Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks ( https://github.com/biocorecrg/ExOrthist ).
- Klíčová slova
- Alternative splicing, Intron-exon structures, Orthology, Paralogy,
- MeSH
- alternativní sestřih MeSH
- exony * MeSH
- genom MeSH
- introny MeSH
- konzervovaná sekvence MeSH
- lidé MeSH
- molekulární evoluce * MeSH
- myši MeSH
- software * MeSH
- výpočetní biologie * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood. RESULTS: Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes. CONCLUSIONS: We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.
- Klíčová slova
- Autism spectrum disorder, Bex3, Gene cluster, Genetic novelty, Neurodevelopmental disorders, Placental mammals, Tceal, Transposon domestication, mTOR,
- MeSH
- CRISPR-Cas systémy MeSH
- DNA vazebné proteiny genetika MeSH
- domestikace * MeSH
- fylogeneze MeSH
- jaderné proteiny genetika MeSH
- lidé MeSH
- molekulární evoluce MeSH
- mozek MeSH
- multigenová rodina * MeSH
- myši inbrední C57BL MeSH
- myši knockoutované MeSH
- myši MeSH
- neurovývojové poruchy genetika MeSH
- placenta MeSH
- placentálové genetika MeSH
- poruchy autistického spektra genetika MeSH
- proteiny nervové tkáně genetika MeSH
- proteiny regulující apoptózu genetika MeSH
- těhotenství MeSH
- TOR serin-threoninkinasy genetika MeSH
- transkripční faktory genetika MeSH
- transpozibilní elementy DNA * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- BEX3 protein, human MeSH Prohlížeč
- DNA vazebné proteiny MeSH
- jaderné proteiny MeSH
- Ngfrap1 protein, mouse MeSH Prohlížeč
- proteiny nervové tkáně MeSH
- proteiny regulující apoptózu MeSH
- TCEAL7 protein, human MeSH Prohlížeč
- TOR serin-threoninkinasy MeSH
- transkripční faktory MeSH
- transpozibilní elementy DNA * MeSH
BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. RESULTS: We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. CONCLUSIONS: The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.
- Klíčová slova
- Adaptation, Detoxification, Epigenetics, Evolution, Fish, Gene duplication, Genomics, Innate immunity, Invasive species, Neogobius melanostomus, Olfaction, Osmoregulation, PacBio, Vision,
- MeSH
- genom * MeSH
- ryby genetika fyziologie MeSH
- zavlečené druhy * MeSH
- zvířata MeSH
- zvláštnosti životní historie * MeSH
- Check Tag
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Endogenous retrovirus (ERV) sequences provide a rich source of information about the long-term interactions between retroviruses and their hosts. However, most ERVs are derived from a subset of retrovirus groups, while ERVs derived from certain other groups remain extremely rare. In particular, only a single ERV sequence has been identified that shows evidence of being related to an ancient Deltaretrovirus, despite the large number of vertebrate genome sequences now available. In this report, we identify a second example of an ERV sequence putatively derived from a past deltaretroviral infection, in the genomes of several species of horseshoe bats (Rhinolophidae). This sequence represents a fragment of viral genome derived from a single integration. The time of the integration was estimated to be 11-19 million years ago. This finding, together with the previously identified endogenous Deltaretrovirus in long-fingered bats (Miniopteridae), suggest a close association of bats with ancient deltaretroviruses.
- Klíčová slova
- Deltaretrovirus, bats, endogenous retrovirus, evolution, genomics, retrovirus,
- MeSH
- Chiroptera klasifikace virologie MeSH
- Deltaretrovirus klasifikace genetika MeSH
- endogenní retroviry klasifikace genetika MeSH
- fylogeneze MeSH
- genom genetika MeSH
- genomika MeSH
- koncové repetice genetika MeSH
- molekulární evoluce MeSH
- rekombinace genetická MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
