Biology subjects

Burguera, D.

Publications and source records attributed to Burguera, D..

7 recordsLinked to original sources

bioRxiv2026

Synchronised developmental partitioning of visual opsins across parental subgenomes in allopolyploid Barbus barbus

Hybridisation and whole-genome duplication generate evolutionary novelty by combining and duplicating divergent parental genomes. Yet, how organisms differentially deploy duplicated gene repertoires across development remains poorly understood. The vertebrate visual system provides an excellent model for addressing this question because colour vision depends on the tightly regulated expression of opsin genes, which often undergo pronounced ontogenetic changes. Here, using comparative transcriptomics, we show that the allopolyploid common barbel (Barbus barbus) has evolved coordinated developmental partitioning of duplicated cone opsin genes. During ontogeny, the short-wavelength-sensitive opsins SWS1 and SWS2 switch expression between parental-subgenome ohnologs, while the middle-wavelength-sensitive RH2 switches between tandem paralogs, with all three transitions being synchronised. In contrast, the long-wavelength-sensitive LWS ohnologs from both parental genomes remain co-expressed throughout development. Single-nucleus RNA sequencing further revealed a strongly rod-dominated retina and largely conserved expression of phototransduction genes across recent ohnologs. The retention of all 14 visual opsin genes and their differential developmental deployment in common barbel highlights the value of independently evolved allopolyploid lineages for investigating the evolutionary consequences of genome duplication. More broadly, our findings show how hybridisation and genome duplication can enable divergent expression of parental gene copies, potentially contributing to sensory adaptation over evolutionary timescales.

evolutionary biology↗

bioRxiv2026

Rapid evolution of cone identity and retinal topography in deep-water crater lake cichlids

Deep-water habitats have been colonized repeatedly by fishes, driving the evolution of visual systems under extremely low-light conditions. Here, we investigated visual adaptation in cichlids from the Barombi Mbo crater lake by comparing shallow- and deep-water species using retinal single-cell transcriptomics and analyses of retinal specializations. The shallow-water species Pungu maclareni expressed a broader repertoire of visual opsins across distinct populations of short- (SWS), medium- (RH2), and long-wavelength-sensitive (LWS) cone photoreceptors. In contrast, the deep-water species Myaka myaka lacked a distinct LWS cone population and instead relied predominantly on RH2A/{beta}-expressing, green-sensitive photoreceptors. To assess whether these deep-water RH2 cones corresponded to canonical RH2 or LWS programmes, we compared conserved photoreceptor markers. Deep-water RH2 cones retained elements of both RH2- and LWS-associated transcriptional programmes, revealing a mixed profile lacking a clear canonical cone-type signature. LWS-associated transcriptional regulators also differed between species, with tbx2a absent from M. myaka cones, consistent with the loss of LWS opsin expression, whereas thrb persisted in M. myaka RH2 cones. We further examined retinal specialization across eight species from the radiation and found that retinal topography also differed in photoreceptor distributions and ganglion cell-based acuity centers in association with habitat depth but also with trophic ecology of the species. Together, our findings show that visual adaptation in a young adaptive radiation involves coordinated changes in visual opsin expression, cone-associated transcriptional programmes, and retinal organization, highlighting how sensory systems can quickly evolve through changes at multiple biological levels in response to ecological conditions.

evolutionary biology↗

bioRxiv2022

Expanded olfactory system in fishes capable of terrestrial exploration

Smell abilities differ greatly among vertebrate species, as reflected by the exceptional size variability of gene families and brain regions involved in odour detection. However, key environmental factors shaping the molecular and phenotypic evolution of the olfactory sensory system remain mostly unknown. Here, we investigate the association between diverse ecological traits and the number of olfactory chemoreceptors in the genomes of more than two hundred ray-finned fishes. We found independent expansions producing large gene repertoires in nocturnal amphibious fishes, generally able to perform active terrestrial exploration. Furthermore, we reinforced this finding with an additional analysis of a clariid species (Channallabes apus), a fish lineage with chemosensory-based aerial orientation. Importantly, we also detected an augmented information-processing capacity in the olfactory bulb of examined nocturnal amphibious species. Overall, we report a convergent magnification of the olfactory system in amphibious fishes potentially enhancing terrestrial orientation, revealing the likelihood of an analogous event in tetrapod ancestors during the water-to-land transition.

evolutionary biology↗

bioRxiv2022

Pervasive evolution of tissue-specificity of ancestral genes differentially shaped vertebrates and insects

Regulation of gene expression is arguably the main mechanism contributing to tissue phenotypic diversity within and between species. Here, we assembled an extensive transcriptomic dataset covering twenty bilaterian species and eight tissues, selecting a specular phylogeny that allowed both the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes. Such pervasive evolution of tissue-specificity was linked to gene duplication coupled with specialization, including an unappreciated prolonged effect of whole genome duplications during recent vertebrate evolution.

genomics↗

bioRxiv2021

The X-linked splicing regulator MBNL3 has been co-opted to restrict placental growth in eutherians

The eutherian placenta is a major site for parental genetic conflict. Here, we identify the X-linked Mbnl3 gene as a novel player in this dispute. Mbnl3 belongs to an RNA binding protein family whose members regulate alternative splicing and other aspects of RNA metabolism in association with cellular differentiation. We find that, in eutherians, Mbnl3 has become specifically expressed in placenta and has undergone accelerated sequence evolution leading to changes in its RNA binding specificities. Although its molecular roles are partly redundant with those of Mbnl2, Mbnl3 has also acquired novel biological functions. In particular, whereas Mbnl2;Mbnl3 double knockout mice display severe placental maturation defects leading to strong histological and functional abnormalities, Mbnl3 knockout alone results in increased placental growth and favors placental and fetal resource allocation during limiting conditions.

evolutionary biology↗

bioRxiv2021

ExOrthist: a tool to infer exon orthologies at any evolutionary distance

Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes among species. However, no existing tool allows the detection of orthologous/paralogous exons. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling to (i) infer exon homologs and orthogroups, (ii) visualize evolution of exon-intron structures, and (iii) assess conservation of alternative splicing patterns. ExOrthist not only evaluates exon sequence conservation but also considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in various evolutionary scenarios, from whole genome duplication to convergence of alternative splicing networks.

genomics↗

bioRxiv2019

Evolved for success in novel environments: the round goby genome

Since the beginning of global trade, hundreds of species have colonized territories outside of their native range. Some of these species proliferate at the expense of native ecosystems, i.e., have become invasive. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales. They also present promising case studies for ecological and evolutionary success in novel environments.\n\nWe seize this unique opportunity to study genomic substrates for ecological success and adaptability to novel environments in a vertebrate. We report a highly contiguous long-read based genome assembly for the most successful temperate invasive fish, the benthic round goby (Neogobius melanostomus), and analyse gene families that may promote its impressive ecological success.\n\nOur approach provides 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 in epigenetic regulators, and the presence of genes that may have contributed to the round gobys capacity to invade cold and salty waters.\n\nA recurring theme across all analyzed gene families are gene expansions. This suggests that gene duplications may promote ecological flexibility, superior performance in novel environments, and underlie the impressive colonization success of the round goby. Gobiidae generally feature fascinating adaptations and are excellent colonizers. Further long-read genome approaches across the goby family may reveal whether the ability to conquer new habitats relates more generally to gene copy number expansions.

ecology↗