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Background: Short interspersed nuclear elements (SINEs) are non-autonomous non-LTR retrotransposons widespread across eukaryotes. They exist both as lineage-specific, fast-evolving elements and as ubiquitous superfamilies characterized by highly conserved domains (HCD). Several of these superfamilies have been described in bivalves, however their overall distribution and impact on host genome evolution are still unknown due to the extreme scarcity of transposon libraries for the clade. In this study, we examined more than 40 bivalve genomes to uncover the distribution of HCD-tRNA-related SINEs, discover novel SINE-LINE partnerships, and understand their possible role in shaping bivalve genome evolution. Results: We found that bivalve HCD SINEs have an ancient origin, and they can rely on at least four different LINE clades. According to a "mosaic" evolutionary scenario, multiple LINE partner can promote the amplification of the same HCD SINE superfamilies while homologues LINE-derived tails are present between different superfamilies. Multiple SINEs were found to be highly similar between phylogenetically related species but separated by extremely long evolutionary timescales, up to ~ 400 million years. Studying their genomic distribution in a subset of five species, we observed different patterns of SINE enrichment in various genomic compartments as well as differences in the tendency of SINEs to form tandem-like and palindromic structures also within intronic sequences. Despite these differences, we observed that SINEs, especially older ones, tend to accumulate preferentially within genes, or in their close proximity, consistently with a model of survival bias for less harmful, short non-coding transposons in euchromatic genomic regions. Conclusion: Here we conducted a wide characterization of tRNA-related SINEs in bivalves revealing their taxonomic distribution and LINE partnerships across the clade. Moreover, through the study of their genomic distribution in five species, we highlighted commonalities and differences with other previously studied eukaryotes, thus extending our understanding of SINE evolution across the tree of life. [ABSTRACT FROM AUTHOR]

The olfactory sense is crucial for organisms, facilitating environmental recognition and interindividual communication. Ithomiini butterflies exemplify this importance not only because they rely strongly on olfactory cues for both inter- and intra-sexual behaviors, but also because they show convergent evolution of specialized structures within the antennal lobe, called macroglomerular complexes (MGCs). These structures, widely absent in butterflies, are present in moths where they enable heightened sensitivity to, and integration of, information from various types of pheromones. In this study, we investigate chemosensory evolution across six Ithomiini species and identify possible links between expression profiles and neuroanatomical. To enable this, we sequenced four new high-quality genome assemblies and six sex-specific antennal transcriptomes for three of these species with different MGC morphologies. With extensive genomic analyses, we found that the expression of antennal transcriptomes across species exhibit profound divergence, and identified highly expressed ORs, which we hypothesize may be associated to MGCs, as highly expressed ORs are absent in Methona , an Ithomiini lineage which also lacks MGCs. More broadly, we show how antennal sexual dimorphism is prevalent in both chemosensory genes and non-chemosensory genes, with possible relevance for behavior. As an example, we show how lipid-related genes exhibit consistent sexual dimorphism, potentially linked to lipid transport or host selection. In this study, we investigate the antennal chemosensory adaptations, suggesting a link between genetic diversity, ecological specialization, and sensory perception with the convergent evolution of MCGs. Insights into chemosensory gene evolution, expression patterns, and potential functional implications enhance our knowledge of sensory adaptations and sexual dimorphisms in butterflies, laying the foundation for future investigations into the genetic drivers of insect behavior, adaptation, and speciation. [ABSTRACT FROM AUTHOR]

Background: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences., Results: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries., Conclusions: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms., (© 2024. The Author(s).)