Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths

Genetics of flight in spongy moths (Lymantria dispar ssp.): functionally integrated profiling of a complex invasive trait

BACKGROUND

Flight can drastically enhance dispersal capacity and is a key trait defining the potential of exotic insect species to spread and invade new habitats. The phytophagous European spongy moths (ESM, Lymantria dispar dispar) and Asian spongy moths (ASM; a multi-species group represented here by L. d. asiatica and L. d. japonica), are globally invasive species that vary in adult female flight capability-female ASM are typically flight capable, whereas female ESM are typically flightless. Genetic markers of flight capability would supply a powerful tool for flight profiling of these species at any intercepted life stage. To assess the functional complexity of spongy moth flight and to identify potential markers of flight capability, we used multiple genetic approaches aimed at capturing complementary signals of putative flight-relevant genetic divergence between ESM and ASM: reduced representation genome-wide association studies, whole genome sequence comparisons, and developmental transcriptomics. We then judged the candidacy of flight-associated genes through functional analyses aimed at addressing the proximate demands of flight and salient features of the ecological context of spongy moth flight evolution.

RESULTS

Candidate gene sets were typically non-overlapping across different genetic approaches, with only nine gene annotations shared between any pair of approaches. We detected an array of flight-relevant functional themes across gene sets that collectively suggest divergence in flight capability between European and Asian spongy moth lineages has coincided with evolutionary differentiation in multiple aspects of flight development, execution, and surrounding life history. Overall, our results indicate that spongy moth flight evolution has shaped or been influenced by a large and functionally broad network of traits.

CONCLUSIONS

Our study identified a suite of flight-associated genes in spongy moths suited to exploration of the genetic architecture and evolution of flight, or validation for flight profiling purposes. This work illustrates how complementary genetic approaches combined with phenotypically targeted functional analyses can help to characterize genetically complex traits.

Analyses of adult transcriptomes from four different populations of the spongy moth, Lymantria dispar L., from China and the USA

The spongy moth Lymantria dispar, formerly known as the gypsy moth, is a forest pest that occurs as two different biotypes: the European spongy moth (ESM), Lymantria dispar dispar, which is distributed in Europe and North America; and the Asian spongy moth (ASM), which consists of subspecies Lymantria dispar asiatica and Lymantria dispar japonica and is distributed in China, Russia, Korea, and Japan. The Asian biotype is classified as a quarantine pest by the U.S. Department of Agriculture because of the superior flight ability of adult females compared to females of the European biotype. To identify genes that potentially account for differences in female flight capability between the two biotypes, we assembled and compared transcriptional profiles of two North American populations of ESM and two Chinese populations of ASM, including samples of unmated female adults and females after mating and oviposition. Of 129,286 unigenes identified, 306 were up-regulated in ASM samples relative to ESM, including genes involved in egg production. In contrast, 2309 unigenes were down-regulated in ASM samples, including genes involved in energy production. Although a previous study found that ASM female flight was reduced after oviposition, a comparison of gene expression before and after mating and oviposition did not reveal any genes which were consistently up- or down-regulated in the two ASM populations.

Transposons and Non-coding Regions Drive the Intrafamily Differences of Genome Size in Insects

Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein–Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution.

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The most comprehensive variation pattern of insects genome size (GS) to date

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GS evolution of the Insecta was reflected by the adaptive Ornstein–Uhlenbeck model

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Ancestral state of insect GS was estimated to be ∼1 Gb

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Intrafamily GS variations were driven by recent transpositions and non-coding regions

Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

The bitter taste, triggered via gustatory receptors, serves as an important natural defense against the ingestion of poisonous foods in animals, and the increased host breadth is usually linked to an increase in the number of gustatory receptor genes. This has been especially observed in polyphagous insect species, such as noctuid species from the Spodoptera genus. However, the dynamic and physical mechanisms leading to these gene expansions and the evolutionary pressures behind them remain elusive. Among major drivers of genome dynamics are the transposable elements but, surprisingly, their potential role in insect gustatory receptor expansion has not been considered yet. In this work, we hypothesized that transposable elements and possibly positive selection would be involved in the highly dynamic evolution of gustatory receptor in Spodoptera spp. We first sequenced de novo the full 465 Mb genome of S. littoralis, and manually annotated the main chemosensory genes, including a large repertoire of 373 gustatory receptor genes (including 19 pseudogenes). We also improved the completeness of S. frugiperda and S. litura gustatory receptor gene repertoires. Then, we annotated transposable elements and revealed that a particular category of class I retrotransposons, the SINE transposons, was significantly enriched in the vicinity of gustatory receptor gene clusters, suggesting a transposon-mediated mechanism for the formation of these clusters. Selection pressure analyses indicated that positive selection within the gustatory receptor gene family is cryptic, only 7 receptors being identified as positively selected. Altogether, our data provide a new good quality Spodoptera genome, pinpoint interesting gustatory receptor candidates for further functional studies and bring valuable genomic information on the mechanisms of gustatory receptor expansions in polyphagous insect species.

