Frontiers Approaches to the Diagnosis of Thrips (Thysanoptera): How Effective Are the Molecular and Electronic Detection Platforms?

Simple Summary

Thrips are important agricultural and forest pests. They cause damage by sucking plant sap and transmitting several plant viruses. Correct identification is the key for epidemiological studies and formulating appropriate management strategies. The application of molecular and electronic detection platforms has improved the morphological character-based diagnosis of thrips species. This article reviews research on molecular and automated identification of thrips species and discusses future research strategies for rapid and high throughput thrips diagnosis.

Abstract

Thrips are insect pests of economically important agricultural, horticultural, and forest crops. They cause damage by sucking plant sap and by transmitting several tospoviruses, ilarviruses, carmoviruses, sobemoviruses, and machlomoviruses. Accurate and timely identification is the key to successful management of thrips species. However, their small size, cryptic nature, presence of color and reproductive morphs, and intraspecies genetic variability make the identification of thrips species challenging. The use of molecular and electronic detection platforms has made thrips identification rapid, precise, sensitive, high throughput, and independent of developmental stages. Multi-locus phylogeny based on mitochondrial, nuclear, and other markers has resolved ambiguities in morphologically indistinguishable thrips species. Microsatellite, RFLP, RAPD, AFLP, and CAPS markers have helped to explain population structure, gene flow, and intraspecies heterogeneity. Recent techniques such as LAMP and RPA have been employed for sensitive and on-site identification of thrips. Artificial neural networks and high throughput diagnostics facilitate automated identification. This review also discusses the potential of pyrosequencing, microarrays, high throughput sequencing, and electronic sensors in delimiting thrips species.

Aphids in focus: unravelling their complex ecology and evolution using genetic and molecular approaches

Aphids are renowned plant parasites of agriculture, horticulture and forestry, causing direct physical damage by sucking phloem and especially by transmission of plant pathogenic viruses. The huge yield loss they cause amounts to hundreds of millions of dollars globally, and because of this damage and the intense efforts expended on control, some 20 species are now resistant to pesticides worldwide. Aphids represent an ancient, mainly northern temperate group, although some species occur in the tropics, often as obligate asexual lineages or even asexual ‘species’. However, besides their notoriety as enemies of plant growers, aphids are also extremely interesting scientifically, especially at the molecular and genetic levels. They reproduce mainly asexually, one female producing 10–90 offspring in 7–10 days and therefore, theoretically, could produce billions of offspring in one growing season in the absence of mortality factors (i.e. climate/weather and antagonists). In this overview, we provide examples of what molecular and genetic studies of aphids have revealed concerning a range of topics, especially fine-grained ecological processes. Aphids, despite their apparently limited behavioural repertoire, are in fact masters (or, perhaps more accurately, mistresses) of adaptation and evolutionary flexibility and continue to flourish in a variety of ecosystems, including the agro-ecosystem, regardless of our best efforts to combat them.

Development and validation of real-time PCR assays based on novel molecular markers for the simultaneous detection and identification of Globodera pallida, G. rostochiensis and Heterodera schachtii

Considering the growing trade of seed potato, reliable diagnostic protocols are required for the detection of regulated nematode species. In this study, a specific and sensitive multiplex Taqman-based real-time PCR method was developed in order to detect and identifyGlobodera pallida,G. rostochiensisandHeterodera schachtii. The newly designed primers and probes enabled the detection of all the target populations tested and with no cross-reaction for closely related non-target species (55 populations tested). The limit of detection (LOD) was one juvenile forG. rostochiensisandG. pallidaand five juveniles forH. schachtii. For monitoring potato cyst nematodes, this analytical tool would extend the number of cyst investigated as five juveniles can be detected among 50 cysts in a sample. Furthermore, this multiplex assay detects DNA of the three targeted species in template DNA obtained directly from float material after nematode extraction from soil.

