Sequence, assembly and count datasets of viruses associated to the pine processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller) (Lepidoptera, Notodontidae) identified from transcriptomic high-throughput sequencing.

The pine processionary moth Thaumetopoea pityocampa is a Lepidopteran pest species occurring in the Western Mediterranean. It causes heavy pine defoliations and it is a public and animal health concern because of its urticating caterpillars. Very little is known about the viruses associated to this species, as only two viruses were described so far. We here present a dataset corresponding to 34 viral transcripts, among which 27 could be confidently assigned to 9 RNA and DNA viral families (Iflaviridae, Reoviridae, Partitiviridae, Permutotetraviridae, Flaviviridae, Rhabdoviridae, Parvoviridae, Baculoviridae and PolyDNAviridae). These transcripts were identified from an original transcriptome assembled for the insect host, using both blast search and phylogenetic approaches. The data were acquired from 2 populations in Portugal and 2 populations in Italy. The transcripts were de novo assembled and used to identify viral sequences by homology searches. We also provide information about the populations and life stages in which each virus was identified. The data produced will allow to enrich the virus taxonomy in Lepidopteran hosts, and to develop PCR-based diagnostic tools to screen colonies across the range and determine the distribution and prevalence of the identified viral species.

Integrated miRNA and transcriptome profiling to explore the molecular determinism of convergent adaptation to corn in two lepidopteran pests of agriculture.

BACKGROUND: The degree to which adaptation to same environment is determined by similar molecular mechanisms, is a topic of broad interest in evolutionary biology, as an indicator of evolutionary predictability. We wished to address if adaptation to the same host plant in phytophagous insects involved related gene expression patterns. We compared sRNA-Seq and RNA-Seq data between two pairs of taxa of Ostrinia and Spodoptera frugiperda sharing maize as host-plant. For the latter, we had previously carried out a reciprocal transplant experiment by feeding of the larvae of the Corn strain (Sf-C) and the Rice strain (Sf-R) on corn versus rice and characterized the mRNA and miRNA responses. RESULTS: First, we predicted the genes encoding miRNA in Ostrinia nubilalis (On) and O. scapulalis (Os). Respectively 67 and 65 known miRNA genes, as well as 196 and 190 novel ones were predicted with Os genome using sncRNAs extracted from whole larvae feeding on corn or mugwort. In On, a read counts analysis showed that 37 (55.22%) known miRNAs and 19 (9.84%) novel miRNAs were differentially expressed (DE) on mugwort compared to corn (in Os, 25 known miRs (38.46%) and 8 novel ones (4.34%)). Between species on corn, 8 (12.5%) known miRNAs and 8 (6.83%) novel ones were DE while only one novel miRNA showed expression variation between species on mugwort. Gene target prediction led to the identification of 2953 unique target genes in On and 2719 in Os, among which 11.6% (344) were DE when comparing species on corn. 1.8% (54) of On miR targets showed expression variation upon a change of host-plant. We found molecular changes matching convergent phenotype, i.e., a set of nine miRNAs that are regulated either according to the host-plant both in On and Sf-C or between them on the same plant, corn. Among DE miR target genes between taxa, 13.7% shared exactly the same annotation between the two pairs of taxa and had function related to insect host-plant interaction. CONCLUSION: There is some similarity in underlying genetic mechanisms of convergent evolution of two distant Lepidopteran species having adopted corn in their host range, highlighting possible adaptation genes.

Coding-Complete Genome Sequence of a Partitivirus Isolated from Pine Processionary Moth Eggs.

Two coding-complete nucleotide sequences of a partitivirus (family Partitiviridae) were discovered in transcriptomic data sets obtained from eggs of the Lepidoptera Thaumetopoea pityocampa Each segment encodes a single open reading frame, and these two segments are predicted to encode an RNA-dependent RNA polymerase and a coat protein, respectively.

Coding-Complete Genome Sequences of an Iteradensovirus and an Alphapermutotetra-Like Virus Identified from the Pine Processionary Moth (Thaumetopoea pityocampa) in Portugal.

