A virus and its vector, pepper yellow leaf curl virus and Bemisia tabaci, two new invaders of Indonesia

Identification of begomoviruses associated with the insect vector Bemisia tabaci and various host plants on Java Island, Indonesia

Begomoviruses are economically important plant viruses and are transmitted by Bemisia tabaci which is a complex of various cryptic species. However, it is uncertain whether most begomoviruses that infect host plants are transmitted by B. tabaci at a similar rate. We compared the begomovirus profiles that were detected in a total of 37 whitefly populations and 52 host plants on Java Island, Indonesia. Seven begomovirus species were detected in B. tabaci at different rates: pepper yellow leaf curl Indonesia virus (PepYLCIV, 56.8%), tomato yellow leaf curl Kanchanaburi virus (TYLCKaV, 46.0%), tomato leaf curl New Delhi virus (ToLCNDV, 21.6%), squash leaf curl China virus (SLCCNV, 21.6%), ageratum yellow vein China virus (AYVCNV, 2.7%), mungbean yellow mosaic India virus (MYMIV, 2.7%), and okra enation leaf curl virus (OELCuV, 2.7%). The begomoviruses were detected at different rates in three cryptic species of B. tabaci. In addition, six begomovirus species were detected in the various host plants at different rates: PepYLCIV (67.3%), TYLCKaV (53.9%), ToLCNDV (13.5%), MYMIV (11.5%), AYVCNV (3.9%), and Tomato yellow leaf curl Thailand virus (TYLCTHV) (1.9%). By comparing the virus presence between whiteflies and plants, five begomoviruses (AYVCNV, MYMIV, PepYLCIV, ToLCNDV, and TYLCKaV) were detected in both samples, but their sequence similarity was highly variable depending on the begomovirus themselves; TYLCKaV was highest (99.4%-100%) than any other viruses. Our study suggests B. tabaci acquire begomoviruses at different rates from plants. This study provides important information on the potential variation in the begomovirus transmission mechanism.

Manipulation of Whitefly Behavior by Plant Viruses

Whiteflies of the Bemisia tabaci complex transmit hundreds of plant viruses belonging to the genera Begomovirus and Crinivirus, among others. Tripartite interactions of whitefly-virus-plant frequently occur during virus infection and transmission. Specifically, virus transmission-related behavior of whitefly, such as preference and feeding, may be altered by viruses and thus exert significant impacts on the outcome of virus spread and epidemics. Here, we provide an overview on the current understanding of the manipulation of whitefly behavior by plant viruses. Plant viruses can significantly modulate whitefly preference and feeding behavior, either directly or in a plant-mediated manner. In general, non-viruliferous whiteflies tend to prefer virus-infected plants, and viruliferous whiteflies are more likely to prefer uninfected plants. In most cases, virus infection of plants and/or whitefly seems to exhibit positive or no effects on whitefly feeding on plants. The significance and evolution of these patterns are then discussed. Finally, we suggest several future directions of research, such as the exploration of temporal dynamics and the dissection of underlying mechanisms of virus-induced changes in whitefly behavior.

Emergence of Asian endemic begomoviruses as a pandemic threat

Plant viruses are responsible for the most devastating and commercially significant plant diseases, especially in tropical and subtropical regions. The genus begomovirus is the largest one in the family Geminiviridae, with a single-stranded DNA genome, either monopartite or bipartite. Begomoviruses are transmitted by insect vectors, such as Bemisia tabaci. Begomoviruses are the major causative agents of diseases in agriculture globally. Because of their diversity and mode of evolution, they are thought to be geographic specific. The emerging begomoviruses are of serious concern due to their increasing host range and geographical expansion. Several begomoviruses of Asiatic origin have been reported in Europe, causing massive economic losses; insect-borne transmission of viruses is a critical factor in virus outbreaks in new geographical regions. This review highlights crucial information regarding Asia's four emerging and highly destructive begomoviruses. We also provided information regarding several less common but still potentially important pathogens of different crops. This information will aid possible direction of future studies in adopting preventive measures to combat these emerging viruses.