Variation in the number of nucleoli and incomplete homogenization of 18S ribosomal DNA sequences in leaf cells of the cultivated Oriental ginseng (Panax ginseng Meyer)

BACKGROUND

Wild ginseng, Panax ginseng Meyer, is an endangered species of medicinal plants. In the present study, we analyzed variations within the ribosomal DNA (rDNA) cluster to gain insight into the genetic diversity of the Oriental ginseng, P. ginseng, at artificial plant cultivation.

METHODS

The roots of wild P. ginseng plants were sampled from a nonprotected natural population of the Russian Far East. The slides were prepared from leaf tissues using the squash technique for cytogenetic analysis. The 18S rDNA sequences were cloned and sequenced. The distribution of nucleotide diversity, recombination events, and interspecific phylogenies for the total 18S rDNA sequence data set was also examined.

RESULTS

In mesophyll cells, mononucleolar nuclei were estimated to be dominant (75.7%), while the remaining nuclei contained two to four nucleoli. Among the analyzed 18S rDNA clones, 20% were identical to the 18S rDNA sequence of P. ginseng from Japan, and other clones differed in one to six substitutions. The nucleotide polymorphism was more expressed at the positions 440-640 bp, and distributed in variable regions, expansion segments, and conservative elements of core structure. The phylogenetic analysis confirmed conspecificity of ginseng plants cultivated in different regions, with two fixed mutations between P. ginseng and other species.

CONCLUSION

This study identified the evidences of the intragenomic nucleotide polymorphism in the 18S rDNA sequences of P. ginseng. These data suggest that, in cultivated plants, the observed genome instability may influence the synthesis of biologically active compounds, which are widely used in traditional medicine.

Contrasting evolutionary patterns of 28S and ITS rRNA genes reveal high intragenomic variation in Cephalenchus (Nematoda): Implications for species delimitation

Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.

Intra-genomic variation in the ribosomal repeats of nematodes

Ribosomal loci represent a major tool for investigating environmental diversity and community structure via high-throughput marker gene studies of eukaryotes (e.g. 18S rRNA). Since the estimation of species' abundance is a major goal of environmental studies (by counting numbers of sequences), understanding the patterns of rRNA copy number across species will be critical for informing such high-throughput approaches. Such knowledge is critical, given that ribosomal RNA genes exist within multi-copy repeated arrays in a genome. Here we measured the repeat copy number for six nematode species by mapping the sequences from whole genome shotgun libraries against reference sequences for their rRNA repeat. This revealed a 6-fold variation in repeat copy number amongst taxa investigated, with levels of intragenomic variation ranging from 56 to 323 copies of the rRNA array. By applying the same approach to four C. elegans mutation accumulation lines propagated by repeated bottlenecking for an average of ~400 generations, we find on average a 2-fold increase in repeat copy number (rate of increase in rRNA estimated at 0.0285-0.3414 copies per generation), suggesting that rRNA repeat copy number is subject to selection. Within each Caenorhabditis species, the majority of intragenomic variation found across the rRNA repeat was observed within gene regions (18S, 28S, 5.8S), suggesting that such intragenomic variation is not a product of selection for rRNA coding function. We find that the dramatic variation in repeat copy number among these six nematode genomes would limit the use of rRNA in estimates of organismal abundance. In addition, the unique pattern of variation within a single genome was uncorrelated with patterns of divergence between species, reflecting a strong signature of natural selection for rRNA function. A better understanding of the factors that control or affect copy number in these arrays, as well as their rates and patterns of evolution, will be critical for informing estimates of global biodiversity.

Intra-genomic ribosomal RNA polymorphism and morphological variation in Elphidium macellum suggests inter-specific hybridization in foraminifera

Elphidium macellum is a benthic foraminifer commonly found in the Patagonian fjords. To test whether its highly variable morphotypes are ecophenotypes or different genotypes, we analysed 70 sequences of the SSU rRNA gene from 25 specimens. Unexpectedly, we identified 11 distinct ribotypes, with up to 5 ribotypes co-occurring within the same specimen. The ribotypes differ by varying blocks of sequence located at the end of stem-loop motifs in the three expansion segments specific to foraminifera. These changes, distinct from typical SNPs and indels, directly affect the structure of the expansion segments. Their mosaic distribution suggests that ribotypes originated by recombination of two or more clusters of ribosomal genes. We propose that this expansion segment polymorphism (ESP) could originate from hybridization of morphologically different populations of Patagonian Elphidium. We speculate that the complex geological history of Patagonia enhanced divergence of coastal foraminiferal species and contributed to increasing genetic and morphological variation.

Geographically localised bursts of ribosomal DNA mobility in the grasshopper Podisma pedestris

We report extraordinary variation in the number and the chromosomal location of ribosomal DNA (rDNA) arrays within populations of the alpine grasshopper Podisma pedestris; even greater differences were found between populations. The sites were detected by in situ hybridisation of labelled rDNA to chromosomal preparations. The total number of rDNA sites in an individual varied from three to thirteen. In the most extreme case, individuals from populations only 10 km apart had no rDNA loci in common. A survey of the geographical distribution of this variation identified clusters of populations with relatively similar chromosomal distribution of rDNA loci. These clusters correspond to those identified earlier by analysis of rDNA sequences. To explain this geographical clustering, we reconstructed the post-glacial colonisation of the region by assuming that the species' distribution has ascended to its current altitudinal range as the climate warmed. The reconstruction suggests that each cluster is descended from a colonisation route up a different alpine valley. That history would imply rapid establishment of rDNA differences, conceivably during the last 10,000 years since the last glaciation. The proposal for rapid change is consistent with the extensive within-population variation, which indicates that the processes responsible for the change in rDNA's chromosomal location continue to occur at a higher rate. We discuss whether our reconstruction of colonisation routes implies movement of the hybrid zone, which would indicate that a neo-XY sex chromosome system has spread through extant populations.

Intraspecific concerted evolution of the rDNA ITS1 in Anopheles farauti sensu stricto (Diptera: Culicidae) reveals recent patterns of population structure

We examined the intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) of Anopheles farauti to determine the level of divergence among populations for this important malarial vector. We isolated 187 clones from 70 individuals and found regional variation among four internal tandem repeats. The data were partitioned prior to analysis given the presence of a paralogous ITS2 sequence, called the 5'-subrepeat, inserted in the ITS1 of most clones. A high level of homogenization and population differentiation was observed for this repeat, which indicates a higher rate of turnover relative to the adjacent 'core' region. Bayesian analysis was performed using several substitutional models on both a combined and a partitioned data set. On the whole, the ITS1 phylogeny and geographic origin of the samples appear to be congruent. Some interesting exceptions indicate the spread of variant repeats between populations and the retention of ancestral polymorphism. Our data clearly demonstrate concerted evolution at the intraspecific level despite intraindividual variation and a complex internal repeat structure from a species that occupies a continuous coastal distribution. A high rate of genomic turnover in combination with a high level of sequence divergence appears to be a major factor leading to its concerted evolution within these populations.

Sequence variation within the rRNA gene loci of 12 Drosophila species

Concerted evolution maintains at near identity the hundreds of tandemly arrayed ribosomal RNA (rRNA) genes and their spacers present in any eukaryote. Few comprehensive attempts have been made to directly measure the identity between the rDNA units. We used the original sequencing reads (trace archives) available through the whole-genome shotgun sequencing projects of 12 Drosophila species to locate the sequence variants within the 7.8-8.2 kb transcribed portions of the rDNA units. Three to 18 variants were identified in >3% of the total rDNA units from 11 species. Species where the rDNA units are present on multiple chromosomes exhibited only minor increases in sequence variation. Variants were 10-20 times more abundant in the noncoding compared with the coding regions of the rDNA unit. Within the coding regions, variants were three to eight times more abundant in the expansion compared with the conserved core regions. The distribution of variants was largely consistent with models of concerted evolution in which there is uniform recombination across the transcribed portion of the unit with the frequency of standing variants dependent upon the selection pressure to preserve that sequence. However, the 28S gene was found to contain fewer variants than the 18S gene despite evolving 2.5-fold faster. We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species.

Finely orchestrated movements: evolution of the ribosomal RNA genes

Evolution of the tandemly repeated ribosomal RNA (rRNA) genes is intriguing because in each species all units within the array are highly uniform in sequence but that sequence differs between species. In this review we summarize the origins of the current models to explain this process of concerted evolution, emphasizing early studies of recombination in yeast and more recent studies in Drosophila and mammalian systems. These studies suggest that unequal crossover is the major driving force in the evolution of the rRNA genes with sister chromatid exchange occurring more often than exchange between homologs. Gene conversion is also believed to play a role; however, direct evidence for its involvement has not been obtained. Remarkably, concerted evolution is so well orchestrated that even transposable elements that insert into a large fraction of the rRNA genes appear to have little effect on the process. Finally, we summarize data that suggest that recombination in the rDNA locus of higher eukaryotes is sufficiently frequent to monitor changes within a few generations.

Ribosomal DNA in the grasshopper Podisma pedestris: escape from concerted evolution

Eukaryote nuclear ribosomal DNA (rDNA) typically exhibits strong concerted evolution: a pattern in which several hundred rDNA sequences within any one species show little or no genetic diversity, whereas the sequences of different species diverge. We report a markedly different pattern in the genome of the grasshopper Podisma pedestris. Single individuals contain several highly divergent ribosomal DNA groups. Analysis of the magnitude of divergence indicates that these groups have coexisted in the Podisma lineage for at least 11 million years. There are two putatively functional groups, each estimated to be at least 4 million years old, and several pseudogene groups, many of which are transcribed. Southern hybridization and real-time PCR experiments show that only one of the putatively functional types occurs at high copy number. However, this group is scarcely amplified under standard PCR conditions, which means that phylogenetic inference on the basis of standard PCR would be severely distorted. The analysis suggests that concerted evolution has been remarkably ineffective in P. pedestris. We propose that this outcome may be related to the species' exceptionally large genome and the associated low rate of deletion per base pair, which may allow pseudogenes to persist.

The attack of the clones: tracking the movement of insecticide-resistant peach-potato aphids Myzus persicae (Hemiptera: Aphididae)

Myzus persicae (Sulzer) collected in Scotland were characterized for four microsatellite loci, intergenic spacer fingerprints and the resistance mechanisms modified acetylcholinesterase (MACE), overproduced carboxylesterase and knockdown resistance (kdr). Microsatellite polymorphisms were used to define a limited number of clones that were either fully susceptible to insecticides or possessed characteristic combinations of resistance mechanisms. Within these clones, intergenic spacer fingerprints could either be very consistent or variable, with the latter indicating ongoing evolution within lineages, most likely derived from the same zygote. Two clones (termed A and B) possessed all three resistance mechanisms and predominated at sites treated with insecticides. Their appearance on seed potatoes and oilseed rape in Scotland in 2001 coincided with extensive insecticide use and severe control failures. Clones C, I and J, with no or fewer resistance mechanisms, were found in samples from 1995 and were dominant at untreated sites in 2001. A comparison of Scottish collections with those from other UK and non-UK sites provides insight into the likely origins, distribution and dynamics of M. persicae clones in a region where asexual (anholocyclic) reproduction predominates, but is vulnerable to migration by novel genotypes from areas of Europe where sexual (holocyclic) reproduction occurs.

