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Marc Robinson-Rechavi<p>Registrations open to our <span class="h-card" translate="no"><a href="https://mstdn.science/@SIB" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>SIB</span></a></span> course for PhD students in Lausanne 🇨🇭 with <span class="h-card" translate="no"><a href="https://ecoevo.social/@rmwaterhouse" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rmwaterhouse</span></a></span> and <span class="h-card" translate="no"><a href="https://mstdn.science/@dessimoz" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>dessimoz</span></a></span> :<br>Biodiversity bioinformatics: from large-scale phylogenomics to gene families and functions<br>with <span class="h-card" translate="no"><a href="https://genomic.social/@bgeedb" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>bgeedb</span></a></span>, OMA and BUSCO inside<br><a href="https://www.sib.swiss/training/course/20240828_COMGE" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">sib.swiss/training/course/2024</span><span class="invisible">0828_COMGE</span></a> <a href="https://ecoevo.social/tags/BiodiversityGenomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BiodiversityGenomics</span></a> <a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/ortholog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ortholog</span></a> <a href="https://ecoevo.social/tags/paralog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paralog</span></a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a></p>
Marc Robinson-Rechavi<p>We posted this cool preprint between Xmas and new year, now time for a thread about the results: Begum et al "Phylogenetic modeling provides evidence for sudden shifts in expression after small-scale duplication in vertebrates and strong support for the ortholog conjecture"<br><a href="https://www.biorxiv.org/content/10.1101/2023.12.29.571877v1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.12.29.571877v1</span></a><br><a href="https://ecoevo.social/tags/paralog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paralog</span></a> <a href="https://ecoevo.social/tags/ortholog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ortholog</span></a> <a href="https://ecoevo.social/tags/GeneDuplication" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GeneDuplication</span></a> <a href="https://ecoevo.social/tags/GenomeDuplication" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GenomeDuplication</span></a> <a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/phylogeny" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>phylogeny</span></a> <a href="https://ecoevo.social/tags/ohnolog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ohnolog</span></a></p>
Marc Robinson-Rechavi<p>E Lau shows very nicely how bioluminescence in ostracods, fireflies and sea pansies can use very different structures yet convergently recruited homologous enzymes. The number of functional genes varies according to lineage-specific duplications. <a href="https://www.biorxiv.org/content/10.1101/2023.04.12.536614v1.abstract" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">biorxiv.org/content/10.1101/20</span><span class="invisible">23.04.12.536614v1.abstract</span></a> <a href="https://ecoevo.social/tags/SMBE2023" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SMBE2023</span></a> <a href="https://ecoevo.social/tags/ConvergentEvolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ConvergentEvolution</span></a> <a href="https://ecoevo.social/tags/paralog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paralog</span></a> <a href="https://ecoevo.social/tags/bioluminescence" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioluminescence</span></a></p>
Marc Robinson-Rechavi<p>Marjorie Liénard: method to express invertebrate opsin proteins in vitro, allowing to show spectral shifts in opsins in butterflies, with notably 2 paralogs of LW providing differentiation in function between the dorsal and ventral parts of the eye <a href="https://www.pnas.org/doi/abs/10.1073/pnas.2008986118" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">pnas.org/doi/abs/10.1073/pnas.</span><span class="invisible">2008986118</span></a> <a href="https://ecoevo.social/tags/SMBE2023" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SMBE2023</span></a> <a href="https://ecoevo.social/tags/opsin" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>opsin</span></a> <a href="https://ecoevo.social/tags/GeneDuplication" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GeneDuplication</span></a> <a href="https://ecoevo.social/tags/paralog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paralog</span></a></p>
Marc Robinson-Rechavi<p>Announcing <a href="https://ecoevo.social/tags/SIB" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SIB</span></a> Comparative genomics course, taught by Christophe Dessimoz, Natasha Glover, <span class="h-card"><a href="https://ecoevo.social/@rmwaterhouse" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rmwaterhouse</span></a></span> and myself, 30 August - 01 September in Lausanne <a href="https://ecoevo.social/tags/UNIL" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>UNIL</span></a> <br>• Introduction to molecular evolution &amp; phylogenetics<br>• Orthology-focused arthropod comparative genomics<br>• Duplication of genes and genomes, expression<br>with <a href="https://ecoevo.social/tags/SIB" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SIB</span></a> resources <a href="https://ecoevo.social/tags/OMA" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OMA</span></a>, <a href="https://ecoevo.social/tags/Orthodb" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Orthodb</span></a> <a href="https://ecoevo.social/tags/BUSCO" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BUSCO</span></a> and <span class="h-card"><a href="https://genomic.social/@bgeedb" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>bgeedb</span></a></span> <a href="https://ecoevo.social/tags/ortholog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ortholog</span></a> <a href="https://ecoevo.social/tags/orthologs" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>orthologs</span></a> <a href="https://ecoevo.social/tags/paralog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paralog</span></a> <a href="https://ecoevo.social/tags/duplication" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>duplication</span></a> <a href="https://ecoevo.social/tags/MolecularEvolution" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>MolecularEvolution</span></a> <a href="https://ecoevo.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Genomics</span></a> <a href="https://ecoevo.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://ecoevo.social/tags/training" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>training</span></a> <span class="h-card"><a href="https://mastodon.social/@P_Palagi" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>P_Palagi</span></a></span> <a href="https://www.sib.swiss/training/course/20230830_COMGE" rel="nofollow noopener" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">sib.swiss/training/course/2023</span><span class="invisible">0830_COMGE</span></a></p>
Marc Robinson-Rechavi<p>Now published in its final form: Parallel evolution of amphioxus and vertebrate small-scale gene duplications by Brasó-Vives et al<br><a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02808-6" rel="nofollow noopener" target="_blank"><span class="invisible">https://</span><span class="ellipsis">genomebiology.biomedcentral.co</span><span class="invisible">m/articles/10.1186/s13059-022-02808-6</span></a><br><a href="https://ecoevo.social/tags/EvoDevo" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EvoDevo</span></a> <a href="https://ecoevo.social/tags/EvolutionaryBiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>EvolutionaryBiology</span></a> <a href="https://ecoevo.social/tags/Genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Genomics</span></a> <a href="https://ecoevo.social/tags/Amphioxus" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Amphioxus</span></a> <a href="https://ecoevo.social/tags/Chordate" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Chordate</span></a> <a href="https://ecoevo.social/tags/ortholog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ortholog</span></a> <a href="https://ecoevo.social/tags/paralog" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>paralog</span></a> <a href="https://ecoevo.social/tags/GeneDuplication" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>GeneDuplication</span></a></p>