PepYLCIV and PepYLCAV resistance gene Pepy-2 encodes DFDGD-Class RNA-dependent RNA polymerase in Capsicum

A begomovirus resistance gene Pepy-2 encoding the DFDGD-Class RNA-dependent RNA polymerase 3a was identified in pepper (C. annuum) through the forward and reverse genetic analyses. In several countries throughout the world, the whitefly-transmitted begomovirus causes massive yield losses in pepper (Capsicum spp.) production. Although introgression of the genetic resistance against begomovirus to commercial cultivars is strongly required, the recently discovered recessive resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, is the only begomovirus resistance gene identified in Capsicum so far. In this study, we fine-mapped another begomovirus resistance gene from PG1-1 (C. annuum), which is resistant to pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV), to further speed up the marker-assisted breeding of begomovirus resistance in peppers. A single dominant locus, Pepy-2, conferring resistance against PepYLCIV in PG1-1 was identified on chromosome 7 by screening recombinants from the F₂ and F₃ segregating populations derived from a cross between PG1-1 and begomovirus susceptible SCM334. In the target region spanning 722 kb, a strong candidate gene, the RNA-dependent RNA polymerase 3a (CaRDR3a), was identified. The whole-genome and transcriptome sequences of PG1-1 and SCM334 revealed a single Guanine (G) deletion in CaRDR3a first exon, causing a frameshift resulting in loss-of-function in SCM334. In addition, multiple loss-of-function alleles of CaRDR3a were identified in the reference sequences of C. annuum, C. chinense, and C. baccatum in the public database. Furthermore, virus-induced gene silencing of CaRDR3a in PG1-1 resulted in the loss of resistance against PepYLCIV. PG1-1 and the DNA marker developed in this study will be useful to breeders using Pepy-2 in their breeding programs.

A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum

A begomovirus resistance gene pepy-1, which encodes the messenger RNA surveillance factor Pelota, was identified in pepper (C. annuum) through map-based cloning and functional characterization. Pepper yellow leaf curl disease caused by begomoviruses seriously affects pepper (Capsicum spp.) production in a number of regions around the world. Ty genes of tomato, which confer resistance to the tomato yellow leaf curl virus, are the only begomovirus resistance genes cloned to date. In this study, we focused on the identification of begomovirus resistance genes in Capsicum annuum. BaPep-5 was identified as a novel source of resistance against pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV). A single recessive locus, which we named as pepper yellow leaf curl disease virus resistance 1 (pepy-1), responsible for PepYLCAV resistance in BaPep-5 was identified on chromosome 5 in an F₂ population derived from a cross between BaPep-5 and the begomovirus susceptible accession BaPep-4. In the target region spanning 34 kb, a single candidate gene, the messenger RNA surveillance factor Pelota, was identified. Whole-genome resequencing of BaPep-4 and BaPep-5 and comparison of their genomic DNA sequences revealed a single nucleotide polymorphism (A to G) located at the splice site of the 9th intron of CaPelota in BaPep-5, which caused the insertion of the 9th intron into the transcript, resulting in the addition of 28 amino acids to CaPelota protein without causing a frameshift. Virus-induced gene silencing of CaPelota in the begomovirus susceptible pepper No.218 resulted in the gain of resistance against PepYLCIV, a phenotype consistent with BaPep-5. The DNA marker developed in this study will greatly facilitate marker-assisted breeding of begomovirus resistance in peppers.

Gas Chromatography-Mass Spectrometry Analysis of Compounds Emitted by Pepper Yellow Leaf Curl Virus-Infected Chili Plants: A Preliminary Study

Pepper yellow leaf curl virus (PYLCV) is a threat to chili plants and can significantly reduce yields. This study aimed as a pilot project to detect PYLCV by analyzing compounds emitted by chili plants using gas chromatography-mass spectrometry (GC-MS). The samples investigated in this research were PYLCV-infected and PYLCV-undetected chili plants taken from commercial chili fields. The infection status was validated by using a polymerase chain reaction (PCR) test. A headspace technique was used to extract the volatile organic compounds emitted by plants. The analysis of GC-MS results began with pre-processing, analyzing sample compound variability with a boxplot analysis, and sample classification by using a multivariate technique. Unsupervised multivariate technique principal component analysis (PCA) was performed to discover whether GC-MS could identify PYLCV-infected or not. The results showed that PYLCV-infected and PYLCV-undetected chili plants could be differentiated, with a total percent variance of the first three principal components reaching 91.32%, and successfully discriminated between PYLCV-infected and PYLCV-undetected chili plants. However, more comprehensive studies are needed to find the potential biomarkers of the infected plants.

