Microsatellite loci are not abundant in all arthropod genomes: analyses in the hard tick, Ixodes scapularis and the yellow fever mosquito, Aedes aegypti

Genetic Melting Pot in Blacklegged Ticks at the Northern Edge of their Expansion Front

Blacklegged ticks (Ixodes scapularis) are considered to be the main vector of Lyme disease in eastern North America. They may parasitize a wide range of bird and mammal hosts. Northward dispersal of blacklegged ticks has been attributed largely to movement of hosts to areas outside of the current range of the tick, in conjunction with climate change. To better understand the drivers of range expansion in the blacklegged tick, we need investigations of the genetic connectivity and differentiation of tick populations at a fine spatial scale using appropriate markers. In this study, we investigated genetic connectivity and differentiation in blacklegged ticks, in an area of putatively recent advance in Ontario and Quebec, Canada, using microsatellite markers. Our findings suggest patchy differentiation of alleles, no spatial pattern of genetic structure, and genetic subdivision within sites, which are consistent with the very limited evidence available near the leading edge of range expansion of blacklegged ticks into Canada. These findings are consistent with the prevailing hypothesis, drawn from a variety of fields of study, suggesting that migratory birds from a variety of regions may be bringing hitchhiking ticks northward into Canada.

Reproductive incompatibility between Amblyomma maculatum (Acari: Ixodidae) group ticks from two disjunct geographical regions within the USA

The Amblyomma maculatum Koch group of ixodid ticks consists of three species: A. maculatum, A. triste, and A. tigrinum. However, since Koch described this group in 1844, the systematics of its members has been the subject of ongoing debate. This is especially true of A. maculatum and A. triste; recent molecular analyses reveal insufficient genetic divergence to separate these as distinct species. Further confounding this issue is the discovery in 2014 of A. maculatum group ticks in southern Arizona (AZ), USA, that share morphological characteristics with both A. triste and A. maculatum. To biologically evaluate the identity of A. maculatum group ticks from southern Arizona, we analyzed the reproductive compatibility between specimens of A. maculatum group ticks collected from Georgia (GA), USA, and southern Arizona. Female ticks from both Arizona and Georgia were mated with males from both the Georgia and Arizona Amblyomma populations, creating two homologous and two heterologous F1 cohorts of ticks: GA ♀/GA ♂, AZ ♀/AZ ♂, GA ♀/AZ ♂, and AZ ♀/GA ♂. Each cohort was maintained separately into the F2 generation with F1 females mating only with F1 males from their same cohort. Survival and fecundity parameters were measured for all developmental stages. The observed survival parameters for heterologous cohorts were comparable to those of the homologous cohorts through the F1 generation. However, the F1 heterologous females produced F2 egg clutches that did not hatch, thus indicating that the Arizona and Georgia populations of A. maculatum group ticks tested here represent different biological species.

Genetic Variation and Differentiation of Hylesia metabus (Lepidoptera: Saturniidae): Moths of Public Health Importance in French Guiana and in Venezuela

Hylesia moths impact human health in South America, inducing epidemic outbreaks of lepidopterism, a puriginous dermatitis caused by the urticating properties of females' abdominal setae. The classification of the Hylesia genus is complex, owing to its high diversity in Amazonia, high intraspecific morphological variance, and lack of interspecific diagnostic traits which may hide cryptic species. Outbreaks of Hylesia metabus have been considered responsible for the intense outbreaks of lepidopterism in Venezuela and French Guiana since the C20, however, little is known about genetic variability throughout the species range, which is instrumental for establishing control strategies on H. metabus. Seven microsatellites and mitochondrial gene markers were analyzed from Hylesia moths collected from two major lepidopterism outbreak South American regions. The mitochondrial gene sequences contained significant genetic variation, revealing a single, widespread, polymorphic species with distinct clusters, possibly corresponding to populations evolving in isolation. The microsatellite markers validated the mitochondrial results, and suggest the presence of three populations: one in Venezuela, and two in French Guiana. All moths sampled during outbreak events in French Guiana were assigned to a single coastal population. The causes and implications of this finding require further research.

