Biology subjects

Rodriguez, E.

Publications and source records attributed to Rodriguez, E..

3 recordsLinked to original sources

bioRxiv2018

A Hybrid de novo Assembly of the Sea Pansy (Renilla muelleri) Genome

BackgroundOver 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral \"forests\" which provide unique niches and three-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several cnidarian genomes are currently available, the majority are from hexacorals. Here, we present a de novo assembly of the R. muelleri genome, making this the first complete draft genome from an octocoral.\n\nFindingsWe generated a hybrid de novo assembly using the Maryland Super-Read Celera Assembler v.3.2.6 (MaSuRCA). The final assembly included 4,825 scaffolds and a haploid genome size of 172 Mb. A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome is smaller (172 Mb) than other publicly available, hexacoral genomes (256-448 Mb), the R. muelleri genome is similar to the hexacoral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models.\n\nConclusionsThe R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity.

genomics↗

bioRxiv2017

Immediate effects of psychosocial stress on attention depend on subjective experience and not directly on stress-related physiological changes

Acute psychosocial stress is associated with physiological, subjective and cognitive changes. In particular, attention, which is considered one of the main processes driving cognition, has been related to different stress outcomes, such as anxiety, cortisol levels and autonomic responses, individually. Nonetheless, their specific contributions to and association with attention is still not fully understood. To study this association, 42 male participants were asked to perform an attentional task just before and immediately after being exposed to either an experimental treatment designed to induce psychosocial stress using the Trier Social Stress Test (TSST) or a matching stress-free control condition. The salivary cortisol concentration, heart rate, and self-reported anxiety were measured to assess the physiological response to stress and the subjective experience during the protocol. As expected, psychosocial stress induced increases in heart rate, salivary cortisol levels and anxiety. The behavioral analysis revealed that members of the control group performed better on the attentional task after the protocol, while members of the TSST group showed no changes. Moreover, after dividing the stress group into sub-groups of participants with high and low anxiety, we observed that participants in the high-anxiety group not only failed to perform better but also performed worse. Finally, after testing several single-level mediation models, we found that anxiety is sufficient to explain the changes in attention and that it mediates the effects between heart rate and cortisol levels on attention. Our results suggest that the immediate effects of acute psychosocial stress on attention are highly dependent on the participants subjective experience, which, in turn, is affected and can mediate stress-related physiological changes.

neuroscience↗

bioRxiv2017

Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the [~]7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 {+/-} 222, with more loci recovered from octocorals (783 {+/-} 138 loci) than hexacorals (475 {+/-}187 loci). Phylogenetically informative sites ranged from 26-49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Re-designing the baits with improved affinities to capture loci within each sub-class will provide a valuable toolset to address systematic questions and further our understanding of the timing of diversifications in the class Anthozoa.

genomics↗