Capsicum-infecting begomoviruses as global pathogens: host-virus interplay, pathogenesis, and management

Whitefly-transmitted begomoviruses are among the major threats to the cultivation of Capsicum spp. (Family: Solanaceae) worldwide. Capsicum-infecting begomoviruses (CIBs) have a broad host range and are commonly found in mixed infections, which, in turn, fuels the emergence of better-adapted species through intraspecies and interspecies recombination. Virus-encoded proteins hijack host factors to breach the well-coordinated antiviral response of plants. Epigenetic modifications of histones associated with viral minichromosomes play a critical role in this molecular arms race. Moreover, the association of DNA satellites further enhances the virulence of CIBs as the subviral agents aid the helper viruses to circumvent plant antiviral defense and facilitate expansion of their host range and disease development. The objective of this review is to provide a comprehensive overview on various aspects of CIBs such as their emergence, epidemiology, mechanism of pathogenesis, and the management protocols being employed for combating them.

Ty-2 and Ty-3a Conferred Resistance are Insufficient Against Tomato Yellow Leaf Curl Kanchanaburi Virus from Southeast Asia in Single or Mixed Infections of Tomato

Tomato yellow leaf curl virus (TYLCV), a monopartite begomovirus that originated in the eastern Mediterranean, has spread worldwide, becoming a serious threat to tomato (Solanum lycopersicum L.) production. Southeast Asia is considered one of the hotspots for begomovirus diversity, and a wide variety of local begomovirus species distinct from TYLCV have been identified. In this study, the protection effect of introgressions of single TYLCV Ty resistance genes, Ty-2 and Ty-3a, in tomato was examined against inoculations of the bipartite begomoviruses Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) and Pepper yellow leaf curl Indonesia virus (PepYLCIV) isolated from Indonesia. Our findings suggest that Ty-2 in the heterozygous state was found to be ineffective against PepYLCIV and TYLCKaV, whereas Ty-3a in the heterozygous state was effective against PepYLCIV and partially effective against TYLCKaV. Quantification of viral DNAs showed correlation between symptom expression and viral DNA accumulation. Moreover, mixed infections of TYLCKaV and PepYLCIV caused notably severe symptoms in tomato plants harboring Ty-3a. In cases of mixed infection, quantifying viral DNAs showed a relatively high accumulation of PepYLCIV, indicating that Ty-3a loses its effectiveness against PepYLCIV when TYLCKaV is also present. This study demonstrates the lack of effectiveness of Ty resistance genes against single and mixed infections of distinct local begomoviruses from Southeast Asia.

Pepper vein yellows virus 9: a novel polerovirus isolated from chili pepper in Indonesia

In 2017, a leaf sample from a single chili pepper (Capsicum annuum) plant exhibiting yellowing was collected from Aceh province, Indonesia. Total RNA was extracted from this sample, and RNA-Seq analysis was conducted. Putative infecting viruses were detected by mapping the obtained reads to the full-length viral genome sequences available in the GenBank database (7457 sequences) and the de novo-assembled contigs. RNA-Seq analysis detected polerovirus, begomovirus, and amalgavirus sequences, and the polerovirus-like sequences showed strong similarity to those of previously reported pepper vein yellows viruses (PeVYVs). The complete viral genome sequence obtained by RT-PCR had a length of 6023 nt, had the typical genome organization of a polerovirus and showed a high degree of sequence similarity to PeVYV-2 from Israel. Moreover, the predicted amino acid sequence of the P0 protein of the Indonesian isolate was 85.1% to 88.8% identical to those of other PeVYVs. In accordance with the polerovirus species demarcation criteria, this isolate should be assigned to a new polerovirus species, and we propose the name "pepper vein yellows virus 9" (PeVYV-9) for this virus.