The Genetic Signature of Range Expansion in a Disease Vector-The Black-Legged Tick

Monitoring and predicting the spread of emerging infectious diseases requires that we understand the mechanisms of range expansion by its vectors. Here, we examined spatial and temporal variation of genetic structure among 13 populations of the Lyme disease vector, the black-legged tick, in southern Quebec, where this tick species is currently expanding and Lyme disease is emerging. Our objective was to identify the primary mode of tick movement into Canada based on observed spatial and temporal genetic patterns. Upon genotyping 10 microsatellite loci from 613 tick specimens, we found multiple genetic signatures of frequent long-distance dispersal events, supporting the hypothesis that migratory birds are the primary carriers of black-legged ticks into southern Quebec. When we compared results from analyses of pairwise differences among ticks collected from 8 different sites at different years between 2011 and 2014, we found that genetic variation observed among tick individuals appeared to be better explained by collection year than sampling locality. This suggests that while cohorts of black-legged ticks can rapidly invade large areas across southern Quebec, they also appear to be undergoing frequent turnover. Finally, the amount of genetic variation in tick populations across our study area appeared to be related to their degree of establishment, with established populations displaying a lower amount of temporal genetic variation than adventitious ones. Given that Lyme disease infection risk in a region can be influenced by the relative presence of established and/or adventitious tick populations, our results are useful for understanding both the seasonality and spatial variation of Lyme disease.

Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs

Microsatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST- and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.

Comparative population genetics of two invading ticks: Evidence of the ecological mechanisms underlying tick range expansions

Two species of ixodid tick, Ixodes affinis Neumann and Amblyomma maculatum Koch, are simultaneously expanding their ranges throughout the mid-Atlantic region of the US. Although we have some understanding of the ecology and life history of these species, the ecological mechanisms governing where and how new populations establish and persist are unclear. To assess population connectivity and ancestry, we sequenced a fragment of the 16S mitochondrial rRNA gene from a representative sample of individuals of both species from populations throughout the eastern US. We found that despite overlapping host preferences throughout ontogeny, each species exhibited very different genetic and geographic patterns of population establishment and connectivity. I. affinis was of two distinct mitochondrial clades, with a clear geographic break separating northern and southern populations. Both I. affinis populations showed evidence of recent expansion, although the southern population was more genetically diverse, indicating a longer history of establishment. A. maculatum exhibited diverse haplotypes that showed no significant relationship with geographic patterns and little apparent connectivity between sites. Heteroplasmy was also observed in the 16S mitochondrial rRNA gene in 3.5% of A. maculatum individuals. Genetic evidence suggests that these species rely on different key life stages to successfully disperse into novel environments, and that host vagility, habitat stability and habitat connectivity all play critical roles in the establishment of new tick populations.

Sequence variability in the mitochondrial 12S rRNA and tRNA Val genes of Ixodes scapularis (Acari: Ixodidae) individuals shown previously to be genetically invariant

The DNA sequences of the mitochondrial (mt) 12S rRNA and tRNA(Val) genes were characterized for 82 blacklegged ticks (Ixodes scapularis) that were genetically identical for Domains IV and V of the mt 16S rRNA gene. Thirty-one haplotypes, differed in sequence by 1-9 bp, were detected among the 82 ticks. Most nucleotide alterations in DNA sequence did not affect the stability of the secondary structures of the RNAs. The magnitude of the DNA sequence variation in the mt 12S rRNA and tRNA(Val) genes among blacklegged ticks suggests that this region of the mitochondrial genome has potential as a genetic marker for examining the population genetics and phylogeography of I. scapularis.

