Abstract
Abstract Mutations are the key substrate of evolution and adaptation. Beside single nucleotide mutations, transposable elements (TEs) have been shown to be a major source of both genetic and phenotypic variation in the model organism Drosophila. TEs can be major players of genome plasticity, and their replication and movement can introduce genetic variability that facilitates localadaptation. This is particularly relevant for the tiger mosquito Aedes albopictus, an invasive species whose genome is extremely rich in TEs and which quickly spread under novel environmental conditions in the invaded regions. In this project we intend to fill a major knowledge gap: clarify the relationship between thermal stress and TEs mobility and determine if temperature is a possible effector of genome plasticity and adaptation in Aalb. We will provide better understanding on whether TEs can play a role in fast local adaptation, and therefore in the invasiveness, of these mosquitoes in Italy. This will ultimately allow us to provide a forecast for the long-term evolution of Ae. albopictus in Italy. To reach this goal, by means of genome sequencing and TEs content characterization we will:1) experimentally test the effects of thermals stress on TEs activity in a Ae. albopictus lab-reared population; 2) verify whether Ae. albopictus wild populations sampled along a thermal gradient in Italy show a TE landscape compatible with the mobilisation pattern observed in the lab experiments; 3) compare the TEs content of Ae. albopictus genome with that of closely related Aedes flavopictus and of emerging invasive species Aedes japonicus and Aedes koreicus to understand if TEs can be associated with invasive success. During the sampling stage of point 2, we also plan to engage local schools, involving students in the sampling process and organising dedicated lectures and activities to explain the role of genomics studies in providing better understanding of these invasive pests. This work will have a significant scientific impact in evolutionary biology, because we will provide a better understanding of the adaptive role of genomic plasticity induced by TEs. This project will also have social and public health impacts, because our results will help the development of predictive tools on the adaptive potential of invasive species, including when experiencing climate change-induced stress.
Results achieved
Mosquitoes phylogenomics. Analyzing species phylogenetic relationships is relevant to a proper understanding of TEs evolution and dynamics. We assembled a nucleotide supermatrix from 166 dipteran genomes spanning the main mosquito subfamilies (62 Anophelinae, 11 Culicini, 9 Aedini, 4 other Culicinae) together with a deliberately broad outgroup of 80 taxa drawn from Culicoidea, Chironomidae, Psychodomorpha and Brachycera. For the phylogenomic reconstruction we used two datasets: i) whole mitochondrial genomes and ii) a supermatrix of 3285 nuclear single-copy orthologs identified using the BUSCO Diptera ortholog set. In the maximum likelihood phylogenomic analysis, both mitochondrial and nuclear analyses recover monophyletic Culicidae. Anophelinae is consistently sister to Culicinae with maximal or near-maximal support in both datasets. Within Culicinae, the nuclear matrix supports the monophyly of major tribes and their relative order; the mitochondrial matrix broadly agrees, but shows localized discordances concentrated in fast-evolving, composition-biased sites. Toxorhynchitini sits close to the origin of the Aedini + Culicini assemblage in the nuclear tree but drifts deeper in the mitochondrial tree. By implementing Bayesian molecular relaxed‐clock models, with both fossil and secondary calibrations, we estimated divergence times with high precision, and explicitly tested the hypothesized temporal offset between genomic compartments. The nuclear chronogram places crown Culicidae in the Jurassic–Early Cretaceous, with major Culicinae radiations in the Cretaceous and expansions through the Paleogene. The mitochondrial chronogram dates deeper nodes older; sensitivity runs (taxon/site subsampling, codon-position recoding, composition-aware partitions) narrow but do not eliminate this nuclear–mitochondrial temporal offset. Transposable elements analysis. To get a better characterization and classification of TE families, a comprehensive lineage-specific TE library has been built on eight publicly available high-quality genomes, including Ae. albopictus. As a general indication, 11792 unique TE families consensus sequences were eventually recovered. Concerning the diversity and relative representation, the obtained TE library contains 33% of DNA transposon, 47% of LTR, 16% of LINEs, 2% of SINEs, 1% of Helitron, and 1% of uncharacterized repeats. The next step of TE dynamics analysis included the characterization of the TEs complement in a wider taxonomic dataset. A total of 49 species were eventually selected, including 29 Anophelinae, 12 Culicinae, 1 Chaoborinae, 2 Chironomidae, 2 Psychodidae, as well as 3 non-nematoceran outgroup species, namely Drosophila melanogaster, D. obscura and Glossina morsitans. Every genome was subject to estimation of genome size and to the TEs content analyses. Moreover, obtained data have been plotted on the phylogeny of the group to further detail the picture of the evolution of TEs in mosquitoes. Using the time-calibrated Bayesian phylogeny, we were able to assess the association between genome size and TE contents patterns in a phylogenetic framework, and test relevant evolutionary scenarios. From the obtained data, emerges clearly how Culicinae share a higher TE content with respect not only Anophelinae but also with respect other considered dipteran genomes. Moreover, the results of the analyses revealed that genome size and TE content are strongly correlated, with Aedes and Culex mosquitoes exhibiting the largest genomes (436 Mbp to 1.5 Gbp) and TE loads (40% of the genome on average; 30 to 62% of the genome). Conversely, Anophelinae genomes are generally small (111 to 346 Mbp) and depleted of TEs (0.3% to 25% of the genome). The diversity of TE communities was evaluated within each genome with Shannon’s and Simpson’s diversity indices, whereby TE orders and families were treated as species and their genomic occupancy as abundance. Species with small genome sizes display highly variable levels of TE diversity, whereas species with large genomes consistently exhibit high TE diversity. This suggests that genome expansion in Culicomorpha is determined by the combined proliferation of multiple TE types, rather than a predominant TE order. Finally, to analyze TE mobilization in relation to thermal stress in Ae. albopictus, we reared mosquito families in high temperature conditions. The lab-reared mosquitoes were divided into trios, each consisting of two parents and one offspring from the same family. For each offspring of each family, a dataset containing only the new insertions found in the offspring but not the parents was produced. Our preliminary results, based on the analysis of just one family, show that there are, on average, around a thousand new TE insertions per offspring that were not present in their parents. Under heat stress, TE families belonging to the DNA families seem to move more compared to the control condition, even if there are instances where families move less under heat stress than would be expected in the absence of stress. This suggests an impact on TE dynamics in stressed mosquitoes. We hypothesise that there is a link between TE content dynamics and adaptation. This will be investigated by comparing the TE landscape of different populations in terms of TE content and distribution. As TE mobilisation can be promoted by environmental stress and Ae. albopictus is characterised by a TE-rich genome, populations experiencing high stress may also exhibit increased TE variability. Our preliminary results revealed a similar number of novel insertions in both the northern and southern populations. This suggests that the two sets of populations have equivalent TE dynamics, and that their different climates may not affect the rate of TE mobilisation. While this could indicate specific TE mobilisation propensity, the number of TE insertions characterising and differentiating the Italian populations from the reference genome point to divergent dynamics in the overall Italian TE landscape. The TE variability of south and north Italy populations is largely associated with divergence from the ancestral population (which is expected to be close to the Foshan strain used to generate the reference genome), and that divergence between them is mostly due to neutral dynamics.Dettagli del progetto
Responsabile scientifico: Andrea Luchetti
Strutture Unibo coinvolte:
Dipartimento di Scienze Biologiche, Geologiche e Ambientali
Coordinatore:
Università degli Studi di Trento(Italy)
Contributo totale Unibo: Euro (EUR) 56.720,00
Durata del progetto in mesi: 24
Data di inizio
05/10/2023
Data di fine:
27/02/2026
