Biology subjects

Gonzalez-Pech, R. A.

Publications and source records attributed to Gonzalez-Pech, R. A..

8 recordsLinked to original sources

bioRxiv2026

Maintenance cost of photosynthesis sets key ecological constraints on zooxanthellate corals

Ecological models using light limitation to explain coral depth distribution have largely disregarded the energetic cost of sustaining photosynthetic activity. Here, we quantified photosystem II (PSII) turnover across a depth-simulated light gradient in a zooxanthellate coral, measuring PSII half-life, D1 protein abundance, and PSII-complex gene expression. Maximum photosynthetic capacity remained stable across irradiance levels while respiration rose and PSII turnover accelerated as a power law, imposing increasing ATP demand at the shallowest depths. Declining D1 protein abundance alongside stable transcript levels demonstrated that this escalating maintenance cost operates through post-transcriptional regulation. Consequently, a decreasing fraction of photosynthetic usable energy is available for translocation to the coral host at high irradiance, as the energy required for PSII repair increases. Integrating these physiological constraints into a bio-optical model revealed that the balance between photosynthetic capacity and its maintenance cost defines an optimal depth, the Photosynthetic Usable Energy Supply (PUES) maximum, where host energetic returns are maximized. This framework provides a mechanistic basis for understanding depth distributions in symbiotic corals and extends as a predictive tool for any photosynthetic organism operating under variable irradiance, including forecasting how environmental degradation contracts viable depth ranges.

ecology↗

bioRxiv2024

The Potential of CCA-associated Bacteria to Fight Antimicrobial-Resistant Pathogens: a Genomic Survey

The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from the CCA Hydrolithon boergesenii. After running antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 100 putative Biosynthetic Gene Clusters (BGCs) across the three genomes. Further analysis uncovered BGCs potentially involved in the biosynthesis of novel antimicrobial compounds. Our study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis and highlights the potential of specialized marine environments like CCA biofilms.

genomics↗

bioRxiv2024

A paleogenomic approach to reconstruct historical responses of coral reefs to anthropogenic change

Coral reefs are declining worldwide due to anthropogenic environmental change. The foundation and health of these ecosystems rely on the harmonious functioning of all members of coral holobionts, i.e., cnidarian host, symbiotic microalgae, and associated microbiome. Coral stress responses often involve shifts in the taxonomic identity of their symbionts and microbiomes. Tracing back changes in coral holobiont composition over prolonged time periods can help us reconstruct health history of reefs and gain a better understanding of coral response to current stressors. Here, we focused on a major Caribbean reef-builder coral, Orbicella faveolata, from Varadero Reef, Colombia. This reef has undergone extensive freshwater sediment discharge and pollution for decades as result of urbanization. We show, for the first time, that paleogenomic and paleoclimatic approaches can be combined to reconstruct historical coral holobiont dynamics potentially associated with anthropogenic disturbances.

molecular biology↗

bioRxiv2019

Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

Dinoflagellates of the family Symbiodiniaceae (Order Suessiales) are predominantly symbiotic, and many are known for their association with corals. The genetic and functional diversity among Symbiodiniaceae is well acknowledged, but the genome-wide sequence divergence among these lineages remains little known. Here, we present de novo genome assemblies of five isolates from the basal genus Symbiodinium, encompassing distinct ecological niches. Incorporating existing data from Symbiodiniaceae and other Suessiales (15 genome datasets in total), we investigated genome features that are common or unique to these Symbiodiniaceae, to genus Symbiodinium, and to the individual species S. microadriaticum and S. tridacnidorum. Our whole-genome comparisons reveal extensive sequence divergence, with no sequence regions common to all 15. Based on similarity of k-mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. We observed extensive structural rearrangements among symbiodiniacean genomes; those from two distinct Symbiodinium species share the most (853) syntenic gene blocks. Functions enriched in genes core to Symbiodiniaceae are also enriched in those core to Symbiodinium. Gene functions related to symbiosis and stress response exhibit similar relative abundance in all analysed genomes. Our results suggest that structural rearrangements contribute to genome sequence divergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This is the first comprehensive comparison of Symbiodiniaceae based on whole-genome sequence data, including comparisons at the intra-genus and intra-species levels.

