A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest

Ecological networks to unravel the routes to horizontal transposon transfers

Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs

The Repetitive Content in Lupin Genomes

International audienceIn this chapter, we present the first detailed evaluation of the repetitive compartment in Lupinus genomes. Low-depth next-generation sequencing (NGS) genomic resources from four closely related smooth-seeded Mediterranean lupin species (L. albus, L. angustifolius, L. luteus, and L. micranthus), exhibiting remarkable differences in genome size and chromosome number have been investigated. The repetitive compartment is composed of a wide diversity of repeats and represents 23¿51% of the genomes. This compartment is essentially comprised of transposable elements (43¿85%), mainly represented by copia and gypsy LTR retrotransposon families. Among the latter, some prominent families (Tekay, Athila, Maximus-SIRE) significantly contribute to genome size differences among species and in shaping different species-specific repeat profiles, regardless of their chromosome numbers. Also particular lineages of these elements have been differentially and recently amplified within species, such as in L. luteus, L. albus, and L. angustifolius. Moreover, this study highlighted the diversity of tandem repeats in lupin genomes,with minisatellites and satellites mostly being species-specific, whereas microsatellites (SSRs) are ubiquitously distributed. Strikingly, L. angustifolius exhibited a tremendous amount of tandem repeats in its genome (26%), including a noteworthy accumulation of one particular hexamer SSR (15.24%of the genome),which demonstrate that also tandem repeatsmay greatly contribute to genomeobesity and dynamics in lupins. Therefore, differential lineage-specific amplifications of retrotransposons and tandem repeats occurred among lupins. Accordingly, this strongly suggests that different processes and mechanisms regulating amplification, proliferation, and clearance of repeats have differentially operated within the same genusamong closely relatedMediterranean species over the last *10¿12 Myr. Further extension of such evaluation to various representatives of the lupins diversity and outgroups will provide a better overview of the repetitive compartment and its evolutionary dynamics in the genus. Additionally, the genomic resources generated by this work represent a valuable basis to start building a repeats database specifically dedicated to best understand the genomic landscape, repeats distribution, and localization in lupins. This will facilitate further investigations on the functional and evolutionary impact of repeats on genes of interest, such as those responsive for important agronomical, adaptive, and defense features

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

Background: The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. Results: We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. Conclusions: The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation