Population genetics and evolutionary history of the intertidal brittle star Ophiothrix (Ophiothrix) exigua in the northern China Sea.

Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.

The complete mitochondrial genome of Mya japonica (Jay, 1857 Myida:myidae).

The soft-shell clam Mya japonica (Jay, 1857) is a commercially important fishery resource. In this study, we identified the complete mitochondrial genome of M. japonica and performed a phylogenetic analysis to explore its genetic relationship with Mya arenaria. The genome is 21,396 bp in length and contains 13 protein-coding genes (PCGs), 23 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 5 D-Loop control regions. The atp8 gene was annotated in Myidae for the first time. Notably, the genome contains an additional trnM, consistent with M. arenaria. The length of the cox2 gene is 1,947 bp, which is 513 bp longer than that in M. arenaria. Its base composition is 29.14% A, 37.26% T, 10.89% C, and 22.71% G. Phylogenetic analysis based on 12 PCGs and 2 rRNAs indicates that M. japonica and M. arenaria form a sister group. In this study, the identification and phylogenetic analysis of the complete mitochondrial genome of M. japonica provide significant information for future taxonomic and evolutionary research of the genus Mya.

Accumulation of trace metal elements in ophiuroids with different feeding types in the North Yellow Sea.

Ophiuroids, as an important group of echinoderms, are widely distributed in marine benthic habitats. Previous studies have identified two primary feeding types of ophiuroids in the Yellow Sea, including carnivorous (Ophiura sarsii vadicola and Stegophiura sladeni) and suspension feeders (Ophiopholis mirabilis). Despite their ecological role in the benthic food webs, little is known about their accumulation of trace metal elements (TMEs). In this study, the content of TMEs (Pb, As, Cd, Hg, Cr, Cu, Zn), methylmercury (MeHg) and δ15N value of three ophiuroids species from the North Yellow Sea were determined. Our results showed that the contents of some TMEs (As, Cd, Cr, Cu and Zn) and MeHg were significantly different in three species of ophiuroid (p < 0.05). There were significant correlations between the accumulations of trace metal elements (Pb, Cd and Zn) and the δ15N value of the ophiuroids (p < 0.05). Additionally, As and Zn exhibited opposite correlations in ophiuroid with two feeding types, which may be related to their host species and different feeding habits. This study provided fundamental data for understanding the distribution of trace metal elements in echinoderms.

Increased microgastropoda sampling give new insights into the phylogenetic relationships of Littorinoidea (Littorinimorpha).

Littorinoidea is one of the most diverse radiations and the most successful group that evolutionary transitions from marine to terrestrial within Littorinimorpha. With such an unmatched diversity, few phylogenetic investigations have attempted to understand their evolutionary relationships, and existing research has primarily focused on typical intertidal species. To address this gap, we conducted the first phylogenomic analysis of the Littorinoidea, leveraging 35 transcriptomes to investigate their internal relationships. Our analyses revealed significant revisions necessary within the Littorinoidea: 1) Pomatias appears distantly related to Littorinidae, suggesting a potential ancestral origin outside of Littorinoidea, challenging traditional classification. The homology of penial innervation within Littorinoidea warrants reevaluation. 2) Lacuna's placement indicates a close relationship with Naticidae, prompting consideration for its removal from Littorinidae. 3) Based on the current phylogenetic research, Peasiella may belong to a distinct family separate from Littorinidae. 4) Our findings support revising the placement of Pteropods within the Littorinimorpha, which is situated phylogenetically between the families Littorinoidea and Naticoidea. Additionally, we highlight the impact of site heterogeneity and evolutionary rate variation on phylogenetic inference. Our study provides a robust phylogenomic framework for the Littorinoidea, emphasizing the importance of including microgastropoda taxa in molecular phylogenetic reconstructions of gastropod subgroups.

Chromosome-level genome assembly and annotation of the cold-water species Ophiura sarsii.

The cold-water species Ophiura sarsii, a brittle star, is a key echinoderm in the Arctic continental shelf region, highly sensitive to climate change. However, the absence of a high-quality genome has hindered a thorough understanding of its adaptive evolution. In this study, we reported the first chromosome-level genome assembly of O. sarsii. The genome assembly totalled 1.57 Gb, encompassing 19 chromosomes with a GC content of 37.11% and a scaffold N50 length of 78.03 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment yielded a completeness estimate of 93.5% for this assembly. We predicted a total of 27,099 protein-coding genes, with 25,079 functionally annotated. The genome was comprised of 58.09% transposable elements. This chromosome-level genome of O. sarsii contributes to our understanding of the origin and evolution of marine organisms.

Chromosome-level genome provides insights into environmental adaptability and innate immunity in the common dolphin (delphinus delphis).