The coding-complete genome sequences of an iteradensovirus (family Parvoviridae) and an alphapermutotetra-like virus (family Permutotetraviridae) were discovered from transcriptomic data sets obtained from Thaumetopoea pityocampa larvae collected in Portugal. Each of the coding-complete genome sequences of these viruses contains three main open reading frames (ORFs).

Complete mitogenome data from a European specimen of Ostrinia scapulalis (Walker, 1859) (Lepidoptera, Pyraloidea, Crambidae, Pyraustinae).

We present an assembly and annotation of the mitogenome of a European specimen of the Adzuki bean borer, Ostrinia scapulalis (Walker, 1859). The data were obtained by combining WGS data issue of a de novo and a previously published sequence library (Gschloessl et al., 2018). We also provide the phylogenetic positioning of the mitogenome within the Ostrinia genus, the Crambidae family and with more distant Lepidoptera species.

New WGS data and annotation of the heterosomal vs. autosomal localization of Ostrinia scapulalis (Lepidoptera, Crambidae) nuclear genomic scaffolds.

Here, we introduce new whole-genome shotgun sequencing and annotation data describing the autosomal vs. Z-heterosomal localization of nuclear genomic scaffolds of the moth species Ostrinia scapulalis. Four WGS libraries (corresponding to 2 males and 2 females) were sequenced with an Illumina HiSeq2500 sequencing technology, and the so-called 'AD-ratio' method was applied to distinguish between autosomal and Z-heterosomal scaffolds based on sequencing depth comparisons between homogametic (male) and heterogametic (female) libraries. A total of 25,760 scaffolds (corresponding to 341.69 Mb) were labelled as autosomal and 1273 scaffolds (15.29 Mb) were labelled as Z-heterosomal, totaling about 357 Mb. Besides, 4874 scaffolds (29.07 Mb) remain ambiguous because of a lack of AD-ratio reproducibility between the two replicates. The annotation method was evaluated a posteriori, by comparing depth-based annotation with the exact localization of known genes. Raw genomic data have been deposited and made accessible via the EMBL ENA BioProject id PRJEB26557. Comprehensive annotation is made accessible via the LepidoDB database (http://bipaa.genouest.org/sp/ostrinia_scapulalis/download/genome/v1.2/).

Animal choruses emerge from receiver psychology.

Synchrony and alternation in large animal choruses are often viewed as adaptations by which cooperating males increase their attractiveness to females or evade predators. Alternatively, these seemingly composed productions may simply emerge by default from the receiver psychology of mate choice. This second, emergent property hypothesis has been inferred from findings that females in various acoustic species ignore male calls that follow a neighbor's by a brief interval, that males often adjust the timing of their call rhythm and reduce the incidence of ineffective, following calls, and from simulations modeling the collective outcome of male adjustments. However, the purported connection between male song timing and female preference has never been tested experimentally, and the emergent property hypothesis has remained speculative. Studying a distinctive katydid species genetically structured as isolated populations, we conducted a comparative phylogenetic analysis of the correlation between male call timing and female preference. We report that across 17 sampled populations male adjustments match the interval over which females prefer leading calls; moreover, this correlation holds after correction for phylogenetic signal. Our study is the first demonstration that male adjustments coevolved with female preferences and thereby confirms the critical link in the emergent property model of chorus evolution.

Genomics of adaptation to host-plants in herbivorous insects.

Herbivorous insects represent the most species-rich lineages of metazoans. The high rate of diversification in herbivorous insects is thought to result from their specialization to distinct host-plants, which creates conditions favorable for the build-up of reproductive isolation and speciation. These conditions rely on constraints against the optimal use of a wide range of plant species, as each must constitute a viable food resource, oviposition site and mating site for an insect. Utilization of plants involves many essential traits of herbivorous insects, as they locate and select their hosts, overcome their defenses and acquire nutrients while avoiding intoxication. Although advances in understanding insect-plant molecular interactions have been limited by the complexity of insect traits involved in host use and the lack of genomic resources and functional tools, recent studies at the molecular level, combined with large-scale genomics studies at population and species levels, are revealing the genetic underpinning of plant specialization and adaptive divergence in non-model insect herbivores. Here, we review the recent advances in the genomics of plant adaptation in hemipterans and lepidopterans, two major insect orders, each of which includes a large number of crop pests. We focus on how genomics and post-genomics have improved our understanding of the mechanisms involved in insect-plant interactions by reviewing recent molecular discoveries in sensing, feeding, digesting and detoxifying strategies. We also present the outcomes of large-scale genomics approaches aimed at identifying loci potentially involved in plant adaptation in these insects.

Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing.

The pine processionary moth Thaumetopoea pityocampa is a Mediterranean lepidopteran defoliator that experiences a rapid range expansion towards higher latitudes and altitudes due to the current climate warming. Its phenology - the time of sexual reproduction - is certainly a key trait for the local adaptation of the processionary moth to climatic conditions. Moreover, an exceptional case of allochronic differentiation was discovered ca. 15 years ago in this species. A population with a shifted phenology (the summer population, SP) co-exists near Leiria, Portugal, with a population following the classical cycle (the winter population, WP). The existence of this population is an outstanding opportunity to decipher the genetic bases of phenology. No genomic resources were so far available for T. pityocampa. We developed a high-throughput sequencing approach to build a first reference transcriptome, and to proceed with comparative analyses of the sympatric SP and WP. We pooled RNA extracted from whole individuals of various developmental stages, and performed a transcriptome characterisation for both populations combining Roche 454-FLX and traditional Sanger data. The obtained sequences were clustered into ca. 12,000 transcripts corresponding to 9265 unigenes. The mean transcript coverage was 21.9 reads per bp. Almost 70% of the de novo assembled transcripts displayed significant similarity to previously published proteins and around 50% of the transcripts contained a full-length coding region. Comparative analyses of the population transcriptomes allowed to investigate genes specifically expressed in one of the studied populations only, and to identify the most divergent homologous SP/WP transcripts. The most divergent pairs of transcripts did not correspond to obvious phenology-related candidate genes, and 43% could not be functionally annotated. This study provides the first comprehensive genome-wide resource for the target species T. pityocampa. Many of the assembled genes are orthologs of published Lepidoptera genes, which allows carrying out gene-specific re-sequencing. Data mining has allowed the identification of SNP loci that will be useful for population genomic approaches and genome-wide scans of population differentiation to identify signatures of selection.

Genetic mapping of two components of reproductive isolation between two sibling species of moths, Ostrinia nubilalis and O. scapulalis.

We report the quantitative trait loci (QTL) mapping of reproductive isolation traits between Ostrinia nubilalis (the European corn borer) and its sibling species O. scapulalis (the Adzuki bean borer), focusing on two traits: mating isolation (mi) and pheromone production (Pher). Four genetic maps were generated from two backcross families, with two maps (one chromosomal map and one linkage map) per backcross. We located 165-323 AFLP markers on these four maps, resulting in the identification of 27-31 linkage groups, depending on the map considered. No-choice mating experiments with the offspring of each backcross led to the detection of at least two QTLs for mi in different linkage groups. QTLs underlying Pher were located in a third linkage group. The Z heterochromosome was identified by a specific marker (Tpi) and did not carry any of these QTLs. Finally, we considered the global divergence between the two sibling species, distortions of segregation throughout the genome, and the location and effect of mi and Pher QTLs in light of the known candidate genes for reproductive isolation within the genus Ostrinia and, more broadly, in phytophagous insects.

'Becoming a species by becoming a pest' or how two maize pests of the genus Ostrinia possibly evolved through parallel ecological speciation events.