Developing Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in three Aedes disease vectors

Aedes aegypti, Aedes notoscriptus, and Aedes albopictus are important vectors of many arboviruses implicated in human disease such as dengue fever. Genetic markers applied across vector species can provide important information on population structure, gene flow, insecticide resistance, and taxonomy, however, robust microsatellite markers have proven difficult to develop in these species and mosquitoes generally. Here we consider the utility and transferability of 15 Ribosome protein (Rp) Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in these 3 Aedes species. Rp EPIC markers designed for Ae. aegypti also successfully amplified populations of the sister species, Ae. albopictus, as well as the distantly related species, Ae. notoscriptus. High SNP and good indel diversity in sequenced alleles plus support for amplification of the same regions across populations and species were additional benefits of these markers. These findings point to the general value of EPIC markers in mosquito population studies.

De novo characterization of the Dialeurodes citri transcriptome: mining genes involved in stress resistance and simple sequence repeats (SSRs) discovery

The citrus whitefly, Dialeurodes citri (Ashmead), is one of the three economically important whitefly species that infest citrus plants around the world; however, limited genetic research has been focused on D. citri, partly because of lack of genomic resources. In this study, we performed de novo assembly of a transcriptome using Illumina paired-end sequencing technology (Illumina Inc., San Diego, CA, USA). In total, 36,766 unigenes with a mean length of 497 bp were identified. Of these unigenes, we identified 17,788 matched known proteins in the National Center for Biotechnology Information database, as determined by Blast search, with 5731, 4850 and 14,441 unigenes assigned to clusters of orthologous groups (COG), gene ontology (GO), and SwissProt, respectively. In total, 7507 unigenes were assigned to 308 known pathways. In-depth analysis of the data showed that 117 unigenes were identified as potentially involved in the detoxification of xenobiotics and 67 heat shock protein (Hsp) genes were associated with environmental stress. In addition, these enzymes were searched against the GO and COG database, and the results showed that the three major detoxification enzymes and Hsps were classified into 18 and 3, 6, and 8 annotations, respectively. In addition, 149 simple sequence repeats were detected. The results facilitate the investigation of molecular resistance mechanisms to insecticides and environmental stress, and contribute to molecular marker development. The findings greatly improve our genetic understanding of D. citri, and lay the foundation for future functional genomics studies on this species.

Invasion biology of Aedes japonicus japonicus (Diptera: Culicidae)

Aedes japonicus japonicus (Theobald) (Diptera: Culicidae) has recently expanded beyond its native range of Japan and Korea into large parts of North America and Central Europe. Population genetic studies begun immediately after the species was detected in North America revealed genetically distinct introductions that subsequently merged, likely contributing to the successful expansion. Interactions, particularly in the larval stage, with other known disease vectors give this invasive subspecies the potential to influence local disease dynamics. Its successful invasion likely does not involve superior direct competitive abilities, but it is associated with the use of diverse larval habitats and a cold tolerance that allows an expanded seasonal activity range in temperate climates. We predict a continued but slower expansion of Ae. j. japonicus in North America and a continued rapid expansion into other areas as this mosquito will eventually be considered a permanent resident of much of North America, Europe, Asia, and parts of Hawaii.

Vector control measures failed to affect genetic structure of Aedes aegypti in a sentinel metropolitan area of Brazil

In order to evaluate subpopulation differentiation, effective population size (Ne) and evidence for population bottlenecks at various geographic levels, Aedes aegypti larvae were collected longitudinally from 2007 to 2009 from four areas in the city of Salvador, Brazil. The DNA from each larva was isolated and genotyped with five independent microsatellite markers. FST and Jost's D revealed significant population structuring (P<0.05) at the municipal and regional levels, while only RST was able to detect genetic differentiation at the level of strata within these areas. Ne analysis from longitudinal data did not show any evidence of significant change in population structure. The census population measured by the house index, however, showed a significant trend toward decrease in these areas. Active vector control measures did contribute to vector reduction, but this was not enough to decrease A. aegypti population genetic diversity in Salvador. The understanding of A. aegypti population dynamics may be helpful for planning and evaluation of control measures to make them more effective.