Application of ITS-2 sequences as markers for identification and phylogenetic inference within the genus Geomylichus (Acari: Listrophoridae)

Phylogenetic relationships among 18 samples from nine nominal species of Geomylichus (Acari: Listrophoridae), were analyzed based on internal transcribed spacer 2 (ITS 2) sequences, Prolistrophorus sp. was used as an outgroup. Maximum likelihood and neighbor-joining analyses indicated that Geomylichus is formed by at least three internal clades. Genetic distance among Prolistrophorus and Geomylichus was 27.8-35.5%, and among species, populations, and infrapopulations of Geomylichus it was 0.4-21.8%, 0.8-2.4%, and 0.8-1.2%, respectively. Differences between the results of this analysis with conventional taxonomy of the group, as well as the overlapping of genetic distances among species, populations, and infrapopulations, suggest that the definition of species within Geomylichus deserves reconsideration. For example, the recognition of inconsistencies among G. texanus populations associated to different host species, resulting from the molecular analysis, led us to collect new morphological evidence now suggesting that this taxon represents more than one species.

Heterogeneity of ITS1 sequences in the biting midge Culicoides impunctatus (Goetghebuer) suggests a population in Argyll, Scotland, may be genetically distinct

Ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, variation in ITS1 from eight Culicoides species was analysed by PCR, DNA restriction analysis, cloning, and sequencing. ITS1 variants were essentially homogenized within a species, as sequences were identical or closely related. However, Culicoides impunctatus ITS1 sequences derived from one (Argyll) of five populations contained considerable genomic diversity. The secondary structure of each ITS1 was computed. The structure aided the production of an accurate alignment and the identification of a large indel. A phylogenetic analysis was performed. Some of the sequences from the diverse Argyll C. impunctatus population were more related to Culicoides imicola, a vector of animal pathogens in the Old World, than they were to the other C. impunctatus sequences. Thus, the rDNA ITS1 regions of individuals in the Argyll C. impunctatus population were not conforming to the general theory of rDNA homogenization through molecular drive.Key words: Culicoides, ITS1, phylogeny, rDNA, secondary structure.

Identifying chironomids (Diptera: Chironomidae) for biological monitoring with PCR-RFLP

Chironomids are excellent biological indicators for the health of aquatic ecosystems, but their use at finer taxonomic levels is hindered by morphological similarity of species at each life stage. Molecular markers have the potential to overcome these problems by facilitating species identification particularly in large-scale surveys. In this study, the potential of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach was tested to rapidly distinguish among chironomids within a geographic area, by considering chironomid species from Melbourne, Australia. By comparing molecular markers with diagnostic morphological traits, RFLP profiles of the cytochrome oxidase I (COI) region were identified that were specific to genera and some common species. These profiles were used to develop an RFLP-based key, which was validated by testing the markers on samples from several wetlands and streams. As well as allowing for rapid identification of species that are difficult to separate on morphological grounds, this approach also has the potential to resolve current taxonomic ambiguities.

Functional and ecological significance of rDNA intergenic spacer variation in a clonal organism under divergent selection for production rate

It has recently been hypothesized that variation in the intergenic spacer (IGS) of rDNA has considerable developmental, evolutionary and ecological significance through effects on growth rate and body C : N : P stoichiometry resulting from the role of the IGS in production of rRNA. To test these ideas, we assessed changes in size and structure of the repetitive region of the IGS, juvenile growth rate (JGR), RNA and phosphorus (P) contents in clonal lineages of Daphnia pulex derived from a single female and subjected to divergent selection on weight-specific fecundity (WSF). As a result of selection, WSF diverged rapidly, with significant reductions within two generations. Other significant changes accompanying shifts in WSF were that juveniles produced by low-WSF females grew more rapidly and had higher RNA and P contents. An increased predominance of long IGS variants was observed in lineages with elevated JGRs and low WSF. The observed variations in IGS length were related to the number of subrepeat units carrying a promoter sequence in the repetitive region. These results strongly support the hypothesized relationships, indicate a genetic mechanism for the evolution of such associations and demonstrate that Daphnia (and perhaps other parthenogens) possess considerable potential for rapid adaptive change in major life-history traits.