The threat of seed-transmissible pepper yellow leaf curl Indonesia virus in chili pepper

Recently, chili pepper (Capsicum annuum) plants in Indonesia have been devastated by a notorious bipartite begomovirus infection named Pepper yellow leaf curl Indonesia virus (PepYLCIV), which causes a distinct decrease in chili pepper production. Pepper yellow diseases have been known since early 2000; however, the spread of this virus thus far is distressing. These diseases can reduce chili yields by 20-100% in Indonesia. As previously known, begomovirus can be transmitted through whitefly to several host plants from the families Solanaceae, Compositae, and Leguminosae. In the field, a single plant was observed with severe symptoms of pepper yellow leaf curl disease, while other plants in the same field were asymptomatic and healthy. The observation leads to the possibility that the virus can be transmitted from previously infected chili pepper plants through seeds, as begomovirus transmission through seeds has been reported before. This study was conducted using seeds from chili peppers infected with viruses from different places in Indonesia. Whole seeds, embryos, and seedlings from PepYLCIV infected seeds were investigated in this study by performing viral genome DNA extraction, uracil DNA glycosylase-PCR, and sequencing analysis. Results revealed that both DNA-A and DNA-B of PepYLCIV in seeds and embryos of infected chili pepper plants were detected. The results also showed that 25-67% of PepYLCIV DNA-A and 50-100% of DNA-B were detected from seedlings grown from infected chili pepper seed collected from different location, thus confirming PepYLCIV as a seed-transmissible virus in chili pepper plants.

Pepper yellow leaf curl Aceh virus: a novel bipartite begomovirus isolated from chili pepper, tomato, and tobacco plants in Indonesia

During 2017, leaf samples of chili pepper (Capsicum annuum), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum) plants exhibiting yellowing and curling symptoms were collected from Aceh province, Indonesia. These samples were used to isolate and sequence viral genomic DNA. Six isolates with complete DNA-A and DNA-B sequences of begomovirus were obtained, all of which showed >99% sequence identity to the others. DNA-A sequences shared the highest nucleotide sequence identity (89.3%-89.7%) with monopartite pepper yellow leaf curl Indonesia virus 2 (PepYLCIV2) and the second-highest sequence identity (87.3%-87.4%) with bipartite pepper yellow leaf curl Indonesia virus (PepYLCIV). The DNA-B sequences shared the highest nucleotide sequence identity (95%-97.5%) with PepYLCIV. Results of recombination analysis indicated that the novel begomovirus was a recombinant. In accordance with the guidelines for begomovirus species demarcation, these isolates should be assigned to a new species, and we have proposed the name ''pepper yellow leaf curl Aceh virus'' (PepYLCAV) for this virus.

Genetic Diversity of Bemisia tabaci (Hemiptera: Aleyrodidae) Species Complex Across Malaysia

The tobacco whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex with members capable of inducing huge economic losses. Precise identification of members of this complex proves essential in managing existing populations and preventing new incursions. Despite records of serious outbreaks of this pest in Malaysia little is known about species status of B. tabaci in this region. To address this, a comprehensive sampling of B. tabaci from different host plants was conducted in 10 states of Malaysia from 2010 to 2012. Members of the complex were identified by sequencing partial mitochondrial cytochrome oxidase subunit I (mtCOI) gene and constructing a Bayesian phylogenetic tree. Seven putative species were identified including Asia I, Mediterranean (MED), China 1, China 2, Asia II 6, Asia II 7, and Asia II 10. The most important finding of the study is the identification of the invasive MED species from locations without previous records of this species. All putative species except Asia I and MED are recorded from Malaysia for the first time. This study provided the first introductory map of B. tabaci species composition in Malaysia and emphasizes the urgent need for further studies to assess the status of MED invasion in this country.

Genetic diversity and geographic distribution of the Bemisia tabaci species complex in Bangladesh

Bemisia tabaci (Gennadius) is a species complex consisting of at least 40 cryptic species. Although the genetic diversity of B. tabaci has been studied in various regions, little is known about distribution in Bangladesh, which is covered by the Bengal delta, the largest delta on Earth. We conducted an extensive survey throughout the country and determined the nucleotide sequence of mitochondrial cytochrome c oxidase subunit 1 (COI) from 110 individuals. We then examined phylogenetic relationships. The results identified four cryptic species that expressed distinct interspecific variation but low intraspecific variation. Asia I was the most abundant, both Asia II 1 and Asia II 5 were moderately abundant, and Asia II 10 was found only in the central region. COI sequences of each cryptic species were distinctive and differentiated into many haplotypes. Our study provides important information to better understand the genetic diversity and geographic distribution of cryptic species in Bangladesh and nearby countries.

Development of a LAMP assay with a portable device for real-time detection of begomoviruses under field conditions

The emergence of begomovirus infection is one of the most important problems affecting production of a variety of vegetable crops worldwide. Infection by begomoviruses has been detected and spread rapidly on Cucurbitaceae and Solanaceae plants in Indonesia. A rapid and simple detection assay for begomoviruses under field conditions for routine sampling of plants is needed. Primers for a loop-mediated isothermal amplification (LAMP) assay were designed based on the sequences of three Indonesian begomoviruses, namely Tomato leaf curl New Delhi virus (ToLCNDV), Pepper yellow leaf curl Indonesia virus (PepYLCIV), and Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV), infecting Cucurbitaceae and Solanaceae plants. LAMP assays using a Genelyzer^™ III portable fluorometer with a toothpick method successfully detected these begomoviruses in infected melon, pepper, and eggplant samples. LAMP assays conducted during a field survey for detection of the three begomoviruses on 104 fresh leaves indicated that most of the samples were positive; the findings were confirmed by PCR using universal primers of begomovirus as a common detection method. These results demonstrate that this simple and rapid LAMP assay using a fluorometer portable device may be used to achieve real-time detection of begomoviruses under field conditions.

Global Population Structure of a Worldwide Pest and Virus Vector: Genetic Diversity and Population History of the Bemisia tabaci Sibling Species Group

The whitefly Bemisia tabaci sibling species (sibsp.) group comprises morphologically indiscernible lineages of well-known exemplars referred to as biotypes. It is distributed throughout tropical and subtropical latitudes and includes the contemporary invasive haplotypes, termed B and Q. Several well-studied B. tabaci biotypes exhibit ecological and biological diversity, however, most members are poorly studied or completely uncharacterized. Genetic studies have revealed substantial diversity within the group based on a fragment of the mitochondrial cytochrome oxidase I (mtCOI) sequence (haplotypes), with other tested markers being less useful for deep phylogenetic comparisons. The view of global relationships within the B. tabaci sibsp. group is largely derived from this single marker, making assessment of gene flow and genetic structure difficult at the population level. Here, the population structure was explored for B. tabaci in a global context using nuclear data from variable microsatellite markers. Worldwide collections were examined representing most of the available diversity, including known monophagous, polyphagous, invasive, and indigenous haplotypes. Well-characterized biotypes and other related geographic lineages discovered represented highly differentiated genetic clusters with little or no evidence of gene flow. The invasive B and Q biotypes exhibited moderate to high levels of genetic diversity, suggesting that they stemmed from large founding populations that have maintained ancestral variation, despite homogenizing effects, possibly due to human-mediated among-population gene flow. Results of the microsatellite analyses are in general agreement with published mtCOI phylogenies; however, notable conflicts exist between the nuclear and mitochondrial relationships, highlighting the need for a multifaceted approach to delineate the evolutionary history of the group. This study supports the hypothesis that the extant B. tabaci sibsp. group contains ancient genetic entities and highlights the vast cryptic diversity throughout the genome in the group.

Isolation and characterization of nine microsatellite loci from Bemisia tabaci (Hemiptera: Aleyrodidae) biotype B

Nine microsatellites were isolated from Bemisia tabaci (Gennadius) biotype B and screened across 60 individuals from two populations (biotype B) to examine polymorphism. Two to 12 alleles were observed per locus. Observed and expected heterozygosities ranged from 0.033 to 0.967 and 0.033 to 0.854, respectively. There was no significant deviation from Hardy-Weinberg equilibrium and no significant linkage disequilibrium between loci. One locus showed evidence for null alleles. These loci will be useful in future studies of the genetic structure of worldwide biotypes and gene flow analyses between and within biotypes of B. tabaci.

Expression and functional characterisation of a soluble form of Tomato yellow leaf curl virus coat protein

BACKGROUND

Tomato yellow leaf curl virus (TYLCV), a member of the genus Begomovirus within the family Geminiviridae, is an important pathogen of tomato in many tropical, subtropical and temperate regions. TYLCV is exclusively transmitted by the whitefly Bemisia tabaci in a circulative manner. The viral coat protein (CP) has been assumed to play important roles in the entry of TYLCV into the insect midgut cells.

