Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins

DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5' region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects' DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1

A soil fungus confers plant resistance against a phytophagous insect by disrupting the symbiotic role of its gut microbiota

Plants generate energy flows through natural food webs, driven by competition for resources among organisms, which are part of a complex network of multitrophic interactions. Here, we demonstrate that the interaction between tomato plants and a phytophagous insect is driven by a hidden interplay between their respective microbiotas. Tomato plants colonized by the soil fungus Trichoderma afroharzianum, a beneficial microorganism widely used in agriculture as a biocontrol agent, negatively affects the development and survival of the lepidopteran pest Spodoptera littoralis by altering the larval gut microbiota and its nutritional support to the host. Indeed, experiments aimed to restore the functional microbial community in the gut allow a complete rescue. Our results shed light on a novel role played by a soil microorganism in the modulation of plant-insect interaction, setting the stage for a more comprehensive analysis of the impact that biocontrol agents may have on ecological sustainability of agricultural systems

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

Molecular Systematics and Traits Evolution in Phasmatodea Leach, 1815 (Hexapoda; Insecta)

Phasmatodea Leach, 1815 (Hexapoda; Insecta) is a polyneopteran order which counts approximately 3000 described species, often known for their remarkable forms of mimicry. In this thesis, I provide a comprehensive systematic framework which includes over 180 species never considered in a phylogenetic framework: the latter can facilitate a better understanding of the processes underlying phasmids evolutionary history. The clade represents in fact an incredible testing ground to study trait evolution and its striking disparity of reproductive strategies and wing morphologies have been of great interest to the evolutionary biology community. Phasmids wings represent one of the first and most notable rejection of Dollo’s law and they played a central role in initiating a long- standing debate on the irreversibility of complex traits loss. Macroevolutionary analyses presented here confirm that wings evolution in phasmids is a reversible process even when possible biases - such as systematic uncertainty and trait-dependent diversification rates - are considered. These findings remark how complex traits can evolve in a dynamic, reversible manner and imply that their molecular groundplan can be preserved despite its phenotypical absence. This concept has been further tested with phylogenetic and transcriptomic approaches in two phasmids parthenogenetic lineages and a bisexual congeneric of the European Bacillus species complex. Leveraging a gene co-expression network approach, male gonad associated genes were retrieved in the bisexual species and then their modifications in the parthenogens were charachterized. Pleiotropy appears to constrain gene modifications associated to male reproductive structures after their loss in parthenogens, so that the lost trait molecular groundplan can be largely preserved in both transcription patterns and sequence evolution. Overall, the results presented in this thesis contribute to shape our understanding of the interplay between the phenotypic and molecular levels in trait evolution

Wood feeding and social living: draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae)

Termites (Insecta, Blattodea, Termitoidae) are a widespread and diverse group of eusocial insects known for their ability to digest wood matter. Herein, we report the draft genome of the subterranean termite Reticulitermes lucifugus, an economically important species and among the most studied taxa with respect to eusocial organization and mating system. The final assembly (~813 Mb) covered up to 88% of the estimated genome size and, in agreement with the Asexual Queen Succession Mating System, it was found completely homozygous. We predicted 16,349 highly supported gene models and 42% of repetitive DNA content. Transposable elements of R. lucifugus show similar evolutionary dynamics compared to that of other termites, with two main peaks of activity localized at 25% and 8% of Kimura divergence driven by DNA, LINE and SINE elements. Gene family turnover analyses identified multiple instances of gene duplication associated with R. lucifugus diversification, with significant lineage-specific gene family expansions related to development, perception and nutrient metabolism pathways. Finally, we analysed P450 and odourant receptor gene repertoires in detail, highlighting the large diversity and dynamical evolutionary history of these proteins in the R. lucifugus genome. This newly assembled genome will provide a valuable resource for further understanding the molecular basis of termites biology as well as for pest contro

Endophytic development of the entomopathogen Beauveria bassiana reduces the immunocompetence of Spodoptera littoralis larvae

Beneficial microorganisms can promote plant growth and defence barriers, offering a valuable alternative to synthetic agrochemicals. Beauveria bassiana is one of the most important entomopathogenic fungi that can colonize a wide variety of plant species as an endophyte, limiting the growth and survival of plant pests and pathogens. Here we contribute to this research topic by studying the effect of tomato plants colonization by B. bassiana on the survival, development, and immunity of Spodoptera littoralis (Lepidoptera, Noctuidae). Endophytic colonization of plants did not affect the survival of larvae feeding on them, which showed a weight increase associated with a higher pupal mortality. Interestingly, encapsulation and nodulation responses of larvae fed with B. bassiana colonized plants were reduced, while, in contrast, phagocytosis slightly increased. These larvae proved to be more sensitive to B. bassiana or Bacillus thuringiensis infection, given their reduced immune competence. “Omic” studies are currently being performed to unravel the molecular mechanism underlying these changes. Our results shed new light on the complex network of multitrophic interactions which underlie the evolution of entomopathogenic lifestyle in soil fungi. KE

Un fungo del genere Trichoderma conferisce resistenza al pomodoro nei confronti delle larve di Spodoptera littoralis alterando il ruolo simbiotico del loro microbiota intestinale

I funghi benefici del genere Trichoderma sono importanti agenti di biocontrollo di patogeni e promuovono la crescita delle piante. In questo lavoro si dimostra che l’interazione tra la pianta di pomodoro e la larva del lepidottero Spodoptera littoralis (Lepidoptera, Noctuidae) viene modulata dal loro microbiota. In particolare, viene descritto il meccanismo grazie al quale la colonizzazione radicale da parte del ceppo T22 di Trichoderma afroharzianum è in grado di conferire alla pianta resistenza nei confronti dell’insetto fitofago. Le larve alimentate con piante di pomodoro colonizzate da T22 mostrano una significativa riduzione della crescita, un marcato ritardo nello sviluppo e una elevata mortalità rispetto ai controlli. Per comprendere le basi funzionali delle alterazioni fenotipiche osservate nelle larve di S. littoralis, che potrebbero essere determinate da una ridotta funzionalità intestinale del fitogafo causata dall’induzione fungina delle barriere di difesa della pianta, sono state valutate le possibili alterazioni strutturali e funzionali di questo organo e del microbiota ad esso associato tramite un approccio morfologico, fisiologico e molecolare. I cambiamenti indotti nella pianta di pomodoro da T. afroharzianum non provocano alcun danno strutturale all’intestino medio delle larve di S. littoralis e/o alterazioni della capacità digestiva, ma determinano una severa disbiosi intestinale. Composizione e funzionalità del microbiota risultano significativamente alterate e questo determina un ridotto supporto nutrizionale con conseguente impatto negativo sullo sviluppo e sulla sopravvivenza del fitofago. Questi effetti possono essere completamente eliminati con la somministrazione orale del microbiota intestinale delle larve controllo o del batterio Enterococcus casseliflavus, il simbionte responsabile della maggior parte dei cambiamenti trascrizionali osservati a carico del microbiota. I risultati ottenuti permettono di fare luce sul meccanismo con il quale un microrganismo del suolo è in grado di regolare l’interazione tra un fitofago e una pianta. La comprensione di questa modulazione, guidata dalla competizione tra organismi per le risorse trofiche, pone le basi per lo sviluppo di nuove strategie per valutare l’impatto ecologico degli agenti di biocontrollo, e quindi per una gestione sostenibile degli agroecosistemi

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects