Sex-specific transcriptomic differences in the immune cells of a key Atlantic-Mediterranean sea urchin

The abundance of the black sea urchin, Arbacia lixula, has been increasing during the last decades likely related to global warming. This thermophilous species has a leading role in maintaining marine barrens in the Mediterranean with the consequent negative impact on coastal rocky ecosystems due to its grazing activity. In this study, we used transcriptomic data from coelomocytes (the cell effectors of the immune system) of females and males of this sea urchin to study potential differences in performance between sexes under laboratory conditions. Differential adaptations, responses to environmental stressors, and resistance against pathogens between sexes may lead to different outcomes in the ongoing expansion of this species in the Mediterranean Sea. Differential expression analyses demonstrated the existence of 120 transcripts, corresponding to 119 genes and two isoforms of the same gene, differentially expressed between coelomocytes of females and males, being 73 up-regulated in males and 47 up-regulated in females. The differential expression patterns were retrieved from a diversity of genes that play different roles related to the immune response due to their antibacterial activity, immune cell activation, cell to cell interaction, intracellular signaling, and detoxification functioning, among others. Our results point out a higher energetic demand of male coelomocytes due to a higher immune activity than females, whereas females have more efficient molecular systems to avoid oxidative stress caused by infections. In conclusion, our study provides evidence of sex-based differences in the expression of genes related to the immune and stress responses in coelomocytes of the sea urchin A. lixula

Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for Next Generation Sequencing

Transcriptomic information provides fundamental insights into biological processes. Extraction of quality RNA is a challenging step, and preservation and extraction protocols need to be adjusted in many cases. Our objectives were to optimize preservation protocols for isolation of high‐quality RNA from diverse echinoderm tissues and to compare the utility of parameters as absorbance ratios and RIN values to assess RNA quality. Three different tissues (gonad, oesophagus and coelomocytes) were selected from the sea urchin Arbacia lixula. Solid tissues were flash‐frozen and stored at −80 °C until processed. Four preservation treatments were applied to coelomocytes: flash freezing and storage at −80 °C, RNAlater and storage at −20 °C, preservation in TRIzol reagent and storage at −80 °C and direct extraction with TRIzol from fresh cells. Extractions of total RNA were performed with a modified TRIzol protocol for all tissues. Our results showed high values of RNA quantity and quality for all tissues, showing nonsignificant differences among them. However, while flash freezing was effective for solid tissues, it was inadequate for coelomocytes because of the low quality of the RNA extractions. Coelomocytes preserved in RNAlater displayed large variability in RNA integrity and insufficient RNA amount for further isolation of mRNA. TRIzol was the most efficient system for stabilizing RNA which resulted on high RNA quality and quantity. We did not detect correlation between absorbance ratios and RNA integrity. The best strategies for assessing RNA integrity was the visualization of 18S rRNA and 28S rRNA bands in agarose gels and estimation of RIN values with Agilent Bioanalyzer chips

Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO2 seeps

Ocean acidification, caused by anthropogenic CO 2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival

Digging the diversity of Iberian bait worms Marphysa (Annelida, Eunicidae)

During a visit to polychaete-rearing facilities in the vicinity of Bay of Cádiz (SW Iberian Peninsula, Atlantic Ocean), we sampled two populations of Marphysa (Annelida, Eunicidae) originally occurring at nearby intertidal soft bottoms, one being more than twice as long as the other at the same age. We analysed them using partial sequences of two mitochondrial genes, 16S rDNA and Cytochrome Oxidase I, and classical morphological observations. Our molecular results confirmed that the two populations corresponded to two different species, with PTP species delimitation values ranging from 0.973 (long-bodied species) to 0.999 (short-bodied species). Morphologically, the short-bodied species resembles the recently redescribed M. sanguinea (Montagu, 1813), but differs mainly in having some parapodia with two subacicular hooks (one bidentate and one unidentate) and three types of pectinate chaetae, Two isodont present all along the body, and one particularly large anodont asymmetric appearing only from mid-posterior parapodia. The long-bodied species resembles Marphysa aegypti Elgetany, El-Ghobashy, Ghoneim and Struck, 2018 both in size and in having very robust, unidentate subacicular hooks (single in most parapodia, two-both similar in size and form-in some posterior parapodia), but differs, among other features, in the maxillary formula, the number of acicula per parapodia and the number and shape of pectinate chaetae. Accordingly, we are here fully illustrating and formally describing the two Iberian populations as Marphysa gaditana sp. nov. (short-bodied) and Marphysa chirigota sp. nov. (long-bodied) and we are emending the description of M. aegypti based on our revision of the type material. Also, we discuss on the distribution of the species of the sanguinea-group and on the relevancy of taxonomically robust studies when dealing with species of commercial interest having the potential of being globally spread through human activities, as well as on the misunderstandings caused by the incorrect use of the "cosmopolitan species" concept.info:eu-repo/semantics/publishedVersio

Digging the diversity of Iberian bait worms Marphysa (Annelida, Eunicidae).

