The genus Ostrinia (Lepidoptera: Crambidae) comprises two of the most important maize pests worldwide, the Asian and the European corn borers. Here, we present an annotated, chromosome-level genome assembly for the most closely related species, the Adzuki bean borer Ostrinia scapulalis , which feeds on various dicotyledon plants. The previous reference genome assembly for this species was generated from short-read sequencing data, resulting in high fragmentation and low completeness. Combining PacBio long read and Hi-C sequencing, we generated a 476 Mb genome with 48 contigs organised into 31 chromosomes (30 autosomes and one Z sex chromosome), with a contig N50 of 16.1 Mbp and BUSCO completeness exceeding 98%. We further combined published and novel RNA-seq data encompassing multiple life stages, tissues, and sexes to annotate 14,261 gene models, reaching a proteome BUSCO completeness of 95%. This highly contiguous reference genome assembly provides a much-improved resource for carrying comparative genomic approaches and better understanding speciation and host plant adaptation in the Ostrinia genus. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE02-0019

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.

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 S f-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.

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).

Additional file 10: Supplementary Excel Table S5. List of gene target predictions of known miRs of On and Os predicted both by MiRanda and TargetScan on mRNA contigs with 3’UTRs.

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.

We studied the Pleistocene diversification of a relatively endemic Mediterranean insect (Ephippiger diurnus; Orthoptera: Tettigoniidae) to understand how species with restricted range may nonetheless exhibit the complex phylogeography normally associated with broad distribution. A time-calibrated molecular phylogeny based on two mitochondrial genes showed that E. diurnus diverged into two major clades, distinguished largely by male song, before or early during the Pleistocene. Several subclades also diverged before the most recent glacial period. Data from 20 microsatellite loci indicated higher genetic diversity in populations along the Mediterranean coast in France, consistent with the hypothesis that glacial refuges were located there. Isolation by distance' accounts for much genetic differentiation between populations, but some adjacent populations are highly differentiated. A Bayesian approach defined genetically distinct clusters and assigned individuals to their most probable cluster. Clusters corresponded to clades in the phylogenetic tree, and we used cluster assignments to estimate interclade gene flow in areas of potential secondary contact. Gene flow is negligible in potential contact areas in the Pyrenees, but a narrow hybrid zone featuring a steep cline exists on the coast. This hybrid zone suggests that the major clades represent distinct species that diverged within a restricted area during the Pleistocene.

The Crau Plain grasshopper, Prionotropisrhodanica Uvarov, 1923 (Orthoptera: Pamphagidae: Thrinchinae), is a rare grasshopper species endemic to the Crau Plain, a steppic habitat in France with unique floristic and faunistic communities. During recent decades, the area covered by these steppic grasslands has been highly reduced and fragmented due to the development of irrigation-based agriculture, roads, as well as industrial and military complexes. The restricted distribution, low population density and poor dispersal ability of P.rhodanica , combined with the destruction of its habitat, has led to the classification of this species as critically endangered in the IUCN Red List of Threatened Species. Decreases in habitat quality due to intensive grazing in the remnant grassland patches constitute an additional threat for P.rhodanica that can impact population dynamics at a relatively small-scale. In this work, we focused on a small area of about 3 km 2 occupied by one of the largest subpopulations observed in 2000–2001. We conducted a single-time snapshot intensive survey of grasshopper density and genetic variation at 11 microsatellite markers. We used a recent method, MAPI, to visualize the spatial genetic structure as a continuous surface and to determine, with the simultaneous use of spatial cross-correlograms, whether the normalized difference vegetation index, which informs on the balance between vegetation productivity and grazing intensity, can explain grasshopper population structure at such a fine scale. We found that both population density and gene flow were strongly and positively correlated to habitat quality (higher productivity of grasslands and/or lower sheep grazing). The spatial scales of interaction between these variables were estimated to be highly similar, in the range of 812–880 meters. This result suggests that P.rhodanica is very sensitive to the quality of the grasslands it inhabits.