Probing functional polymorphisms in the dengue vector, Aedes aegypti

BACKGROUND

Dengue is the most prevalent arboviral disease world-wide and its primary vector is the mosquito Aedes aegypti. The current lack of commercially-available vaccines makes control of vector populations the only effective strategy to prevent dengue transmission. Aedes aegypti geographic populations exhibit great variability in insecticide resistance and susceptibility to dengue infection. The characterization of single nucleotide polymorphisms (SNPs) as molecular markers to study quantitatively this variation is needed greatly because this species has a low abundance of microsatellite markers and limited known restriction fragments length polymorphisms (RFLPs) and single-strand conformation polymorphism (SSCP) markers.

RESULTS

We used RNA-seq to characterize SNPs in three Ae. aegypti strains, including the Liverpool (LVP) strain, from which the current genome annotation is derived. We identified 131,764 unique genome locations with at least one alternative nucleotide to what is reported in the reference annotation. These comprised changes in both open-reading frames (ORFs) and untranslated regions (UTRs) of transcripts. An in depth-look at sequence variation in immunity genes revealed that those associated with autophagy, MD2-like receptors and Peptidoglycan Recognition Proteins had more sequence variation in their 3'UTRs than mutations associated with non-synonymous changes. This supports the conclusion that these genes had maintained their functional specificity while being adapted to different regulatory domains. In contrast, a number of peroxidases, serpins and Clip-domain serine proteases exhibited conservation of putative UTR regulatory sequences while displaying diversification of the ORFs. Transcriptome evidence also was found for ~2500 novel transcriptional units (NTUs) not annotated in the reference genome.

CONCLUSIONS

The transcriptome-wide assessment of within and inter-strain polymorphisms in Ae. aegypti adds considerably to the number of molecular markers available for genetic studies in this mosquito. Additionally, data supporting NTU discovery emphasizes the need for continuous amendments of the reference genome annotation.

Long microsatellites and unusually high levels of genetic diversity in the Orthoptera

Much remains to be learned about the mutational processes governing the evolution of microsatellite repeat regions and the associated levels of genetic diversity observed at microsatellite markers across populations or species. An extensive survey of microsatellite variation in 210 insect species from six major orders revealed that within Orthopterans, which are characterized by giant genomes, levels of genetic diversity were ~20% higher and microsatellite repeat arrays were longer than in any other group. Because of the mutation dependence on repeat length, this result suggests a higher microsatellite loci mutation rate in the Orthoptera. We deem it plausible that differences among insect orders, either in mismatch repair systems or in abundance of transposable element-derived microsatellites, can shape the size distribution of both genomes and microsatellite repeat regions. Our findings emphasise that observed levels of genetic diversity can greatly vary across species (orders at least) because of molecular differences in the mechanisms that determine microsatellite size, and are therefore critical to conservation and population genetics studies, where microsatellite repeat variability is primarily interpreted in terms of population demography and history.

Rapid and cost-effective screening of newly identified microsatellite loci by high-resolution melting analysis

This study describes a new method for identifying microsatellite loci that will reliably amplify and show high degree of polymorphism in a given species. Microsatellites are the most powerful codominant markers available today, but the development of novel loci remains a labour-intensive and expensive process. In de novo isolation, approaches using next generation sequencing (NGS) are gradually replacing ones using Escherichia coli libraries, resulting in unparalleled numbers of candidate loci available. We present a systematic review of published microsatellite primer notes and show that, on average, about half of all candidate loci are lost due to insufficient PCR amplification, monomorphism or multicopy status in the genome, no matter what isolation strategy is used. Thus, the screening of candidate loci remains a major step in marker development. Re-assessing capillary-electrophoresis genotyped loci via high-resolution melting analysis (HRM), we evaluate the usefulness of HRM for this step. We demonstrate its applicability in a genotyping case study and introduce a fast, HRM-based workflow for the screening of microsatellite loci. This workflow may readily be applied to NGS-based marker development and has the potential to cut the costs of traditional testing by half to three quarters.

Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances

Background

The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha).

Principal Findings

By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations).

Significance

De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes.

Genome-based polymorphic microsatellite development and validation in the mosquito Aedes aegypti and application to population genetics in Haiti

Background

Microsatellite markers have proven useful in genetic studies in many organisms, yet microsatellite-based studies of the dengue and yellow fever vector mosquito Aedes aegypti have been limited by the number of assayable and polymorphic loci available, despite multiple independent efforts to identify them. Here we present strategies for efficient identification and development of useful microsatellites with broad coverage across the Aedes aegypti genome, development of multiplex-ready PCR groups of microsatellite loci, and validation of their utility for population analysis with field collections from Haiti.

Results

From 79 putative microsatellite loci representing 31 motifs identified in 42 whole genome sequence supercontig assemblies in the Aedes aegypti genome, 33 microsatellites providing genome-wide coverage amplified as single copy sequences in four lab strains, with a range of 2-6 alleles per locus. The tri-nucleotide motifs represented the majority (51%) of the polymorphic single copy loci, and none of these was located within a putative open reading frame. Seven groups of 4-5 microsatellite loci each were developed for multiplex-ready PCR. Four multiplex-ready groups were used to investigate population genetics of Aedes aegypti populations sampled in Haiti. Of the 23 loci represented in these groups, 20 were polymorphic with a range of 3-24 alleles per locus (mean = 8.75). Allelic polymorphic information content varied from 0.171 to 0.867 (mean = 0.545). Most loci met Hardy-Weinberg expectations across populations and pairwise F_ST comparisons identified significant genetic differentiation between some populations. No evidence for genetic isolation by distance was observed.

Conclusion

Despite limited success in previous reports, we demonstrate that the Aedes aegypti genome is well-populated with single copy, polymorphic microsatellite loci that can be uncovered using the strategy developed here for rapid and efficient screening of genome supercontig assemblies. These loci are suitable for genetic and population studies using multiplex-PCR.

Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research

The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies.

Assortative pairing in Ixodes ricinus (Acari: Ixodidae), the European vector of Lyme borreliosis

In sexual organisms, the way in which gametes associate can greatly influence the maintenance of genetic variation, the structure of this variation in space, and ultimately organismal evolution. Based on patterns of genetic structure previously found, we explicitly tested whether adults of the sheep tick Ixodes ricinus pair according to their genetic relatedness. We sampled tick pairs from the vegetation in four natural populations and genotyped individual ticks at seven microsatellite loci. Based on this data, we observed highly significant assortative mating in two of the four locations, a pattern that could not be accounted for by a spatial autocorrelation in the distribution of related ticks. One explanation for these observations may be the existence of local host associations that develop independently in different populations. Assortative mating in I. ricinus will have clear consequences for its population dynamics and, through processes of adaptation and transmission, may significantly alter the epidemiological patterns of the pathogens it carries, including the Lyme disease agent Borrelia burgdorferi s.l. Future tests will now be required to examine the mechanisms leading to this pattern and its epidemiological consequences.

Lessons from a beetle and an ant: coping with taxon-dependent differences in microsatellite development success

Microsatellites are powerful markers often isolated de novo for species yet to be investigated. Enriched genomic libraries are usually used for isolation purposes. We critically evaluate the outcome of an enrichment-based protocol applied to two insect species (the ant Lasius austriacus and the beetle Pityogenes chalcographus) which yielded contrasting numbers of suitable loci. Our findings of differences in microsatellite isolation are consistent with the available data on differences in genomic characteristics across these taxa. In the beetle repeated isolation of identical motifs, difficulties in primer development, and multibanded products caused loss of most candidate clones. We identified critical steps during marker development.

Microsatellite flanking region similarities among different loci within insect species

Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.