During a visit to polychaete-rearing facilities in the vicinity of Bay of Ca´diz (SW Iberian Peninsula, Atlantic Ocean), we sampled two populations of Marphysa (Annelida, Eunicidae) originally occurring at nearby intertidal soft bottoms, one being more than twice as long as the other at the same age. We analysed them using partial sequences of two mitochondrial genes, 16S rDNA and Cytochrome Oxidase I, and classical morphological observations. Our molecular results confirmed that the two populations corresponded to two different species, with PTP species delimitation values ranging from 0.973 (long-bodied species) to 0.999 (short-bodied species). Morphologically, the short-bodied species resembles the recently redescribed M. sanguinea (Montagu, 1813), but differs mainly in having some parapodia with two subacicular hooks (one bidentate and one unidentate) and three types of pectinate chaetae, Two isodont present all along the body, and one particularly large anodont asymmetric appearing only from mid-posterior parapodia. The long-bodied species resembles Marphysa aegypti Elgetany, El-Ghobashy, Ghoneim and Struck, 2018 both in size and in having very robust, unidentate subacicular hooks (single in most parapodia, two-both similar in size and form-in some posterior parapodia), but differs, among other features, in the maxillary formula, the number of acicula per parapodia and the number and shape of pectinate chaetae. Accordingly, we are here fully illustrating and formally describing the two Iberian populations as Marphysa gaditana sp. nov. (short-bodied) and Marphysa chirigota sp. nov. (long-bodied) and we are emending the description of M. aegypti based on our revision of the type material. Also, we discuss on the distribution of the species of the sanguinea-group and on the relevancy of taxonomically robust studies when dealing with species of commercial interest having the potential of being globally spread through human activities, as well as on the misunderstandings caused by the incorrect use of the "cosmopolitan species" concept

Connectivity of the Pulley Ridge with remote locations as inferred from satellite- tracked drifter trajectories

Using historical (1994-2017) satellite‐tracked surface drifter trajectory data, we conduct a probabilistic Lagrangian circulation study which sheds light on the connectivity of Pulley Ridge with other locations in the Gulf of Mexico and adjacent areas. The analysis reveals that Pulley Ridge is connected with the North Atlantic, the Caribbean Sea, and most of the Gulf of Mexico. Preferred connecting pathways are identified and arrival times to potential reef sites computed. The study demonstrates the importance of Pulley Ridge as a source for neighboring regions like the Dry Tortugasa, the Florida Keys, Campeche Bank, and the east Florida coast as well as a self‐recruitment area for species with short competence time. The study further suggests that the reefs in the Caribbean Sea, the Dry Tortugas, the western Florida Keys, and the West Florida Shelf can act as sources for Pulley Ridge, indicating the importance of Pulley Ridge as a central refugium for species in the Gulf of Mexico

Cryptic speciation and genetic structure of widely distributed brittle stars (Ophiuroidea) in Europe

The development of molecular techniques has led to the detection of numerous cases of cryptic speciation within widely distributed marine invertebrate species and important taxonomic revisions in all the major marine taxa. In this study, we analysed a controversial marine species complex in the genus Ophiothrix, a widespread taxon in European waters traditionally assigned to two nominal species, Ophiothrix fragilis and O. quinquemaculata. These species are important components of the rocky shores and deep marine benthos along the North Atlantic and Mediterranean littoral. Their status (including variants of both species) has remained contentious due to overlapping variability in morphological characters. In this study, we analysed the genetic and morphological differences of Ophiothrix lineages along the Atlantic and Mediterranean coasts. We also assessed population genetic structure in the Atlantic and Mediterranean basins by sequencing two mitochondrial genes, the 16S rRNA gene and COI gene, of 221 specimens from 13 locations. Phylogenetic analyses demonstrated the existence of two genetically distinct lineages, attributable to two different species although unrelated to previous taxonomic distinctions. Morphological differences could also be detected between these lineages. Samples from the Northeast Atlantic and one from the deep Mediterranean grouped within Lineage I, whereas Lineage II pooled together the southern Atlantic and rocky shallow Mediterranean samples. In the northern region of the Iberian Peninsula and at a deep locality in the Mediterranean, both lineages overlap. Speciation processes likely happened during the Mio–Pliocene transition (about 4.8–7.5 million years ago), when marine-level oscillations led to the blockage of major marine corridors in Europe and promoted genetic isolation by vicariance. Secondary contact between lineages following sea-level increases and recolonization during the refilling of the Mediterranean after the Miocene salinity crisis could explain the present-day distribution of genetic variability. No barriers to gene flow along the Atlanto-Mediterranean area were detected for Lineage II, and the lack of genetic structure could be caused by a mixture of several factors, such as wide dispersal potential, recent demographic expansion and large population size

