem caused by these viruses. This paper provides an overview of the most outstanding achievements in the research on the TYLCV complex that could lead to more effective control strategies.

Recommendations for the classification and nomenclature of the DNA-β satellites of begomoviruses

The symptom-modulating, single-stranded DNA satellites (known as DNA-β) associated with begomoviruses (family Geminiviridae) have proven to be widespread and important components of a large number of plant diseases across the Old World. Since they were first identified in 2000, over 260 full-length sequences (∼1,360 nucleotides) have been deposited with databases, and this number increases daily. This has highlighted the need for a standardised, concise and unambiguous nomenclature for these components, as well as a meaningful and robust classification system. Pairwise comparisons of all available full-length DNA-β sequences indicate that the minimum numbers of pairs occur at a sequence identity of 78%, which we propose as the species demarcation threshold for a distinct DNA-β. This threshold value divides the presently known DNA-β sequences into 51 distinct satellite species. In addition, we propose a naming convention for the satellites that is based upon the system already in use for geminiviruses. This maintains, whenever possible, the association with the helper begomovirus, the disease symptoms and the host plant and provides a logical and consistent system for referring to already recognised and newly identified satellites.

Displacement of Tomato yellow leaf curl virus (TYLCV)-Sr by TYLCV-Is in tomato epidemics in Spain

ABSTRACT A progressive displacement of tomato yellow leaf curl virus (TYLCV)-Sr by TYLCV-Is was observed in tomato epidemics in southern Spain based on incidence data of both virus species obtained during surveys conducted between 1996 and 1998. Ecological factors that might be involved in such a displacement, such as competition of TYLCV-Sr and TYLCV-Is in tomato, transmission by local biotypes (B and Q) of Bemisia tabaci, and presence in weeds and alternate crops, have been analyzed. No selective advantage is observed for TYLCV-Sr or TYLCV-Is in tomato plants either infected via Agrobacterium tumefaciens or via B. tabaci. However, TYLCV-Is is more efficiently vectored by local biotypes of B. tabaci; and common bean, a bridge crop between tomato crops, is a host for TYLCV-Is but not TYLCV-Sr. Therefore, common bean acts as a reservoir for TYLCV-Is. These two factors are probably responsible for the displacement of TYLCV-Sr by TYLCV-Is as the causative agent of epidemics in tomato in southern Spain.

Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus

Abstract The family Geminiviridae includes plant-infecting circular single-stranded DNA viruses that have geminate particle morphology. Members of this family infect both monocotyledonous and dicotyledonous plants and have a nearly global distribution. With the advent of new molecular tools and low-cost sequencing, there has been a significant increase in the discovery of new geminiviruses in various cultivated and non-cultivated plants. In this communication, we highlight the establishment of three new genera (Becurtovirus, Eragrovirus and Turncurtovirus) to accommodate various recently discovered geminiviruses that are highly divergent and, in some cases, have unique genome architectures. The genus Becurtovirus has two viral species, Beet curly top Iran virus (28 isolates; leafhopper vector Circulifer haematoceps) and Spinach curly top Arizona virus (1 isolate; unknown vector), whereas the genera Eragrovirus and Turncurtovirus each have a single assigned species: Eragrostis curvula streak virus (6 isolates; unknown vector) and Turnip curly top virus (20 isolates; leafhopper vector Circulifer haematoceps), respectively. Based on analysis of all of the genome sequences available in public databases for each of the three new genera, we provide guidelines and protocols for species and strain classification within these three new genera.

Tomato Yellow Leaf Curl Virus-Is Causes a Novel Disease of Common Bean and Severe Epidemics in Tomato in Spain

Field surveys were conducted in the autumn of 1997 in the main tomato (Lycopersicon esculentum)-growing regions of southern Spain following a severe tomato yellow leaf curl epidemic in tomato. Tomato yellow leaf curl virus (TYLCV)-Is was found to have spread to all regions and to coexist with TYLCV-Sr, which has been present since 1992. TYLCV-Is was also shown to be the causal agent of bean leaf crumple, a novel disease that has caused severe economic losses in fresh-market common bean (Phaseolus vulgaris) crops of southern Spain since September 1997. The disease was reproduced by infecting beans with cloned TYLCV-Is obtained from infected tomato plants collected in Almería. This is the first report of bean leaf crumple disease and the first report of a geminivirus in bean from Spain.