The common dolphin (Delphinus delphis) is widely distributed worldwide and well adapted to various habitats. Animal genomes store clues about their pasts, and can reveal the genes underlying their evolutionary success. Here, we report the first high-quality chromosome-level genome of D. delphis. The assembled genome size was 2.56 Gb with a contig N50 of 63.85 Mb. Phylogenetically, D. delphis was close to Tursiops truncatus and T. aduncus. The genome of D. delphis exhibited 428 expanded and 1,885 contracted gene families, and 120 genes were identified as positively selected. The expansion of the HSP70 gene family suggested that D. delphis has a powerful system for buffering stress, which might be associated with its broad adaptability, longevity, and detoxification capacity. The expanded IFN-α and IFN-ω gene families, as well as the positively selected genes encoding tripartite motif-containing protein 25, peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, and p38 MAP kinase, were all involved in pathways for antiviral, anti-inflammatory, and antineoplastic mechanisms. The genome data also revealed dramatic fluctuations in the effective population size during the Pleistocene. Overall, the high-quality genome assembly and annotation represent significant molecular resources for ecological and evolutionary studies of Delphinus and help support their sustainable treatment and conservation.

The mitochondrial genome of Monoserius pennarius (Linnaeus, 1758) from the East China Sea.

The species Monoserius pennarius (Linnaeus, 1758), is particularly abundant in the tropical Indo-West Pacific east of Sri Lanka, yet very limited genetic information exists for this species. Here, we report the assembled-linear mitochondrial genome of M. pennarius collected from the East China Sea. The 15,197 bp mitogenome contains 13 protein-coding genes (PCGs), two tRNA genes, and two rRNA genes. Notably, the gene order in this mitogenome differs from that of other hydrozoans within the same taxonomic order. Phylogenetic analysis, based on 13 concatenated mitochondrial PCGs, recovered M. pennarius as a sister of Nemalecium lighti (Hargitt, 1924), outside the other Leptothecata hydrozoans, suggesting paraphyly of Leptothecata. The mitogenome of M. pennarius, serving as the first publicly available for the family Aglaopheniidae, holds foreseeable value for investigating Leptothecata evolution.

Occurrence and distribution of phycotoxins in the Antarctic Ocean.

Lipophilic phycotoxins (LPTs) and domoic acid (DA) in Antarctic seawater, as well as parts of the South Pacific and the Southern Indian Oceans were systematically investigated. DA and six LPTs, namely pectenotoxin-2 (PTX2), okadaic acid (OA), yessotoxin (YTX), homo-yessotoxin (h-YTX), 13-desmethyl spirolide C (SPX1), and gymnodimine (GYM), were detected. PTX2, as the dominant LPTs, was widely distributed in seawater surrounding Antarctica, whereas OA, YTX, and h-YTX were irregularly distributed across the region. The total concentration of LPTs in surface seawater ranged from 0.10 to 13.57 ng/L (mean = 2.20 ng/L). ∑LPT levels were relatively higher in the eastern sea areas of Antarctica than in the western sea areas. PTX2 was the main LPT in the vertical profiles, and the PTX2 concentration was significantly higher in the epipelagic zone than water depths below 200 m. The predominant sources of PTX2 and OA in Antarctic sea areas are likely to be Dinophysis.

Biomineralization in a cold environment: Insights from shield compositions and transcriptomics of polar sternaspids (Sternaspidae, Polychaeta).

The survival and physiological functions of polar marine organisms are impacted by global climate changes. Investigation of the adaptation mechanisms underlying biomineralization in polar organisms at low temperatures is important for understanding mineralized organismal sensitivity to climate change. Here, we performed electron probe analysis on the shields of Antarctic polychaete Sternaspis sendalli and Arctic polychaete Sternaspis buzhinskajae (Sternaspidae), and sequenced the transcriptomes of the tissues surrounding shields to examine biomineral characteristics and adaptive mechanisms in persistently cold environments. Compared to the temperate relative species, the relative abundance of iron, phosphorus, calcium, magnesium, nitrogen, sulfur and silicon in two polar sternaspid shields was similar to Sternaspis chinensis. However, the diversity and expression levels of biomineralization-related shell matrix proteins differed between the polar and temperate species, suggesting distinct molecular mechanisms underlying shield formation in cold environments. Tubulin and cyclophilin were upregulated compared to the temperate species. Furthermore, 42 positively selected genes were identified in Antarctic S. sendalli, with functions in cytoskeletal structure, DNA repair, immunity, transcription, translation, protein synthesis, and lipid metabolism. Highly expressed genes in both polar species were associated with cytoskeleton, macromolecular complexes and cellular component biosynthesis. Overall, this study reveals conserved elemental composition yet distinct biomineralization processes in the shields of polar sternaspids. The unique expression of biomineralization related genes and other cold-adaptation related genes provide molecular insights into biomineralization in cold marine environments.