RESULTS

Testing the hypothesis that CP plays an important role in TYLCV acquisition by B. tabaci, a soluble form of the CP was expressed and purified. The purified recombinant CP made it possible to examine the function of TYLCV CP without other viral proteins. In an in vivo binding assay, specific binding of TYLCV CP to B. tabaci midguts was detected when purified CP was fed to B. tabaci. In addition, real-time polymerase chain reaction analysis of virus titre revealed that B. tabaci fed with purified CP had reduced the level of virus in their midgut compared with those fed with bovine serum albumin or maltose-binding protein. These results suggest that binding of TYLCV CP to the B. tabaci midgut specifically inhibits virus acquisition.

CONCLUSIONS

The findings that TYLCV CP binds to B. tabaci midguts and decreases virus acquisition provide direct evidence that CP mediates the attachment of TYLCV to receptors on the epithelial cells of the B. tabaci midgut.

Plant-mediated whitefly-begomovirus interactions: research progress and future prospects

Plant-mediated interactions between begomoviruses and whiteflies exert important influences on the population dynamics of vectors and the epidemiology of plant diseases. In this article, we synthesize the relevant literature to identify patterns to the interactions. We then review studies on the ecological, biochemical and molecular mechanisms underlying the interactions and finally elaborate on the most interesting issues for future research. The interactions between begomoviruses and the insect vector, the whitefly Bemisia tabaci, via their shared host plants can be mutualistic, neutral or negative. However, in contrast to a pattern of improved performance of vectors on virus-infected plants that has been observed with persistently transmitted RNA viruses, the number of cases exhibiting mutualistic, neutral or negative effects in the indirect interactions between begomoviruses and whiteflies appear evenly distributed. With regard to the mechanisms of plant-mediated positive effects on whiteflies, two case studies indicate that suppression of plant defence and/or alteration in plant nutrition as a result of virus infection can be important. Our review shows that we are only just beginning to understand the tripartite interactions between begomoviruses, whiteflies and plants. Future efforts in this area should try to expand the number and diversity of pathosystems for investigation to reveal the patterns of interactions, to investigate the molecular and biochemical mechanisms of the interactions using a multidisciplinary approach, and to examine the virus-plant-vector interactions in the field and in natural plant communities.

Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia

Over the past three decades diseases caused by whitefly-transmitted geminiviruses (begomoviruses) have emerged to be important constraints to the production of solanaceous crops, particularly tomato (Solanum lycopersicum) and peppers (Capsicum spp.), in many tropical and subtropical regions of the world. The most studied of these is Tomato yellow leaf curl virus (TYLCV), which has spread to many other areas from its likely origin in the Mediterranean basin region. The virus is usually associated with the polyphagous and virus-vectoring-efficient B-biotype of its vector whitefly (Bemisia tabaci). However, in Southeast and East Asia, a wide variety of distinct local begomovirus species have been identified from tomato and pepper crops over this period, and TYLCV was detected in Japan only in about 1996, China in 2006 and Korea in 2008, despite B-biotype whiteflies being present in several of the countries of the region since at least the early 1990s. Continental Southeast Asia appears to be a major center of diversity for begomoviruses and some species may have spread across the region; Tomato yellow leaf curl Thailand virus (TYLCTHV) appears to have spread from the Thailand-Myanmar region into southern China and is now displacing the local tomato-infecting species in Taiwan, and Tomato yellow leaf curl Kanchanaburi virus (TYLCKaV) appears to have spread from the Thailand-Vietnam region to Java, Indonesia. Since many of the native tomato- or pepper-infecting begomoviruses and associated satellite DNAs have also been detected in local weed species, it seems likely that their ancestors originated in these weed hosts, but with the expansion and intensification of tomato and pepper production in the region, there was selection for recombinant or mutant forms with greater virulence on tomato and/or pepper. Expansion and intensification of these crops may also have resulted in increased populations of local, and if present, B- or Q-biotype whiteflies, aiding the increase and spread of local begomovirus species.