Evolutionary dynamics of multilocus microsatellite arrangements in the genome of the butterfly Bicyclus anynana, with implications for other Lepidoptera

The sequences flanking microsatellites isolated from the butterfly Bicyclus anynana display high levels of similarity among different loci. We examined sequence data for evidence of the two mechanisms most likely to generate these similarities, namely recombination mediated events, such as unequal crossing over or gene conversion and through transposition of mobile elements (MEs). Many sequences contained tandemly arranged microsatellites, lending support to recombination as the multiplication mechanism. There is, however, also support for ME-mediated multiplication of microsatellites and their flanking sequences. Homology with a known Lepidopteran ME was found in B. anynana microsatellite regions, and polymorphic microsatellite markers with partial similarities in their flanking sequences were passed on to the next generation independently, indicating that they are not linked. Therefore, the rise of these similarities appears to be mediated through both processes, either as an interaction between the two, or by each being responsible for part of the observations. A large proportion of microsatellites embedded in repetitive DNA is representative for most studied butterflies and moths, and a BLAST survey of the B. anynana sequences revealed four short microsatellite-associated sequences that were present in many species of Lepidoptera. The similarities usually start to deviate beyond these sequences, which suggests that they define the extremes of a repeated unit. Further study of these conserved sequences may help to understand the mechanism underlying the multiplication events, and answer the question of why these redundancies are predominantly found in this insect group.

Higher genetic variation estimated by microsatellites compared to isoenzyme markers in Aedes aegypti from Rio de Janeiro

Aedes aegypti populations from five districts in Rio de Janeiro were analyzed using five microsatellites and six isoenzyme markers, to assess the amount of variation and patterns of gene flow at local levels. Microsatellite loci were polymorphic enough to detect genetic differentiation of populations collected at small geographic scales (e.g. within a city). Ae. aegypti populations were highly differentiated as well in the city center as in the outskirt. Thus, dengue virus propagation by mosquitoes could be as efficient in the urban area as in the outskirt of Rio de Janeiro, the main entry point of dengue in Brazil.

The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3' tandem repeats and the poly(dA) tail

A novel family of tRNA-related SINEs named gecko was discovered in the yellow fever mosquito, Aedes aegypti. Approximately 7200 copies of gecko were distributed in the A. aegypti genome with a significant bias toward A + T-rich regions. The 3' end of gecko is similar in sequence and identical in secondary structure to the 3' end of MosquI, a non-LTR retrotransposon in A. aegypti. Nine conserved substitutions and a deletion separate gecko into two groups. Group I includes all gecko that end with poly(dA) and a copy that ends with AGAT repeats. Group II comprises gecko elements that end with CCAA or CAAT repeats. Members within each group cannot be differentiated when the 3' repeats are excluded in phylogenetic and sequence analyses, suggesting that the alterations of 3' tails are recent. Imperfect poly(dA) tail was recorded in group I and partial replication of the 3' tandem repeats was frequently observed in group II. Genomic evidence underscores the importance of slippage retrotransposition in the alteration and expansion of the tandem repeat during the evolution of gecko sequences, although we do not rule out postinsertion mechanisms that were previously invoked to explain the evolution of Alu-associated microsatellites. We propose that the 3' tandem repeats and the poly(dA) tail may be generated by similar mechanisms during retrotransposition of both SINEs and non-LTR retrotransposons and thus the distinction between poly(dA) retrotransposons such as L1 and non-poly(dA) retrotransposons such as I factor may not be informative.

