Arbacia lixula
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA302829 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12114551_1.fastq.gz | Fastqsanger.gz | |||
| SRR12114551_2.fastq.gz | Fastqsanger.gz | |||
| SRR12114552_1.fastq.gz | Fastqsanger.gz | |||
| SRR12114552_2.fastq.gz | Fastqsanger.gz | |||
| SRR12114553_1.fastq.gz | Fastqsanger.gz |
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Project description:Developmental microbiome of the sea urchin Arbacia lixula
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Project description:The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.
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Project description:As the ocean warms, the thermal tolerance of marine invertebrates is key to determining their distributional change, where acclimation to low pH may impact the thermal range of optimal development. We compared thermal tolerance of progeny from a low pH-acclimated sea urchin (Arbacia lixula) population from the CO2 vents of Ischia (Italy) and a nearby population living at ambient pH. The percentages of normally developing gastrulae and two-armed larvae were determined across 10 temperatures representing present and future temperature conditions (16-34°C). Vent-acclimated sea urchins showed a greater percentage of normal development at 24 h, with a larger optimal developmental temperature range than control sea urchins (12.3°C versus 5.4°C range, respectively). At 48 h, upper lethal temperatures for 50% survival with respect to ambient temperatures were similar between control (+6.8°C) and vent (+6.2°C) populations. Thus, acclimation to low pH did not impact the broad thermal tolerance of A. lixula progeny. With A. lixula's barrens-forming abilities, its wide thermotolerance and its capacity to acclimate to low pH, this species will continue to be an important ecological engineer in Mediterranean macroalgal ecosystems in a changing ocean.
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Project description:The genetic structure of 13 populations of the amphiatlantic sea urchin Arbacia lixula, as well as temporal genetic changes in three of these localities, were assessed using ten hypervariable microsatellite loci. This thermophilous sea urchin is an important engineer species triggering the formation of barren grounds through its grazing activity. Its abundance seems to be increasing in most parts of the Mediterranean, probably favoured by warming conditions. Significant genetic differentiation was found both spatially and temporally. The main break corresponded to the separation of western Atlantic populations from those in eastern Atlantic and the Mediterranean Sea. A less marked, but significant differentiation was also found between Macaronesia (eastern Atlantic) and the Mediterranean. In the latter area, a signal of differentiation between the transitional area (Alboran Sea) and the rest of the Mediterranean was detected. However, no genetic structure is found within the Mediterranean (excluding Alboran) across the Siculo-Tunisian Strait, resulting from either enough gene flow to homogenize distance areas or/and a recent evolutionary history marked by demographic expansion in this basin. Genetic temporal variation at the Alboran Sea is as important as spatial variation, suggesting that temporal changes in hydrological features can affect the genetic composition of the populations. A picture of genetic homogeneity in the Mediterranean emerges, implying that the potential expansion of this keystone species will not be limited by intraspecific genetic features and/or potential impact of postulated barriers to gene flow in the region.
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