Spatio-temporal patterns of genetic change amongst populations of cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa

The greatest current threat to cassava in sub-Saharan Africa, is the continued expansion of plant virus pandemics being driven by super-abundant populations of the whitefly vector, Bemisia tabaci. To track the association of putatively genetically distinct populations of B. tabaci with pandemics of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), a comprehensive region-wide analysis examined the phylogenetic relationships and population genetics of 642 B. tabaci adults sampled from cassava in six countries of East and Central Africa, between 1997 and 2010, using a mitochondrial DNA cytochrome oxidase I marker (780 bases). Eight phylogenetically distinct groups were identified, including one, designated herein as 'East Africa 1' (EA1), not previously described. The three most frequently occurring groups comprised >95% of all samples. Among these, the Sub-Saharan Africa 2 (SSA2) group diverged by c. 8% from two SSA1 sub-groups (SSA1-SG1 and SSA1-SG2), which themselves were 1.9% divergent. During the 14-year study period, the group associated with the CMD pandemic expansion shifted from SSA2 to SSA1-SG1. Population genetics analyses of SSA1, using Tajima's D, Fu's Fs and Rojas' R2 statistics confirmed a temporal transition in SSA1 populations from neutrally evolving at the outset, to rapidly expanding from 2000 to 2003, then back to populations more at equilibrium after 2004. Based on available evidence, hybrid introgression appears to be the most parsimonious explanation for the switch from SSA2 to SSA1-SG1 in whitefly populations driving cassava virus pandemics in East and Central Africa.

Will the real Bemisia tabaci please stand up?

Since Panayiotis Gennadius first identified the whitefly, Aleyrodes tabaci in 1889, there have been numerous revisions of the taxonomy of what has since become one of the world's most damaging insect pests. Most of the taxonomic revisions have been based on synonymising different species under the name Bemisia tabaci. It is now considered that there is sufficient biological, behavioural and molecular genetic data to support its being a cryptic species complex composed of at least 34 morphologically indistinguishable species. The first step in revising the taxonomy of this complex involves matching the A. tabaci collected in 1889 to one of the members of the species complex using molecular genetic data. To do this we extracted and then amplified a 496 bp fragment from the 3' end of the mitochondrial DNA cytochrome oxidase one (mtCOI) gene belonging to a single whitefly taken from Gennadius' original 1889 collection. The sequence identity of this 123 year-old specimen enabled unambiguous assignment to a single haplotype known from 13 Mediterranean locations across Greece and Tunisia. This enabled us to unambiguously assign the Gennadius A. tabaci to the member of the B. tabaci cryptic species complex known as Mediterranean or as it is commonly, but erroneously referred to, as the 'Q-biotype'. Mediterranean is therefore the real B. tabaci. This study demonstrates the importance of matching museum syntypes with known species to assist in the delimitation of cryptic species based on the organism's biology and molecular genetic data. This study is the first step towards the reclassification of B. tabaci which is central to an improved understanding how best to manage this globally important agricultural and horticultural insect pest complex.

Viruses of pepper crops in the Mediterranean basin: a remarkable stasis

Compared to other vegetable crops, the major viral constraints affecting pepper crops in the Mediterranean basin have been remarkably stable for the past 20 years. Among these viruses, the most prevalent ones are the seed-transmitted tobamoviruses; the aphid-transmitted Potato virus Y and Tobacco etch virus of the genus Potyvirus, and Cucumber mosaic virus member of the genus Cucumovirus; and thrips-transmitted tospoviruses. The last major viral emergence concerns the tospovirus Tomato spotted wilt virus (TSWV), which has undergone major outbreaks since the end of the 1980s and the worldwide dispersal of the thrips vector Frankliniella occidentalis from the western part of the USA. TSWV outbreaks in the Mediterranean area might have been the result of both viral introductions from Northern America and local reemergence of indigenous TSWV isolates. In addition to introductions of new viruses, resistance breakdowns constitute the second case of viral emergences. Notably, the pepper resistance gene Tsw toward TSWV has broken down a few years after its deployment in several Mediterranean countries while there has been an expansion of L³-resistance breaking pepper mild mottle tobamovirus isolates. Beyond the agronomical and economical concerns induced by the breakdowns of virus resistance genes in pepper, they also constitute original models to understand plant-virus interactions and (co)evolution.