genomics↗

bioRxiv2019

Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

Symbiodiniaceae are predominantly symbiotic dinoflagellates critical to corals and other reef organisms. Symbiodinium is a basal symbiodiniacean lineage and includes symbiotic and free-living taxa. However, the molecular mechanisms underpinning these distinct lifestyles remain little known. Here, we present high-quality de novo genome assemblies for the symbiotic Symbiodinium tridacnidorum CCMP2592 (genome size 1.3 Gbp) and the free-living Symbiodinium natans CCMP2548 (genome size 0.74 Gbp). These genomes display extensive sequence divergence, sharing only ~1.5% conserved regions ([≥]90% identity). We predicted 45,474 and 35,270 genes for S. tridacnidorum and S. natans, respectively; of the 58,541 homologous gene families, 28.5% are common to both genomes. We recovered a greater extent of gene duplication and higher abundance of repeats, transposable elements and pseudogenes in the genome of S. tridacnidorum than in that of S. natans. These findings demonstrate that genome structural rearrangements are pertinent to distinct lifestyles in Symbiodinium, and may contribute to the vast genetic diversity within the genus, and more broadly in Symbiodiniaceae. Moreover, the results from our whole-genome comparisons against a free-living outgroup support the notion that the symbiotic lifestyle is a derived trait in, and that the free-living lifestyle is ancestral to, Symbiodinium.

genomics↗

bioRxiv2019

Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates

Dinoflagellates are taxonomically diverse, ecologically important phytoplankton in marine and freshwater environments. Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. For each genome, guided using full-length transcriptome data, we predicted >50,000 high-quality genes. About 68% of the genome is repetitive sequence; long terminal repeats likely contribute to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). Of all genes, [~]40% are encoded unidirectionally, [~]25% comprised of single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial, origin of ice-binding domains in cold-adapted dinoflagellates. Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Since most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light environments.

genomics↗

bioRxiv2019

Evidence that inconsistent gene prediction can mislead analysis of algal genomes

Comparative algal genomics often relies on predicted gene models from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis, remain poorly understood. Here, using available genome data from six dinoflagellate species in Symbiodiniaceae, we identified potential methodological biases in the published gene models that were predicted using different approaches. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted gene models resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas those published earlier were largely biased by the distinct approaches used in each instance. Importantly, these biases mislead the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative genomics, particularly for non-model algal genomes.

genomics↗

bioRxiv2017

Transcriptomic Resilience of a Coral Holobiont to Low pH

Ocean acidification is considered as one of the major threats for coral reefs at a global scale. Marine calcifying organisms, including stony corals, are expected to be the most affected by the predicted decrease of the surface water pH at the end of the century. The severity of the impacts on coral reefs remains as matter of controversy. Although previous studies have explored the physiological response of stony corals to changes in pH, the response of the holobiont (i.e. the coral itself plus its symbionts) remains largely unexplored. In the present study, we assessed the changes in overall gene expression of the coral Montipora digitata and its microalgal symbionts after a short (three days) and a longer (42 days) exposure to low pH (7.6). The short-term exposure to low pH caused small differences in the expression level of the host, impacting mostly genes associated with stress response in other scleractinians. Resilience to Acidification of a Coral Holobiont Longer exposure to low pH resulted in no significant changes in gene expression of the coral host. Gene expression in the eukaryotic symbionts remained unaltered at both exposure times. Our findings suggest resilience, in terms of gene expression, of the Montipora digitata holobiont to pH decrease, as well as capability to acclimatize to extended periods of exposure to low pH.

ecology↗