We present a draft genome assembly with a de novo prediction and automated functional annotation of coding genes, and a reference transcriptome of the Adzuki bean borer, Ostrinia scapulalis, based on RNA sequencing of various tissues and developmental stages. The genome assembly spans 419 Mb, has a GC content of 37.4% and includes 26,120 predicted coding genes. The reference transcriptome holds 33,080 unigenes and contains a high proportion of a set of genes conserved in eukaryotes and arthropods, used as quality assessment of the reconstructed transcripts. The new genomic and transcriptomic data presented here significantly enrich the public sequence databases for the Crambidae and Lepidoptera, and represent useful resources for future researches related to the evolution and the adaptation of phytophagous moths. The genome and transcriptome assemblies have been deposited and made accessible via a NCBI BioProject (id PRJNA390510) and the LepidoDB database (http://bipaa.genouest.org/sp/ostrinia_scapulalis/).

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/).

The pine processionary moth Thaumetopoea pityocampa (Lepidoptera: Notodontidae) is the main pine defoliator in the Mediterranean region. Its urticating larvae cause severe human and animal health concerns in the invaded areas. This species shows a high phenotypic variability for various traits, such as phenology, fecundity and tolerance to extreme temperatures. This study presents the construction and analysis of extensive genomic and transcriptomic resources, which are an obligate prerequisite to understand their underlying genetic architecture. Using a well-studied population from Portugal with peculiar phenological characteristics, the karyotype was first determined and a first draft genome of 537Mb total length was assembled into 68,292 scaffolds (N50 = 164kb). From this genome assembly, 29,415 coding genes were predicted. To circumvent some limitations for fine-scale physical mapping of genomic regions of interest, a 3X coverage BAC library was also developed. In particular, 11 BACs from this library were individually sequenced to assess the assembly quality. Additionally, de novo transcriptomic resources were generated from various developmental stages sequenced with HiSeq and MiSeq Illumina technologies. The reads were de novo assembled into 62,376 and 63,175 transcripts, respectively. Then, a robust subset of the genome-predicted coding genes, the de novo transcriptome assemblies and previously published 454/Sanger data were clustered to obtain a high-quality and comprehensive reference transcriptome consisting of 29,701 bona fide unigenes. These sequences covered 99% of the cegma and 88% of the busco highly conserved eukaryotic genes and 84% of the busco arthropod gene set. Moreover, 90% of these transcripts could be localized on the draft genome. The described information is available via a genome annotation portal (http://bipaa.genouest.org/sp/thaumetopoea_pityocampa/).

Background: Most phytophagous insects have morphological, behavioral and physiological adaptations allowing them to specialize on one or a few plant species. Identifying the mechanisms involved in host plant specialization is crucial to understand the role of divergent selection between different environments in species diversification, and to identify sustainable targets for the management of insect pest species. In the present study, we measured larval phenotypic and transcriptomic responses to host plants in two related phytophagous lepidopteran species: the European corn borer (ECB), a worldwide pest of maize, and the adzuki bean borer (ABB), which feeds of various dicotyledons. Our aim was to identify the genes and functions underlying host specialization and/or divergence between ECB and ABB. Results: At the phenotypic level, we observed contrasted patterns of survival, weight gain and developmental time between ECB and ABB, and within ECB and ABB reared on two different host plants. At the transcriptomic level, around 8% of the genes were differentially expressed (DE) between species and/or host plant. 70% of these DE genes displayed a divergent pattern of expression between ECB and ABB, regardless of the host, while the remaining 30% were involved in the plastic response between hosts. We further categorized plastic DE genes according to their parallel or opposite pattern between ECB and ABB to specifically identify candidate genes involved in the species divergence by host specialization. These candidates highlighted a comprehensive response, involving functions related to plant recognition, digestion, detoxification, immunity and development. Last, we detected viral, bacterial, and yeast genes whose incidence contrasted ECB and ABB samples, and maize and mugwort conditions. We suggest that these microorganism communities might influence the survival, metabolism and defense patterns observed in ECB and ABB larvae. Conclusions: The comprehensive approach developed in the present study allowed to identify phenotypic specialization patterns and underlying candidate molecular mechanisms, and highlighted the putative role of microorganisms in the insect-host plant interaction. These findings offer the opportunity to pinpoint specific and sustainable molecular or physiological targets for the regulation of ECB pest populations.