New agricultural pest species attacking introduced crops may evolve from pre-existing local herbivores by ecological speciation, thereby becoming a species by becoming a pest. We compare the evolutionary pathways by which two maize pests (the Asian and the European corn borers, ACB and ECB) in the genus Ostrinia (Lepidoptera, Crambidae) probably diverged from an ancestral species close to the current Adzuki bean borer (ABB). We typed larval Ostrinia populations collected on maize and dicotyledons across China and eastern Siberia, at microsatellite and mitochondrial loci. We found only two clusters: one on maize (as expected) and a single one on dicotyledons despite differences in male mid-tibia morphology, suggesting that all individuals from dicotyledons belonged to the ABB. We found evidence for migrants and hybrids on both host plant types. Hybrids suggest that field reproductive isolation is incomplete between ACB and ABB. Interestingly, a few individuals with an 'ABB-like' microsatellite profile collected on dicotyledons had 'ACB' mtDNA rather than 'ABB-like' mtDNA, whereas the reverse was never found on maize. This suggests asymmetrical gene flow directed from the ACB towards the ABB. Hybrids and backcrosses in all directions were obtained in no-choice tests. In laboratory conditions, they survived as well as parental strain individuals. In Xinjiang, we found ACB and ECB in sympatry, but no hybrids. Altogether, our results suggest that reproductive isolation between ACB and ABB is incomplete and mostly prezygotic. This points to ecological speciation as a possible evolutionary scenario, as previously found for ECB and ABB in Europe.

When history repeats itself: exploring the genetic architecture of host-plant adaptation in two closely related lepidopteran species.

The genus Ostrinia includes two allopatric maize pests across Eurasia, namely the European corn borer (ECB, O. nubilalis) and the Asian corn borer (ACB, O. furnacalis). A third species, the Adzuki bean borer (ABB, O. scapulalis), occurs in sympatry with both the ECB and the ACB. The ABB mostly feeds on native dicots, which probably correspond to the ancestral host plant type for the genus Ostrinia. This situation offers the opportunity to characterize the two presumably independent adaptations or preadaptations to maize that occurred in the ECB and ACB. In the present study, we aimed at deciphering the genetic architecture of these two adaptations to maize, a monocot host plant recently introduced into Eurasia. To this end, we performed a genome scan analysis based on 684 AFLP markers in 12 populations of ECB, ACB and ABB. We detected 2 outlier AFLP loci when comparing French populations of the ECB and ABB, and 9 outliers when comparing Chinese populations of the ACB and ABB. These outliers were different in both countries, and we found no evidence of linkage disequilibrium between any two of them. These results suggest that adaptation or preadaptation to maize relies on a different genetic architecture in the ECB and ACB. However, this conclusion must be considered in light of the constraints inherent to genome scan approaches and of the intricate evolution of adaptation and reproductive isolation in the Ostrinia spp. complex.

De novo transcriptomic resources for two sibling species of moths: Ostrinia nubilalis and O. scapulalis.

BACKGROUND: This study aimed at enhancing the transcriptomic resources for two sibling species of moths, Ostrinia scapulalis (Adzuki bean borer) and Ostrinia nubilalis (European corn borer), as a foundation for future researches on their divergence history. Previous works on these species had shown that their genetic divergence was low, while they were reproductively isolated in natura and specialized on different host plants. Comparative genomic resources will help facilitate the understanding of the mechanisms involved in this isolation and adaptation to the host plants. Despite their fundamental interest, these species still lack the genomic resources to thoroughly identify candidate genes for functions of interest. We present here a high throughput sequencing and de novo transcriptome assembly for these two sibling species in line with this objective of comparative genomics. RESULTS: Based on 322,504 and 307,622 reads of 454 sequencing for O. scapulalis and O. nubilalis respectively, we reconstructed 11,231 and 10,773 transcripts, of which 40% were functionally annotated by BLAST analyzes. We determined the level of completeness of both assemblies as well as the recovery level of published Ostrinia genomic resources. Gene ontology (GO) of common and species-specific de novo transcripts did not reveal GO terms significantly enriched in one or the other species. By applying stringent homology searches on transcripts common to O. scapulalis and O. nubilalis, we identified a set of homologous transcripts, with a mean nucleotide identity value of 98.1%. In this set, the most divergent transcripts revealed candidate genes involved in developmental, sensorial and pathogen defense processes. CONCLUSIONS: This data greatly increases the genomic resources of Ostrinia species and constitute a solid skeleton for future comparative analyzes of expression or diversity, despite we show that the transcriptomes for both species have not been assembled at full completion. In addition, we provide a set of homologous transcripts together with their annotation as a source of candidate genes for comparative analyzes.