Symbiotic relationship of Comaster schlegelii (Crinoidea: Comatulidae) And Gymnolophus obscura (Ophiuroidea: Ophiotrichidae) derived from stable isotope and fatty acid analyses.

Coral reef community exhibit high species diversity and a broad range of biological relationships including widespread symbiosis and complex food utilization patterns. In our study, we investigated the symbiotic relationship between the commonly crinoid host Comaster schlegelii and its ophiuroid obligatory symbiont Gymnolophus obscura. Using a combination of fatty acid biomarkers and stable isotopic compositions, we explored differences in their organic matter utilization strategies and nutritional relationships. The result of stable isotopes revealed that G. obscura had higher δ15N values than its crinoid host. Particulate organic matter and phytoplankton were identified as the primary food sources for both species, however C. schlegelii showed a higher proportional contribution from benthic microalgae. Fatty acid markers showed that C. schlegelii was more dependent on benthic microalgae such as diatoms, and less on debritic organic matter and bacteria than G. obscura. Elevated δ15N values of G. obscura and similar food source contribution rates between the host and symbiont suggest that ophiuroid feeds on materials filtered by crinoids and have similar diet to the host. Our results provide insights into the symbiotic patterns of crinoids and ophiuroids, while also supplying foundational data on how symbiotic reef species select organic matter utilization strategies to adapt to their environment.

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats.

IMPORTANCE: Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Metabolomic insights into neurological effects of BDE-47 exposure in the sea cucumber Apostichopus japonicus.

The persistent organic pollutant 2,2',4,4'-Tetrabromodiphenyl ether (BDE-47), a prevalent congener among polybrominated diphenyl ethers (PBDEs), exhibits potent bioaccumulation and toxicity. Despite extensive research into the adverse effects of BDE-47, its neurotoxicity in sea cucumbers remains unexplored. Given the crucial role of the sea cucumber's nervous system in survival and adaptation, evaluating the impacts of BDE-47 is vital for sustainable aquaculture and consumption. In this study, we employed ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Triple-TOF-MS) to analyze metabolomic changes in neuro-related tissues of Apostichopus japonicus exposed to low (0.1 µg/L), medium (1.0 µg/L), and high (10.0 µg/L) BDE-47 concentrations. We identified significantly changed metabolites in each exposure group (87 in low, 79 in medium, and 102 in high), affecting a variety of physiological processes such as steroid hormone balance, nucleotide metabolism, energy metabolism, neurotransmitter levels, and neuroprotection. In addition, we identified concentration-dependent, common, and some other metabolic responses in the neuro-related tissues. Our findings reveal critical insights into the neurotoxic effects of BDE-47 in sea cucumbers and contribute to risk assessment related to BDE-47 exposure in the sea cucumber industry, paving the way for future neurotoxicological research in invertebrates.

The complete mitochondrial genome of Cuspidaria undata (Bivalvia, Anomalodesmata, Cuspidariidae).

The mitochondrial genome of Cuspidaria undata (Verrill, 1884) was sequenced in full using Illumina HiSeq 2500. The circular mitochondrial DNA (mtDNA) was 16,266 bp in size, encoded 37 genes, and contained 13 protein-coding genes (PCGs), 2 rRNAs and 22 tRNAs. The gene order of the 13 PCGs in this species exhibited extensive rearrangement and differences in comparison to other Cuspidariidae, indicating that gene order is not conserved within this family. Phylogenetic analysis based on 13 PCGs and 2 rRNAs recovered a monophyletic Cuspidariidae.

Transcriptomic response of intertidal brittle star Ophiothrix exigua to seasonal variation.

Adaptation to seasonal change is essential for survival, and is especially critical for organisms living in physically harsh environments. Brittle stars (Ophiothrix), known as a keystone species, inhabiting the intertidal rocky ecosystem are affected by multiple stressors, but molecular insights into their adaptation remain poorly studied. In the present study, transcriptomic responses of Ophiothrix exigua from the intertidal habitats of the North Pacific Ocean during summer and winter are reported. A total of 12,844 differentially expressed genes (DEGs) were identified. Of these, 7102 genes were up-regulated and 5742 genes were down-regulated in summer relative to winter. One hundred fifty-two key DEGs, including 31 up-regulated and 121 down-regulated genes, were categorized into three major subcategories and seven subclasses. The key DEGs included heat shock cognate protein 70 (HSC70), toll-like receptor-2 (TLR2), cAMP-dependent protein kinase catalytic subunit beta-like isoform X2 (PKA), serine/threonine-protein kinase mTOR (MTOR), and ras-related c3 botulinum toxin substrate 1 isoform X1 (RAC1). Glutathione peroxidase-like (GPX) and tubulin superfamily members (TUBA, TUBB) were consistent across seasons. The main defense-related pathways in brittle star were phagosome, apoptosis, and glutathione metabolism. These findings would greatly enhance our understanding of the genomic basis of environmental adaptation in intertidal invertebrates.