SEQUENCE VARIATION OF THE RIBOSOMAL DNA SECOND INTERNAL TRANSCRIBED SPACER REGION IN TWO SPATIALLY DISTINCT POPULATIONS OF AMBLYOMMA AMERICANUM (L.) (ACARI: IXODIDAE)

Sequence analysis of the ribosomal DNA second internal transcribed spacer (ITS 2) region in 2 spatially distinct populations of Amblyomma americanum (L.) revealed intraspecific variation. Nucleotide sequences from multiple DNA extractions and several polymerase chain reaction amplifications of eggs from mixed-parentage samples from both populations of ticks revealed that 12 of 1,145 (1.0%) sites varied. Three of the 12 sites of variation were distinct between the 2 A. americanum populations, which corresponded to a rate of 0.26%. Phylogenetic analysis based on ITS 2 sequences provided strong support (i.e., bootstrap value of 80%) that wild A. americanum clustered into a distinguishable group separate from those derived from colony ticks.

Quantitative trait loci that control dengue-2 virus dissemination in the mosquito Aedes aegypti

The mosquito Aedes aegypti is the most important vector of yellow fever and dengue fever flaviviruses. Ae. aegypti eradication campaigns have not been sustainable and there are no effective vaccines for dengue viruses. Alternative control strategies may depend upon identification of mosquito genes that condition flavivirus susceptibility and may ultimately provide clues for interrupting transmission. Quantitative trait loci affecting the ability of Ae. aegypti to develop a dengue-2 infection in the midgut have been mapped previously. Herein we report on QTL that determine whether mosquitoes with a dengue-2-infected gut can then disseminate the virus to other tissues. A strain selected for high rates of dengue-2 dissemination was crossed to a strain selected for low dissemination rates. QTL were mapped in the F(2) and again in an F(5) advanced intercross line. QTL were detected at 31 cM on chromosome I, at 32 cM on chromosome II, and between 44 and 52 cM on chromosome III. Alleles at these QTL were additive or dominant in determining rates of dengue-2 dissemination and accounted for approximately 45% of the phenotypic variance. The locations of dengue-2 midgut infection and dissemination QTL correspond to those found in earlier studies.

Mosquito transposable elements

The completion of the genome assembly for the African malaria mosquito, Anopheles gambiae, and continuing genomic efforts for the yellow fever mosquito, Aedes aegypti, have allowed the use of bioinformatics tools to identify and characterize a diverse array of transposable elements (TEs) in these and other mosquito genomes. An overview of the types and number of both RNA-mediated and DNA-mediated TEs that are found in mosquito genomes is presented. A number of novel and interesting TEs from these species are discussed in more detail. These findings have significant implications for our understanding of mosquito genome evolution and for future modifications of natural mosquito populations through the use of TE-mediated genetic transformation.

Aedes aegypti genomics

The mosquito, Aedes aegypti, is the primary, worldwide arthropod vector for the yellow fever and dengue viruses. As it is also one of the most tractable mosquito species for laboratory studies, it has been and remains one of the most intensively studied arthropod species. This has resulted in the development of detailed genetic and physical maps for Ae. aegypti and considerable insight into its genome organization. The research community is well-advanced in developing important molecular tools that will facilitate a whole genome sequencing effort. This includes generation of BAC clone end sequences, physical mapping of selected BAC clones and generation of EST sequences. Whole genome sequence information for Ae. aegypti will provide important insight into mosquito chromosome evolution and allow for the identification of genes and gene function. These functions may be common to all mosquitoes or perhaps unique to individual species, possibly specific to host-seeking and blood-feeding behaviors, as well as the innate immune response to pathogens encountered during blood-feeding. This information will be invaluable to the global effort to develop novel strategies for preventing arthropod-borne disease transmission.