Genetic architecture of sexual selection: QTL mapping of male song and female receiver traits in an acoustic moth.

Models of indirect (genetic) benefits sexual selection predict linkage disequilibria between genes that influence male traits and female preferences, owing to non-random mate choice or physical linkage. Such linkage disequilibria can accelerate the evolution of traits and preferences to exaggerated levels. Both theory and recent empirical findings on species recognition suggest that such linkage disequilibria may result from physical linkage or pleiotropy, but very little work has addressed this possibility within the context of sexual selection. We studied the genetic architecture of sexually selected traits by analyzing signals and preferences in an acoustic moth, Achroia grisella, in which males attract females with a train of ultrasound pulses and females prefer loud songs and a fast pulse rhythm. Both male signal characters and female preferences are repeatable and heritable traits. Moreover, female choice is based largely on male song, while males do not appear to provide direct benefits at mating. Thus, some genetic correlation between song and preference traits is expected. We employed a standard crossing design between inbred lines and used AFLP markers to build a linkage map for this species and locate quantitative trait loci (QTL) that influence male song and female preference. Our analyses mostly revealed QTLs of moderate strength that influence various male signal and female receiver traits, but one QTL was found that exerts a major influence on the pulse-pair rate of male song, a critical trait in female attraction. However, we found no evidence of specific co-localization of QTLs influencing male signal and female receiver traits on the same linkage groups. This finding suggests that the sexual selection process would proceed at a modest rate in A. grisella and that evolution toward exaggerated character states may be tempered. We suggest that this equilibrium state may be more the norm than the exception among animal species.

Scanning the European corn borer (Ostrinia spp.) genome for adaptive divergence between host-affiliated sibling species.

It has recently been shown that the European corn borer, a major pest of maize crops, is actually composed of two genetically differentiated and reproductively isolated taxa, which are found in sympatry over a wide geographical range in Eurasia. Each taxon is adapted to specific host plants: Ostrinia nubilalis feeds mainly on maize, while O. scapulalis feeds mainly on hop or mugwort. Here, we present a genome scan approach as a first step towards an integrated molecular analysis of the adaptive genomic divergence between O. nubilalis and O. scapulalis. We analysed 609 AFLP marker loci in replicate samples of sympatric populations of Ostrinia spp. collected on maize, hop and mugwort, in France. Using two genome scan methods based on the analysis of population differentiation, we found a set of 28 outlier loci that departed from the neutral expectation in one or the other method (of which a subset of 14 loci were common to both methods), which showed a significantly increased differentiation between O. nubilalis and O. scapulalis, when compared to the rest of the genome. A subset of 12 outlier loci were sequenced, of which 7 were successfully re-amplified as target candidate loci. Three of these showed homology with annotated lepidopteran sequences from public nucleotide databases.

Modeling survival and mark loss in molting animals: recapture, dead recoveries, and exuvia recoveries.

Capture-mark-recapture (CMR) analyses aim primarily at estimating relevant life history parameters, despite the fact that some individuals are not always recaptured, even if alive on the study site. Applying such approaches to species with a complex life cycle, such as insects, remains challenging because each change of stage tends to cause mark loss through molting. We developed a multistate model based on three exclusive events ("dead", "surviving and molting", and "surviving and staying in the same larval stage") to estimate probabilities of survival and mark loss. Estimates of biologically relevant parameters were derived from those of the probabilities of transition between these states. The model was applied to data from radio-tracking diodes glued on grasshoppers. The estimates of recapture probabilities decreased throughout the season for animals remaining alive, while the detection of dead animals and lost diodes was exhaustive. The survival probability was higher for larvae than for adults (0.98 vs. 0.96), and mark loss was stronger in larvae than in adults (0.09 vs. 0.06). We show that the survival rate of a species with a high rate of mark loss can be estimated using multistate models, provided that marks can be recovered after being lost. These models are flexible enough to test for several effects that potentially affect survival and mark loss probabilities.

Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright-Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex 'quartet' of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.