EcoTILLING for the identification of allelic variants of melon eIF4E, a factor that controls virus susceptibility

BackgroundTranslation initiation factors of the 4E and 4G protein families mediate resistance to several RNA plant viruses in the natural diversity of crops. Particularly, a single point mutation in melon eukaryotic translation initiation factor 4E (eIF4E) controls resistance to Melon necrotic spot virus (MNSV) in melon. Identification of allelic variants within natural populations by EcoTILLING has become a rapid genotype discovery method.ResultsA collection of Cucumis spp. was characterised for susceptibility to MNSV and Cucumber vein yellowing virus (CVYV) and used for the implementation of EcoTILLING to identify new allelic variants of eIF4E. A high conservation of eIF4E exonic regions was found, with six polymorphic sites identified out of EcoTILLING 113 accessions. Sequencing of regions surrounding polymorphisms revealed that all of them corresponded to silent nucleotide changes and just one to a non-silent change correlating with MNSV resistance. Except for the MNSV case, no correlation was found between variation of eIF4E and virus resistance, suggesting the implication of different and/or additional genes in previously identified resistance phenotypes. We have also characterized a new allele of eIF4E from Cucumis zeyheri, a wild relative of melon. Functional analyses suggested that this new eIF4E allele might be responsible for resistance to MNSV.ConclusionThis study shows the applicability of EcoTILLING in Cucumis spp., but given the conservation of eIF4E, new candidate genes should probably be considered to identify new sources of resistance to plant viruses. Part of the methodology described here could alternatively be used in TILLING experiments that serve to generate new eIF4E alleles.

High similarity among the tomato yellow leaf curl virus isolates from the West Mediterranean Basin: the nucleotide sequence of an infectious clone from Spain

SummaryAn isolate of tomato yellow leaf curl geminivirus, from the first epidemic outbreaks that occurred in Murcia, Spain (TYLCV-M) in 1992, was cloned and its nucleotide sequence was determined. The circular single stranded DNA consisted of 2777 nucleotides. The genome organization resembled that of other TYLCV sequenced so far; regulatory signal sequences for bidirectional transcription and for polyadenylation of the transcripts were localized in the sequence. Infectivity of the cloned DNA was demonstrated by subcloning a 1.8 mer of TYLCV-M in pBin19 and agroinoculating it into tomato andNicotiana benthamiana plants. Symptoms and viral DNA forms in agroinfected plants did not differ from those of field infected ones. Sequence comparisons with other TYLCV isolates show a high homogeneity between isolates from the West Mediterranean Basin, suggesting the presence of a geographical cluster.

Typing of Tomato Yellow Leaf Curl Viruses in Europe

Tomato yellow leaf curl disease is spreading in southern Europe, where it has quickly become a serious problem. In recent years, several virus isolates have been characterised. Although with some genetic variability, all isolates found in Europe belong to one of two species Tomato yellow leaf curl-Sardinia (TYLCV-Sar) or Tomato yellow leaf curl-Israel (TYLCV-Is). Several methods were tested to identify and type TYLCV isolates from field samples: (1) RFLP of a DNA fragment amplified from the coat protein gene; (2) PAGE of a fragment amplified from the C2 gene; (3) dot-blot hybridisation. All methods enabled the detection of the TYLCVs and provided good indications for attributing them to one species or the other. However, for typing purposes, the RFLP method was the most reliable, due to the easily recognisable pattern produced by the two virus species present in Europe. Dot-blot hybridisation is less expensive for identifying TYLCVs in large numbers of samples, particularly when a mixture of two probes is used. PAGE of the C2 fragment is the fastest of the methods tested.

Severe yellowing outbreaks in tomato in Spain associated with infections of Tomato chlorosis virus

Since 1997, yellowing disease outbreaks have occurred in tomato (Lycopersicon esculentum) crops in southern Spain. The outbreaks were associated with high populations of the whitefly Bemisia tabaci. Symptoms consisted mainly of interveinal yellowing that developed initially on lower leaves and then progressed to the upper part of the plant. Affected plants were less vigorous and yielded less due to reduced fruit growth and delayed ripening. During 1998 and 1999, the yellowing disease was widespread and occurred at high incidences in the Málaga province. The disease agent was readily transmissible from tomato to tomato by B. tabaci biotype Q. Samples from symptomatic tomato plants were analyzed and shown to be infected with Tomato chlorosis virus (ToCV) (genus Crinivirus, family Closteroviridae). This is the first report of ToCV epidemics in Europe.