The Spruce Budworm Genome: Reconstructing the Evolutionary History of Antifreeze Proteins

Insects have developed various adaptations to survive harsh winter conditions. Among freeze-intolerant species, some produce "antifreeze proteins" (AFPs) that bind to nascent ice crystals and inhibit further ice growth. Such is the case of the spruce budworm, Choristoneura fumiferana (Lepidoptera: Tortricidae), a destructive North American conifer pest that can withstand temperatures below -30°C. Despite the potential importance of AFPs in the adaptive diversification of Choristoneura, genomic tools to explore their origins have until now been limited. Here we present a chromosome-scale genome assembly for C. fumiferana, which we used to conduct comparative genomic analyses aimed at reconstructing the evolutionary history of tortricid AFPs. The budworm genome features 16 genes homologous to previously reported C. fumiferana AFPs (CfAFPs), 15 of which map to a single region on chromosome 18. Fourteen of these were also detected in five congeneric species, indicating Choristoneura AFP diversification occurred before the speciation event that led to C. fumiferana. Although budworm AFPs were previously considered unique to the genus Choristoneura, a search for homologs targeting recently sequenced tortricid genomes identified seven CfAFP-like genes in the distantly related Notocelia uddmanniana. High structural similarity between Notocelia and Choristoneura AFPs suggests a common origin, despite the absence of homologs in three related tortricids. Interestingly, one Notocelia AFP formed the C-terminus of a "zonadhesin-like" protein, possibly representing the ancestral condition from which tortricid AFPs evolved. Future work should clarify the evolutionary path of AFPs between Notocelia and Choristoneura and assess the role of the "zonadhesin-like" protein as precursor of tortricid AFPs.

Sequencing, Assembly and Annotation of the Whole-Insect Genome of Lymantria dispar dispar, the European Gypsy Moth

The European gypsy moth, Lymantria dispar dispar (LDD), is an invasive insect and a threat to urban trees, forests and forest-related industries in North America. For use as a comparator with a previously published genome based on the LD652 pupal ovary-derived cell line, as well as whole-insect genome sequences obtained from the Asian gypsy moth subspecies L. dispar asiatica and L. dispar japonica, the whole-insect LDD genome was sequenced, assembled and annotated. The resulting assembly was 998 Mb in size, with a contig N50 of 662 Kb and GC content of 38.8%. Long interspersed nuclear elements (LINEs) constitute 25.4% of the whole-insect genome, and a total of 11,901 genes predicted by automated gene finding encoded proteins exhibiting homology with reference sequences in the NCBI NR and/or UniProtKB databases at the most stringent similarity cutoff level (i.e., the gold tier). These results will be especially useful in developing a better understanding of the biology and population genetics of L. dispar and the genetic features underlying Lepidoptera in general.

Potential Differences and Methods of Determining Gypsy Moth Female Flight Capabilities: Implications for the Establishment and Spread in Novel Habitats

The introduction of the Asian gypsy moth into novel environments continues with frequent interceptions in North America. There is a concern that these subspecies will pose a greater threat to the forests and urban environments of North America than the established gypsy moths (Lymantria dispardispar L.), due to their greater capacity for female flight. Asian gypsy moth populations vary in many key traits, including female flight capabilities. The potential impacts of female flight, in combination with the other key traits, on the ecology and spread of this insect are first discussed in this communication. This also provides the first review of most of the current literature on the variations in flight capability and flight distance of gypsy moth populations, as well as variation in other traits of concern and the potential methods of identification, with special attention paid to the Asian subspecies Lymantria dispar japonica Motschulsky and Lymantria dispar asiatica Vinkovskij. There are currently good tools for identifying the general origin of introduced gypsy moth populations, but these do not provide enough information to effectively manage introductions. Gypsy moth key traits differ among populations, even within each subspecies of the gypsy moth, so introduction of gypsy moths from other world areas into locations where the gypsy moth is already present could result in unwanted changes in gypsy moth biology. It also appears that the introduction of flight-capable females could enhance a population’s dispersal capability and require modifications to management protocols used for flightless females. Therefore, rapid tools to assess key traits in introduced populations are needed to adequately plan for, or deal with, new introductions into novel habitats.