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PubMed2026

An RPA-assisted homogeneous electrochemical DNA sensor for on-site eDNA detection toward early warning of crown-of-thorns starfish outbreaks.

Crown-of-thorns starfish (COTS) outbreaks seriously threaten coral reef ecosystems, while conventional monitoring approaches are time-consuming and often lack sufficient sensitivity for early warning. Existing electrochemical DNA sensors usually require complex electrode-surface immobilization procedures, which can lead to uneven probe distribution, significant steric hindrance, and poor stability. Meanwhile, the low concentration of environmental DNA (eDNA) in marine environments further complicates detection. To overcome these challenges, this study developed a homogeneous electrochemical DNA sensor assisted by recombinase polymerase amplification (RPA) for COTS eDNA detection. Target DNA was first amplified by RPA, and the amplification products were then hybridized in solution with capture probe (CP)-modified magnetic beads (MB) and biotin-labeled signal probe (SP) to form sandwich-structured MB complexes. These complexes were subsequently magnetically enriched and immobilized on the electrode surface for electrochemical signal readout. Under optimized conditions, the sensor displayed a linear response to COTS genomic DNA from 3.77 fg/μL to 1 ng/μL, with an LOD of 2.02 fg/μL and an LOQ of 3.77 fg/μL. The sensor was applied to Xisha Islands samples, and the results agreed with droplet digital PCR (ddPCR) (P > 0.05), demonstrating its potential for sensitive and reliable on-site COTS eDNA detection.

Animals↗

PubMed2025

Contrasting Patterns of Connectivity Between Populations of Euphotic and Mesophotic Hydroids in Reunion Island Support the Deep Reef Refuge Hypothesis.

In the context of coral reef decline, mesophotic coral ecosystems (MCEs, 30-150 m) offer hope for the recovery of degraded euphotic reefs. The Deep Reef Refuge Hypothesis (DRRH) postulates the potential of mesophotic reefs to reseed euphotic reefs. This hypothesis needs to be further tested by estimating connectivity along the depth gradient. Mesophotic data are lacking worldwide, particularly in the southwestern Indian Ocean (SWIO). Here, using a total of 2218 samples collected at depths ranging from 10 to 103 m, we estimated the connectivity of 7 hydroid species sampled at euphotic, upper, and lower mesophotic depths around Reunion Island using a multi-species comparative framework. Population genetic analyses using 8-17 microsatellite markers per species (80 markers in total) as well as Bayesian inference were performed to estimate population structure and contemporary migration rates to highlight connectivity patterns and directionality of gene flow between depths. The results revealed three main genetic patterns depending on the species: a horizontal stepping stone pattern between areas around the island, a vertical stepping stone pattern between adjacent depths, and a quasi-panmictic pattern. Each species showed some specificity within these patterns, but overall, at least 4 of the 7 species support the assumption of vertical connectivity from the Deep Reef Refuge Hypothesis, highlighting the importance of studying multiple species. The existence of vertical connectivity between euphotic and mesophotic depths in the southwestern Indian Ocean confirms the importance of mesophotic coral ecosystems for conservation efforts and our global understanding of coral reef ecosystem dynamics.

Animals↗

PubMed2026

DNA methylation-based ageing in a deuterostome invertebrate: an epigenetic clock for the crown-of-thorns seastar (Acanthaster cf. solaris).

Accurate and reliable ageing tools are essential for wildlife conservation and management. While DNA methylation has emerged as a promising tool for age estimation in vertebrates, its application to invertebrates remains contested and has been limited to arthropods. Here, we develop an epigenetic clock for the Pacific crown-of-thorns seastar (CoTS; Acanthaster cf. solaris), a destructive coral predator contributing to habitat degradation across Indo-Pacific reefs. Using Oxford Nanopore Technologies, we generated whole-genome DNA methylation profiles across five age groups and identified 1910 CpG sites with methylation patterns significantly associated with age. We then fitted age prediction models using elastic net regression and evaluated predictive performance with leave-one-out cross-validation (LOOCV), achieving a mean absolute error of 0.31 ± 0.22 years, corresponding to 4-6% of the CoTS lifespan (5-8 years). This accuracy suggests the potential to differentiate annual cohorts, supporting future management-relevant inference. To facilitate practical implementation, we constructed an optimized epigenetic clock from 14 CpG sites consistently selected across LOOCV iterations. Our results demonstrate that DNA methylation-based age estimation is feasible in a deuterostome invertebrate, extending epigenetic ageing approaches beyond arthropods and establishing their potential to advance age determination and management in invertebrates that lack reliable ageing methods.

Animals↗

PubMed2026

Insights Into the Structural Features, Codon Usage Patterns, and Phylogenetic Analysis in Neoniphon argenteus (Teleostei: Holocentriformes) Based on Complete Mitochondrial Genome.

Neoniphon argenteus, a widely distributed nocturnal coral reef fish in the family Holocentridae, plays an important role in maintaining coral reef ecosystem health, yet its phylogenetic position remains poorly resolved. To bridge this gap, we sequenced and analyzed the complete mitochondrial genome of a specimen from the South China Sea to characterize its structural features, codon usage patterns, and phylogenetic relationships. The 16,569 bp mitogenome (GenBank: PP190474.1) encodes 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and two non-coding regions, exhibiting a distinct A + T bias. All tRNAs fold into typical cloverleaf secondary structures except tRNA-Ser (AGN), which lacks the dihydrouridine (DHU) arm. The control region contains palindromic motifs (TACAT/ATGTA) capable of forming hairpin structures and five conserved sequence blocks, whereas the OL region harbors a conserved 5'-GCCGG-3' motif. RSCU analysis revealed 31 frequently used codons (RSCU > 1) with a pronounced preference for A/C-ending codons. The ΔRSCU method identified 10 candidate optimal codons (GCA, CAA, GAA, GGA, AUU, CUA, CCA, CGA, ACA, and GUC). Selection pressure analysis using EasyCodeML and site-specific models indicated that all PCGs are predominantly under purifying selection, with no significant evidence of pervasive positive selection. ND6 exhibited elevated pairwise Ka/Ks ratios (mean = 1.209 ± 0.047), consistent with reduced selective constraint rather than adaptive evolution. Phylogenetic analysis of 19 Holocentriformes species using maximum likelihood and Bayesian inference with partitioned models based on 13 PCGs and two rRNA genes (12S and 16S) assigned all taxa to two well-supported subfamilies (Holocentrinae and Myripristinae). Within Holocentrinae, Neoniphon species form a monophyletic clade nested within a paraphyletic Sargocentron, suggesting that the genus Sargocentron as currently defined is not monophyletic. This study provides useful baseline molecular data for further exploration of the evolutionary history of N. argenteus and other members of Holocentriformes.

Holocentridae↗