Enjoying the warming Mediterranean: transcriptomic responses to temperature changes of a thermophilous keystone species in benthic communities

Information about the genomic processes underlying responses to temperature changes is still limited in non‐model marine invertebrates. In this sense, transcriptomic analyses can help to identify genes potentially related to thermal responses. We here investigated, via RNA‐seq, whole‐transcriptomic responses to increased and decreased temperatures in a thermophilous keystone sea urchin, Arbacia lixula, whose populations are increasing in the Mediterranean. This species is a key driver of benthic communities' structure due to its grazing activity. We found a strong response to experimentally induced cold temperature (7°C), with 1,181 differentially expressed transcripts relative to the control condition (13°C), compared to only 179 in the warm (22°C) treatment. A total of 84 (cold treatment) and three (warm treatment) gene ontology terms were linked to the differentially expressed transcripts. At 7°C the expression of genes encoding different heat shock proteins (HSPs) was upregulated, together with apoptotic suppressor genes (e.g., Bcl2), genes involved in the infection response and/or pathogen‐recognition (e.g., echinoidin) and ATP‐associated genes, while protein biosynthesis and DNA replication pathways were downregulated. At 22°C neither HSPs induction nor activation of the previously mentioned pathways were detected, with the exception of some apoptotic‐related activities that were upregulated. Our results suggest a strong transcriptional response associated with low temperatures, and support the idea of low water temperature being a major limitation for A. lixula expansion across deep Mediterranean and northern Atlantic waters

Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae)

Background: Knowledge about the distribution of the genetic variation of marine species is fundamental to address species conservation and management strategies, especially in scenarios with mass mortalities. In the Mediterranean Sea, Petrosia ficiformis is one of the species most affected by temperature-related diseases. Our study aimed to assess its genetic structure, connectivity, and bottleneck signatures to understand its evolutionary history and to provide information to help design conservation strategies of sessile marine invertebrates. Results: We genotyped 280 individuals from 19 locations across the entire distribution range of P. ficiformis in the Atlanto-Mediterranean region at 10 microsatellite loci. High levels of inbreeding were detected in most locations (especially in the Macaronesia and the Western Mediterranean) and bottleneck signatures were only detected in Mediterranean populations, although not coinciding entirely with those with reported die-offs. We detected strong significant population differentiation, with the Atlantic populations being the most genetically isolated, and show that six clusters explained the genetic structure along the distribution range of this sponge. Although we detected a pattern of isolation by distance in P. ficiformis when all locations were analyzed together, stratified Mantel tests revealed that other factors could be playing a more prominent role than isolation by distance. Indeed, we detected a strong effect of oceanographic barriers impeding the gene flow among certain areas, the strongest one being the Almeria-Oran front, hampering gene flow between the Atlantic Ocean and the Mediterranean Sea. Finally, migration and genetic diversity distribution analyses suggest a Mediterranean origin for the species. Conclusions: In our study Petrosia ficiformis showed extreme levels of inbreeding and population differentiation, which could all be linked to the poor swimming abilities of the larva. However, the observed moderate migration patterns are highly difficult to reconcile with such poor larval dispersal, and suggest that, although unlikely, dispersal may also be achieved in the gamete phase. Overall, because of the high genetic diversity in the Eastern Mediterranean and frequent mass mortalities in the Western Mediterranean, we suggest that conservation efforts should be carried out specifically in those areas of the Mediterranean to safeguard the genetic diversity of the species

Phylogenetic relationships of Gymnothorax bacalladoi Böhlke and Brito (1987) a poorly known moray of the Macaronesian islands

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