The complete mitochondrial genome of Comaster schlegelii (Crinoidea, Comatulida).

Comaster schlegelii, belonging to the family Comatulidae, is a variable feather star distributed in the Pacific Ocean. The complete mitochondrial genome of this species was 15,887 bp in length, consisting of 13 protein-coding genes, 22 transport RNA genes, two ribosomal RNA genes and one control region. The whole mitochondrial genome of C. schlegelii had a high AT content of 72.73%. The phylogenetic relationship was reconstructed with 16 relevant echinoderms, which revealed C. schlegelii was closely clustered with Anneissia pinguis in the family Comatulidae.

Complete mitochondrial genome of Dibranchus japonicus (Actinopterygii, Lophiiformes, Ogcocephalidae), from the West Pacific Ocean.

Dibranchus japonicus is a benthic fish living in the deep Pacific Ocean. Here, we described the complete mitochondrial genome of this species, with the sequences about 17,233 bp in length, containing 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The gene arrangement of this species was identical with others from family Ogcocephalidae. The content of GC and AT for D. japonicus was 45.41% and 54.59%, respectively. Phylogenetic analysis, based on 13 PCGs and two rRNA genes, revealed the close relationship between D. japonicus and other species of Ogcocephalidae, which was consistent with the morphology.

The first complete mitochondrial genome of Notostomus gibbosus (Caridea, Acanthephyridae).

Notostomus gibbosus is a deep-sea shrimp, belonging to Caridea, Acanthephyridae. The whole complete mitochondrial genome of N. gibbosus was 17,956 bp in length, with 37 genes, containing 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. The GC content of N. gibbosus was 39.43%. The genomic structure and gene arrangement were identical to those of Caridea species. The phylogenetic analysis of 13 protein-coding genes showed a close relationship to the genera Acanthephyra.

The complete mitochondrial genome of Oplophorus spinosus (Brullé, 1839) (Caridea, Oplophoridae).

We determined the complete mitochondrial genome of Oplophorus spinosus with a typical circular structure. The complete mitogenomes of O. spinosus was 17,346 bp in length, with 37 genes containing 13 protein-coding genes, 22 tRNAs, two rRNAs, and a confirmed D-loop zone. The GC content of O. spinosus was 34.39%. The phylogenetic results showed that O. spinosus was most closed to O. typus, providing useful mitochondrial information for its further evolutionary and taxonomy study.

Gut Microbial Composition and Diversity in Four Ophiuroid Species: Divergence Between Suspension Feeder and Scavenger and Their Symbiotic Microbes.

Gut microbiota have important roles in the survival and adaptation of the host. Ophiuroids, as the worldwide dominant benthos, have ecological roles in benthic-pelagic coupling in the sea floor. However, little is known about the composition and diversity of their gut microbiota and its potential functions in benthic ecosystems. In present study, we preformed 16S rRNA sequencing and function analysis in four dominant species (Stegophiura sladeni, Ophiopholis mirabilis, Ophiura sarsii vadicola, and Ophiura kinbergi) with two feeding types (suspension feeding/herbivores and scavenger/carnivores) from the Yellow Sea, China. Results showed that 56 phyla and 569 genera of microbiota were identified among ophiuroid guts. Multivariate and diversity analyses showed that the ophiuroid gut microbiota were independent and have higher biodiversity to the sediment microbial in the Yellow Sea. Phyla Proteobacteria, Firmicutes, Tenericutes, and Bacteroidetes were the dominant bacteria, with more than 80% abundance among the four ophiuroid species. A comparison among the gut microbial compositions among four ophiuroids showed the similarity of two offshore carnivore ophiuroids (S. sladeni and O. sarsii vadicola) and variation in the dominant microbiota types of three nearshore ophiuroids (S. sladeni, O. mirabilis, and O. kinbergi). The functional analysis revealed the significant differences of the environment-related expression in S. sladeni gut microbiota between nearshore and offshore environments. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional annotation showed the significant divergence of metabolism pathways between two nearshore species, the herbivores O. mirabilis and carnivores S. sladeni, such as the Lipid metabolism, Carbohydrate metabolism, and Metabolism of cofactors and vitamins. The homolog search and phylogenetic analysis identified the first gut symbiotic Candidatus Hepatoplasma in S. sladeni with important roles for the nutrient metabolisms. Overall, our study reported the comprehensive data of ophiuroid gut microbiota, while the functional microbiome provides insight into the physiology and environmental adaptation in ophiuroids.