Intraspecific DNA variation in nuclear genes of the mosquito Aedes aegypti

Single nucleotide polymorphisms (SNPs) are an abundant source of genetic variation among individual organisms. To assess the usefulness of SNPs for genome analysis in the yellow fever mosquito, Aedes aegypti, we sequenced 25 nuclear genes in each of three strains and analysed nucleotide diversity. The average frequency of nucleotide variation was 12 SNPs per kilobase, indicating that nucleotide variation in Ae. aegypti is similar to that in other organisms, including Drosophila and the malaria vector Anopheles gambiae. Transition polymorphisms outnumbered transversion polymorphisms, at a ratio of about 2:1. We examined codon usage and confirmed that mutational bias favours G and C ending codons. Codon bias was most pronounced in highly expressed genes. Nucleotide diversity estimates indicated that substitution rates are positively correlated in coding and non-coding regions. Nucleotide diversity varied from one gene to another. The unequal distribution of SNPs among Ae. aegypti nuclear genes suggests that single base variations are non-neutral and are subject to selective constraints. Our analysis showed that ubiquitously expressed genes have lower polymorphism rates and are likely under strong purifying selection, whereas tissue specific genes and genes with a putative role in parasite defence exhibit higher levels of polymorphism that may be associated with diversifying selection.

A preliminary linkage map of the hard tick, Ixodes scapularis

A linkage map of the Ixodes scapularis genome was constructed, based upon segregation amongst 127 loci. These included 84 random amplified polymorphic DNA (RAPD) markers, 32 Sequence-Tagged RAPD (STAR) markers, 5 cDNAs, and 5 microsatellites in 232 F1 intercross progeny from a single, field-collected P1 female. A preliminary linkage map of 616 cM was generated across 14 linkage groups with one marker every 10.8 cM. Assuming a genome size of approximately 109 bp, the relationship of physical to genetic distance was found to be approximately 300 kb/cM in the I. scapularis genome.

Sex-biased genetic structure in the vector of Lyme disease, Ixodes ricinus

We analyzed 725 Ixodes ricinus ticks (the principal vector of Lyme disease in Europe) collected in Switzerland in 1995 and 1996 (three and eight samples, respectively) and in Tunisia in 1996 (one sample) with five microsatellite markers. We found highly significant genetic differentiation between Swiss and Tunisian samples but detected almost no differentiation within Switzerland, even between those samples separated by the Alps. Interestingly, we found that I. ricinus females were more genetically related to one another than were males at a local scale, which would indicate a higher dispersal rate of immature males. Possible explanations for these findings in terms of sex-specific association of ticks with certain hosts (e.g., birds) and their epidemiological consequences are discussed.

Linkage map organization of expressed sequence tags and sequence tagged sites in the mosquito, Aedes aegypti

A composite genetic linkage map for the yellow fever mosquito Aedes aegypti was constructed based on restriction fragment length polymorphism (RFLP), single nucleotide polymorphism (SNP) and single strand conformation polymorphism (SSCP) markers. The map consists of 146 marker loci distributed across 205 cM, and includes several morphological mutant marker loci. Most of the genetic markers are derived from random cDNAs or Ae. aegypti genes of known function. A number of markers are derived from random genomic DNAs, including several cloned RAPD-PCR fragments, and also several cDNAs from Drosophila melanogaster. Most of the random cDNAs (80.2%) have high BlastX sequence identities to known genes, with the majority of matches to genes from D. melanogaster. Access to sequence data for all markers will facilitate their continued development for use in high-throughput SNP marker analyses and also provides additional physical anchor points for an anticipated genome sequencing effort.

SSCP analysis of cDNA markers provides a dense linkage map of the Aedes aegypti genome

An intensive linkage map of the yellow fever mosquito, Aedes aegypti, was constructed using single-strand conformation polymorphism (SSCP) analysis of cDNA markers to identify single nucleotide polymorphisms (SNPs). A total of 94 A. aegypti cDNAs were downloaded from GenBank and primers were designed to amplify fragments <500 bp in size. These primer pairs amplified 94 loci, 57 (61%) of which segregated in a single F(1) intercross family among 83 F(2) progeny. This allowed us to produce a dense linkage map of one marker every 2 cM distributed over a total length of 134 cM. Many A. aegypti cDNAs were highly similar to genes in the Drosophila melanogaster genome project. Comparative linkage analysis revealed areas of synteny between the two species. SNP polymorphisms are abundant in A. aegypti genes and should prove useful in both population genetics and mapping studies.