Combining DNA sequences and morphology in systematics: testing the validity of the dragonfly species Cordulegaster bilineata

Morphological and molecular techniques are rarely combined when answering questions of taxonomic validity. In this study, we combine morphological techniques with DNA sequences to determine the validity of the dragonfly species Cordulegaster bilineata. The two dragonfly species C. bilineata and C. diastatops are very similar in size, body color, and morphological characters, and due to these similarities, the status of C. bilineata as a valid species is in question. In this study we compare morphological measurements of males and internal transcribed spacer 1 (ITS-1) sequences of rDNA between the two taxa. The hamule measurements (where copulation occurs) of males show little difference between the taxa in question, but the anal appendage measurements (where the male first contacts the female) show marked divergence between the two taxa. Cluster analysis with these anal appendage measurements correctly assigns almost all individuals measured into their respective taxon. PCR amplification products of ITS-1 display a approximately 50 bp size difference between C. bilineata (n = 4) and C. diastatops (n = 5) regardless of collection site. Sequence data for these amplifications show 51 bp missing in one locus in the ITS-1 of C. bilineatarelative to C. diastatops. A lone population of C. diastatops from Wisconsin has three individuals with ITS-1 products that match the size of both C. bilineata and C. diastatops. One individual from this population appears to yield two ITS-1 amplification products that match both C. bilineata and C. diastatops. Although this population may be evidence for hybridization between the two taxa, such hybridization is not necessarily sufficient to disqualify the validity of a separate species designation for C. bilineata. Morphology and ITS-1 sequences depict a high degree of divergence that is consistent with species-level differences.

Defining orthologous groups among multicopy genes prior to inferring phylogeny, with special emphasis on the Triticeae (Poaceae)

Sequence information from multicopy genes has been widely used for phylogenetic inference. Among those sequences analyzed, nuclear 5S rRNA genes, the two internal transcribed spacer regions (ITS1 and ITS2) of the 18S-26S rDNA genes, and the intergenic spacer (IGS) regions of the same 18S-26S rDNA genes have all been used at the specific, generic, familial and tribal levels. Many investigations have used direct sequencing of PCR products to generate sequence data. The merits of an alternate approach, namely, cloning prior to sequencing followed by careful alignment of numerous cloned sequences to discern groups of putative orthologous sequences that may then be useful for the inference of relationships among species and genera, are examined and discussed. This process discerns patterns resulting from several cycles of careful alignment followed by manual editing conducted by eye--an exacting operation especially when sequences are unequal in length due to the presence of additions/deletions. Based upon examples taken from our work on the sequencing of individual 5S rDNA clones from several wheat and barley species (Triticum and Hordeum respectively), and the re-analysis of data of others taken from several studies using the nuclear genes mentioned above, we are able to identify groups of putative orthologous sequences that we have named "unit classes". Furthermore, comparisons between provisional orthologous sequences isolated from different species are required for the inference of phylogenetic relationships between them. Paralogous sequences from different unit classes can be compared to infer evolutionary relationships among repeat types only, i.e. among unit classes. In several cases, the analysis of the sequence diversity obtained from different clones permitted the assignment of unit classes to specific haplomes.

Polymerase chain reaction-restriction fragment length polymorphism of ribosomal internal transcribed spacer region analysis on polyacrylamide gel electrophoresis reveals two haplotypes coexisting in Myzus persicae

Aphids are geographically and economically the most important group of phytophagous insects. They are responsible for various damage on cultivated plants. In our laboratory, we are interested in their ability to transmit phytoviruses such as Rhabdovirus, Cucumovirus, Potyvirus, and Caulimavirus which cause many crop diseases. The present work deals with the study of vectors as analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of internal transcribed spacer (ITS) regions. Electrophoresis of PCR-RFLP products using EcoRV, AluI and DraI restriction enzymes on 10% polyacrylamid gel reveals the coexistence of two different haplotypes in the same individual genome. This result seems to explain some features of aphid evolution.