Isolation and characterization of eight polymorphic microsatellite loci for the coconut pest, Brontispa longissima (Coleoptera: Hispidae)

Brontispa longissima is one of the most serious insect pests of coconut in Southeast Asia; it was first discovered on Hainan Island in June 2002. Despite the economic risk associated with this pest, genetic aspects of the invasion process have remained relatively unexplored. Using microsatellite markers, we investigated the population structure, genetic variability and pattern of invasion in various geographic populations. The methodology was based on a modified biotin-capture method. Eight polymorphic microsatellite loci were isolated and characterized for the pest. The allele number per locus varied from 2 to 3 (N = 30). The expected and observed heterozygosities of the eight loci ranged from 0.042 to 0.509 and from 0.042 to 0.963, respectively. Although the frequency of polymorphisms was not very high in this population, the microsatellite loci that were isolated will be useful for investigating the genetic diversity and migration routes of B. longissima populations.

Genetic identity of the Bemisia tabaci species complex and association with high cotton leaf curl disease (CLCuD) incidence in Pakistan

BACKGROUND

The cotton whitefly, Bemisia tabaci (Gennadius), is a cryptic species complex, and members of the complex have become serious pests in Pakistan because of their feeding and their ability to transmit cotton leaf curl virus (CLCuV). Here, an analysis was made of the identity of B. tabaci collected from cotton and a range of non-cotton hosts in the cotton-growing zones in Punjab and Sindh, the main cotton-producing provinces of Pakistan, using a portion of the mitochondrial cytochrome oxidase 1 gene. The geographic distribution of the different members of the complex was then compared with the incidence of CLCuD.

RESULTS

Using the Dinsdale nomenclature, the results revealed three putative species, Asia 1, Asia II 1 and Middle East-Asia Minor 1. Asia II 1 (also referred to in the literature as biotypes K, P, PCG-1, PK1, SY and ZHJ2) was only recorded from Punjab cotton plants, whereas Asia 1 (also referred to in the literature as biotypes H, M, NA and PCG-2) was found in both Sindh and Punjab. Middle East-Asia Minor 1 (commonly known as biotype B and B2) was found only in Sindh. Moreover, Asia II 1 was associated with high incidences of CLCuD, whereas regions where Middle East-Asia Minor 1 was present had a lower incidence. Phylogenetic analysis showed that the Middle East-Asia Minor 1 population in Sindh formed a distinct genetic subgroup within the putative species, suggesting that the Sindh province of Pakistan may form part of its home range. So far, no individuals from the putative species Mediterranean (commonly known as biotypes Q, J and L) have been found in Pakistan.

CONCLUSIONS

The capacity to manage pests and disease effectively relies on knowledge of the identity of the agents causing the damage. In the case of CLCuD in Pakistan, this knowledge has been obscured to some extent because of the inconsistent approach to identifying and distinguishing the different B. tabaci associated with CLCuD. The situation has now been clarified, and a strong association between disease incidence and vector identity and abundance has been shown. Given this advance, future research can now focus on factors that influence the capacity of different vector species to transmit the viruses that cause CLCuD, the reason for differences in vector abundance and the lack of geographic overlap between the cryptic vector species. This knowledge will contribute to the development of improved methods with which to manage the disease in Pakistan.

The invasion route for an insect pest species: the tobacco aphid in the New World

Biological invasions are rapid evolutionary events in which populations are usually subject to a founder event during introduction followed by rapid adaptation to the new environment. Molecular tools and Bayesian approaches have shown their utility in exploring different evolutionary scenarios regarding the invasion routes of introduced species. We examined the situation for the tobacco aphid, Myzus persicae nicotianae, a recently introduced aphid species in Chile. Using seven microsatellite loci and approximate Bayesian computation, we studied populations of the tobacco aphid sampled from several American and European countries, identifying the most likely source populations and tracking the route of introduction to Chile. Our population genetic data are consistent with available historical information, pointing to an introduction route of the tobacco aphid from Europe and/or from other putative populations (e.g. Asia) with subsequent introduction through North America to South America. Evidence of multiple introductions to North America from different genetic pools, with successive loss of genetic diversity from Europe towards North America and a strong bottleneck during the southward introduction to South America, was also found. Additionally, we examined the special case of a widespread multilocus genotype that was found in all American countries examined. This case provides further evidence for the existence of highly successful genotypes or 'superclones' in asexually reproducing organisms.