We present here a comprehensive analysis of the transcriptomic response to plant environments in ovipositing females of two sibling species of phytophagous moths affiliated to different host ranges: the European corn borer (ECB) and the adzuki bean borer (ABB). We first assembled and annotated a de novo reference transcriptome based on a high throughput RNA sequencing of females placed in different plant environments, then we measured differences in gene expression between ECB and ABB, and also within each moth species between environments. We further related the differentially expressed (DE) genes to the host preference in ECB and ABB and highlighted the functional categories involved. More specifically, we conducted an analysis on chemosensory genes previously characterized in ECB, ABB and other related Ostrinia species, as these genes are considered as good candidates for the host recognition before oviposition. Overall, we recorded more DE genes in ECB than in ABB samples, what could highlight the higher strength of the host specialization in ECB compared to ABB as observed at the behavioral level. We also noticed that the genes involved in the preference for their respective host were different between ECB and ABB. At the functional level, the response to plant environment in ECB and ABB during oviposition involved many processes, including the chemosensory repertoire as expected, but also metabolism of carbohydrates, lipids, proteins, and amino acids, detoxification mechanisms and immunity. All together, our results allowed identifying genes and functions candidates for specialization and also for the species divergence between ECB and ABB. By ad-hoc categorization, we discriminated some genes responding to the environment with similar or divergent pattern in ECB and ABB. Among them, we highlighted new lines of research like carbohydrates metabolism or virus and retrovirus dynamics.

Background: Divergent selection has been shown to promote speciation in many taxa and especially in phytophagous insects. In the Ostrinia species complex, the European corn borer (ECB) and adzuki bean borer (ABB) are two sibling species specialized to different host plants. The first is a well-known maize pest, whereas the second is a polyphagous species associated with various dicotyledons. Their specialization to host plants is driven by morphological, behavioral and physiological adaptations. In particular, previous studies have shown that ECB and ABB display marked behavior with regard to plant choice during oviposition, involving specific preference and avoidance mechanisms. In this study, our goal was to identify the mechanisms underlying this host-plant specialization in adult females through an analysis of their gene expression. We assembled and annotated a de novo reference transcriptome and measured differences in gene expression between ECB and ABB females, and between environments. We related differentially expressed genes to host preference behavior, and highlighted the functional categories involved. We also conducted a specific analysis of chemosensory genes, which are considered to be good candidates for host recognition before oviposition. Results: We recorded more differentially expressed genes in ECB than in ABB samples, and noticed that the majority of genes potentially involved in the host preference were different between the two species. At the functional level, the response to plant environment in adult females involved many processes, including the metabolism of carbohydrates, lipids, proteins, and amino acids; detoxification mechanisms and immunity; and the chemosensory repertoire (as expected). Until now, most of the olfactory receptors described in Ostrinia spp. had been tested for their putative role in pheromone recognition by males. Here we observed that one specific olfactory receptor was clearly associated with ECB's discrimination between maize and mugwort conditions, highlighting a potential new candidate involved in plant odor discrimination in adult females. Conclusions: Our results are a first step toward the identification of candidate genes and functions involved in chemosensory processes, carbohydrate metabolism, and virus and retrovirus dynamics. These candidates provide new avenues for research into understanding the role of divergent selection between different environments in species diversification.

Host specialization plays a key role in the extreme diversification of phytophagous insects. Whereas proximate mechanisms of specialization have been studied extensively, their consequences for species divergence remain unclear. Preference for, and performance on hosts are thought to be a major source of divergence in phytophagous insects. We assessed these major components of specialization in two moth species, the European corn borer (ECB) and the Adzuki bean borer (ABB), by testing their oviposition behaviour in different conditions (choice or no-choice set-ups) and their performances, by reciprocal transplant at the larval stage on the usual host and an alternative host plant. We demonstrated that both ABB and ECB have a strong preference for their host plants for oviposition, but that relative larval performances on the usual host and an alternative host differed according to the experiment and the trait considered (weight or survival). Finally, we show for the first time that the preference for maize in ECB conceals a strong avoidance of mugwort. The differences in performance, attraction and avoidance between ECB and ABB are discussed in the light of the underlying mechanisms and divergence process.