Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

<p>Abstract</p> <p>Background</p> <p>Developing lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null" alleles. Previous studies identified sequences flanking simple sequence repeat (SSR) units that are shared among many lepidopteran species and can be grouped into microsatellite-associated DNA families. These families are thought to be associated with unequal crossing-over during DNA recombination or with transposable elements (TEs).</p> <p>Results</p> <p>We identified full-length lepidopteran non-LTR retrotransposable elements of the RTE clade in <it>Heliconius melpomene </it>and <it>Bombyx mori</it>. These retroelements possess a single open reading frame encoding the Exonuclease/Endonuclease/Phosphatase and the Reverse Transcriptase/nLTR domains, a 5' UTR (untranslated region), and an extremely short 3' UTR that regularly consists of SSR units. Phylogenetic analysis supported previous suggestions of horizontal transfer among unrelated groups of organisms, but the diversity of lepidopteran RTE elements appears due to ancient divergence of ancestral elements rather than introgression by horizontal transfer. Similarity searches of lepidopteran genomic sequences in GenBank identified partial RTE elements, usually consisting of the 3' terminal region, in 29 species. Furthermore, we identified the C-terminal end of the Reverse Transcriptase/nLTR domain and the associated 3' UTR in over 190 microsatellite markers from 22 lepidopteran species, accounting for 10% of the lepidopteran microsatellites in GenBank. Occasional retrotransposition of autonomous elements, frequent retrotransposition of 3' partial elements, and DNA replication slippage during retrotransposition offers a mechanistic explanation for the association of SSRs with RTE elements in lepidopteran genomes.</p> <p>Conclusions</p> <p>Non-LTR retrotransposable elements of the RTE clade therefore join a diverse group of TEs as progenitors of SSR units in various organisms. When microsatellites are isolated using standard SSR enrichment protocols and primers designed at complementary repeated regions, amplification from multiple genomic sites can cause scoring difficulties that compromise their utility as markers. Screening against RTE elements in the isolation procedure provides one strategy for minimizing this problem.</p

A brave new world for an old world pest: Helicoverpa armigera (Lepidoptera: Noctuidae) in Brazil

The highly polyphagous Old World cotton bollworm Helicoverpa armigera is a quarantine agricultural pest for the American continents. Historically H. armigera is thought to have colonised the American continents around 1.5 to 2 million years ago, leading to the current H. zea populations on the American continents. The relatively recent species divergence history is evident in mating compatibility between H. zea and H. armigera under laboratory conditions. Despite periodic interceptions of H. armigera into North America, this pest species is not believed to have successfully established significant populations on either continent. In this study, we provide molecular evidence via mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and cytochrome b (Cyt b) partial gene sequences for the successful recent incursion of H. armigera into the New World, with individuals being detected at two sites (Primavera do Leste, Pedra Preta) within the State of Mato Grosso in Brazil. The mtDNA COI and Cyt b haplotypes detected in the Brazilian H. armigera individuals are common throughout the Old World, thus precluding identification of the founder populations. Combining the two partial mtDNA gene sequences showed that at least two matrilines are present in Brazil, while the inclusion of three nuclear DNA Exon-Primed Intron-Crossing (EPIC) markers identified a further two possible matrilines in our samples. The economic, biosecurity, resistance management, ecological and evolutionary implications of this incursion are discussed in relation to the current agricultural practices in the Americas

Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil

The Old World bollworm Helicoverpa armigera is now established in Brazil but efforts to identify incursion origin(s) and pathway(s) have met with limited success due to the patchiness of available data. Using international agricultural/horticultural commodity trade data and mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene markers, we inferred the origins and incursion pathways into Brazil. We detected 20 mtDNA haplotypes from six Brazilian states, eight of which were new to our 97 global COI-Cyt b haplotype database. Direct sequence matches indicated five Brazilian haplotypes had Asian, African, and European origins. We identified 45 parsimoniously informative sites and multiple substitutions per site within the concatenated (945 bp) nucleotide dataset, implying that probabilistic phylogenetic analysis methods are needed. High diversity and signatures of uniquely shared haplotypes with diverse localities combined with the trade data suggested multiple incursions and introduction origins in Brazil. Increasing agricultural/horticultural trade activities between the Old and New Worlds represents a significant biosecurity risk factor. Identifying pest origins will enable resistance profiling that reflects countries of origin to be included when developing a resistance management strategy, while identifying incursion pathways will improve biosecurity protocols and risk analysis at biosecurity hotspots including national portsESC and IBM were supported by CSIRO Health and Biosecurity, the Brazilian Government’s, Science without Boarders (Ciência sem Fronteiras) summer internship program (242166/2012–1 (ESC); 209297/2013-1 (IBM)), and Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) scholarships. CA was supported by a CSIRO OCE Post Doctoral Fellowship (R-03255-01). WTT and TKW acknowledged funing support from CSIRO Health & Biosecurity ‘Genes of Biosecurity Significance’ (R-8681-1). CC acknowledges funding support from FAPEG (Fundação de amparo a pesquisa do estado de Goiás) (Grant number: Helicoverpa/2013102670001419)

Two species into one: bottleneck history of Helicoverpa zea from Helicoverpa armigera revealed by DNA barcoding

The use of mitochondrial DNA Cytochrome Oxidase I (mtDNA COI) gene in species identification has gained popularity in recent years, with its effectiveness in identifying cryptic and new species demonstrated in birds and Lepidoptera. The noctuid moths of the genus Helicoverpa include two of the most devastating agricultural pest species: H. armigera of the old world, and H. zea found exclusively in the north and south American continents. Both of these species are polyphagous targeting >150 crop species. Phylogenies of H. armigera and H. zea have to-date been constructed based on coding nuclear DNA sequences and morphological characters, but a mtDNA phylogeny of H. zea and H. armigera has been lacking. Differentiating H. zea and H. armigera based on morphological characters relies almost exclusively on characters of the male genitalia, although accurate identification has remained problematic due to over-lapping ranges in character measurements. H. zea and H. armigera are presently recognised as two separate species despite successful bi-directional, ‘inter-specific’, mating experiments that gave rise to viable offspring, and the trapping of H. zea males when using H. armigera sex pheromones in the North American continent. Using a 511 base pair sequence of a partial mtDNA COI gene, we analysed the phylogenetic relationships amongst 228 H. armigera individuals sampled from China, Australia, Africa, India and Pakistan, plus 14 H. zea from North America, H. punctigera from Australia and H. assulta from India, using Heliothis virescens as an outgroup. Our mtDNA COI phylogeny of Helicoverpa species indicates that H. punctigera is ancestral to H. assulta which is in turn ancestral to H. armigera and H. zea. Furthermore, the long branch-length of H. zea from the H. armigera clade suggests a recent bottleneck event in H. zea’s separation from H. armigera. H. zea and H. armigera show an intermediate level of nucleotide diversity, lying between expected values for intra-specific and inter-specific sequence comparisons, possibly suggesting rapid nucleotide divergence in H. zea due to selection pressures imposed on movement by agricultural practices

DNA barcoding confirmed the occurrence of invasive vegetable leaf miner, Liriomyza sativae Blanchard (Diptera:Agromyzidae) in Northeast India

The vegetable leaf miner, Liriomyza sativae (Diptera:Agromyzidae), is an invasive polyphagous species originally known to be found in America and now spread in many parts of Africa, Asia, and the Pacific region. During 2016, L. sativae was observed for the first time infesting tomato (Solanum lycopersicum L.) leaves in experimental farms of an institute at Umiam (Meghalaya state of northeastern India). Based on museum specimens, this species was reported from India on tomato during 1994. Nevertheless, no further information is hitherto available from India apart from just new record. Considering the pest status of L. sativae across the globe, it is crucial to understand its expansion range, severity, biological attributes, and seasonal incidence on tomato in India. Taxonomic identification of different species of Liriomyza leaf miners is very complex due to morphological resemblance, and consequently, species-level identification is often done incorrectly by mistaking one species for another. Therefore, we characterized L. sativae at the molecular level and developed species specific DNA barcodes by using mitochondrial cytochrome oxidase gene. Moreover, the information on the correct distribution, seasonal incidence, and basic biological attributes of different stages of L. sativae is reported and discussed

Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea

Background: Helicoverpa armigera and H. zea are amongst the most significant polyphagous pest lepidopteran species in the Old and New Worlds respectively. Separation of H. armigera and H. zea is difficult and is usually only achieved through morphological differences in the genitalia. They are capable of interbreeding to produce fertile offspring. The single species status of H. armigera has been doubted, due to its wide distribution and plant host range across the Old World. This study explores the global genetic diversity of H. armigera and its evolutionary relationship to H zea. Results: We obtained partial (511 bp) mitochondrial DNA (mtDNA) Cytochrome Oxidase-I(COI) sequences for 249 individuals of H. armigera sampled from Australia, Burkina Faso, Uganda, China, India and Pakistan which were associated with various host plants. Single nucleotide polymorphisms (SNPs) within the partial COI gene differentiated H. armigera populations into 33 mtDNA haplotypes. Shared haplotypes between continents, low F-statistic values and low nucleotide diversity between countries (0.0017 – 0.0038) suggests high mobility in this pest. Phylogenetic analysis of four major Helicoverpa pest species indicates that H. punctigera is basal to H. assulta, which is in turn basal to H. armigera and H. zea. Samples from North and South America suggest that H. zea is also a single species across its distribution. Our data reveal short genetic distances between H. armigera and H. zea which seem to have been established via a founder event from H. armigera stock at around 1.5 million years ago.Conclusion: Our mitochondrial DNA sequence data supports the single species status of H. armigera across Africa, Asia and Australia. The evidence for inter-continental gene flow observed in this study is consistent with published evidence of the capacity of this species to migrate over long distances. The finding of high genetic similarity between Old World H. armigera and New World H. zea emphasises the need to consider work on both pests when building pest management strategies for either

Not Available

Not AvailableCotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), is a serious pest of several crops throughout the world, representing millions of United States of America dollars worth of damage. This pest can adapt to various cropping systems in a wide geographical range and has high migratory potential. It features high fecundity and can develop resistance to almost all insecticides used for its management. Several investigations to develop microsatellite markers for H. armigera have not been successful because of the paucity of microsatellites in the lepidopteran genome. As well, collections of H. armigera from cotton fields of southern and western India were not yet studied for molecular genetic diversity. The current study aimed to screen publicly available expressed sequence tag resources for simple sequence repeats and assess their potential as DNA markers for assessment of gene flow between collections of southern and western India. We identified 30 polymorphic microsatellites for potential use in diversity analysis of H. armigera collections. Genetic diversity analysis revealed that the collections were widely diverse with population differentiation index (Fst) of 0.17. Furthermore, gene flow analysis revealed a mean frequency of private alleles of 11% within the collections. The microsatellite resources we developed could be widely used for molecular diversity or population genetic research involving this important pest of cotton and food crops.Not Availabl

Maximum Likelihood (ML) tree of (Harm-1 to Harm-31), (Hzea-1, Hzea-2), and based on partial COI haplotypes sequences

<p><b>Copyright information:</b></p><p>Taken from "Mitochondrial DNA analysis of field populations of (Lepidoptera: Noctuidae) and of its relationship to "</p><p>http://www.biomedcentral.com/1471-2148/7/117</p><p>BMC Evolutionary Biology 2007;7():117-117.</p><p>Published online 14 Jul 2007</p><p>PMCID:PMC1934911.</p><p></p> Numbers above the nodes indicate bootstrap support. The outgroup used was . The inclusion of additional haplotypes Harm-32, Harm-33, and Hzea-3 to Hzea-11 did not alter the overall topology, and bootstrap values of the ML tree after 1,000 bootstrap replications remained high, with all haplotypes confidently clustered (bootstrap value = 96) within the clade. remained basal to (bootstrap value = 99), and the /clade (bootstrap value = 78) shared a most common ancestor with (bootstrap value = 97) (data not shown)