Search Results (43)

The green sea turtle (Chelonia mydas), a widely distributed species, plays a crucial role in maintaining the marine ecosystem. However, studies on C. mydas require accurate and comprehensive genome annotation information. Long-read direct transcriptome data of C. mydas were obtained using direct RNA sequencing on the Oxford Nanopore Technologies (ONT) platform from blood tissue of a single captive individual. A total of 4061 novel transcripts were obtained by comparing long-read direct transcripts with genome annotation of C. mydas. We also predicted 2402 CDSs on the novel transcripts. Among them, 1208 (50.29%) had functional annotation information in the databases. In addition, we predicted and analyzed AS events, fusion transcripts, methylation sites, poly(A)s, and lncRNAs in the C. mydas long-read direct transcriptome. Overall, our study provides the a long-read direct blood transcriptome for C. mydas to complement and improve its genome annotation. This valuable resource will contribute to future research on C. mydas. Additionally, the analyses of transcriptome structure mentioned above may provide new insights and ideas for the study of C. mydas. Full article

This study aimed to assess the species diversity and genetic structure of Meretrix clams around Hainan Island using mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding. The genus Meretrix is a common and economically important group of bivalves in the intertidal zones of Hainan Island, widely distributed in estuarine and nearshore sandy habitats and playing a significant role in local fisheries and aquaculture. In recent years, studies on Meretrix in Hainan have mainly focused on morphological identification and species records from limited coastal areas; however, due to the high phenotypic plasticity of shell morphology and the relatively subtle differences among species, traditional morphology-based identification remains challenging. Meanwhile, molecular systematic investigations of Meretrix in Hainan are still limited, particularly systematic studies using DNA barcoding to assess species diversity and geographic distribution patterns. A total of 141 individuals were collected from ten intertidal sites. Four species were identified—M. lyrata, M. lamarckii, M. meretrix and M. petechialis—with interspecific genetic distances (17.6–22.7%) far exceeding intraspecific variation (0.3–0.9%). Phylogenetic analysis based on COI sequences clearly distinguished four Meretrix species from the waters around Hainan Island, with each species forming a well-supported monophyletic clade, supporting their status as independent evolutionary lineages. In addition, two markedly divergent genetic lineages were detected within M. petechialis, suggesting that this species may possess a relatively complex population structure, one of which is typically found in northern Chinese waters, suggesting possible human-mediated introduction. Species richness was higher on the eastern coast, potentially influenced by regional hydrodynamic conditions. This study provides baseline DNA barcode data for Meretrix species in Hainan and supports the need for integrative management of this economically important resource. Full article

Sex determination in teleost fishes exhibits remarkable evolutionary plasticity; however, the underlying mechanisms remain largely elusive for many species of high economic importance. Herein, we provide the first genome-wide investigation of the genetic basis of sex determination in the European anchovy (Engraulis encrasicolus), an ecologically and commercially vital clupeiform fish. Using low-pass whole-genome resequencing of 100 sexually mature individuals (50 females and 50 males), we conducted a genome-wide association study (GWAS) and F_ST scans to identify sex-linked loci and characterize sex-determining regions (SDRs). Our analyses revealed two major candidate SDRs located on chromosomes 14 and 18, encompassing multiple sex-associated single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Among these, the amhr2 (anti-Müllerian hormone type 2 receptor) gene on Chr14 displayed the strongest and most consistent association with phenotypic sex, marked by several male-specific missense SNPs and InDel variants. Comparative and transcriptomic analyses confirmed sex-biased expression of amhr2 and other SDR-linked genes, potentially indicating a male heterogametic (XY-like) genetic sex determination system. These results provide the first molecular evidence for a candidate SDR in E. encrasicolus, raise the possibility of involvement of amhr2 and additional loci in sex determination, and highlight rapid sex chromosome turnover within Clupeiformes. Our findings not only expand the understanding of teleost sex determination evolution but also establish a genomic foundation for developing molecular tools for sex identification and population management in anchovy fisheries. Full article

Leptobotia rotundilobus is a newly described species in the subfamily Leptobotinae (Teleostei: Cypriniformes), which is endemic to China. Research on this recently discovered species is preliminary, characterized by limited baseline data and the absence of a fully sequenced mitochondrial genome. To elucidate the structural features of the mitochondrial genome of L. rotundilobus, we performed whole-genome sequencing using next-generation sequencing technology and analyzed its genomic composition, gene content, and structural variation through genome assembly and bioinformatics. The complete circular sequence, spanning 16,593 bp, comprises 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (D-loop), all arranged in the canonical order. The overall base composition of the genome was determined to be 30.8% adenine (A), 24.4% thymine (T), 28.6% cytosine (C), and 16.2% guanine (G). This A+T bias (55.2%) is consistent with the mitochondrial genomes of other Leptobotia, which may affect secondary structure. The ratio of non-synonymous (Ka) to synonymous substitutions (Ks) of 13 PCGs of 16 Leptobotinae species is far less than 1 (0.012–0.063), indicating strong negative or purifying selection on the mitogenome in these species. Moreover, to investigate the phylogenetic relationships within the subfamily Leptobotinae, particularly within the genus Leptobotia, we constructed multiple phylogenetic trees of the mitogenome and concatenated 13 PCGs of 39 sequences with Sinibotia superciliaris as an outgroup. The phylogentic trees using the maximum likelihood (ML) and Bayesian inference (BI) methods consistently indicate that: (1) after correcting the species identification error, L. rotundilobus is closely related to L. micra; and (2) the species of Leptobotia and Parabotia each form a monophyletic group. This study provides new insights into the taxonomy and phylogenetic relationships of Leptobotinae, with a particular focus on the genus Leptobotia, thereby contributing to the clarification of the systematics, origin, and evolution of Botiidae. Full article

This study documents the presence of two uncommon tetraodontiform fishes and reviews the occurrence of species from this order in Spanish marine waters. Two tetraodontid specimens (Family Tetraodontidae) were caught in the Atlantic waters off the coast of Galicia, northwestern Spain. A specimen of Sphoeroides pachygaster was collected in 2021 off the Costa da Vela, while a specimen of Ephippion guttifer was captured in 2025 in the Ría de Pontevedra, both locations situated in southern Galicia. Morphological analyses, supported by photographic evidence and DNA barcoding, confirmed the preliminary taxonomic identification of the two species. Histological reproductive analysis of the Ephippion guttifer specimen revealed a female in the spawning-capable phase. These findings constitute the first verified record of S. pachygaster and the second of E. guttifer in Galician waters. An updated comprehensive list of tetraodontiform species found in Spanish waters across five geographical demarcations was compiled. Historically, a total of 26 species across five families have been reported in Spanish waters, with 22 in the Canary Islands and 15 in the Spanish Iberian Peninsula and Balearic Islands. Additionally, a review of the presence of neurotoxic tetrodotoxins (TTXs) or paralytic shellfish toxins (PSTs) in each species is included, providing an up-to-date overview of a largely unexplored field in European waters. The increasing occurrence of tetraodontiform fishes in Spanish waters provides further evidence of the progressive tropicalization of the Spanish marine environment. Full article

South China’s freshwater biodiversity has been shaped by Quaternary climatic oscillations and persistent geological barriers. We investigated the phylogeography and conservation implications of the primary freshwater fish Microphysogobio kachekensis across mainland China and Hainan Island using mitochondrial (cyt b and control region) and nuclear (RAG2 and rpS7-1) markers from 200 individuals. Mitochondrial analyses recovered two major lineages and multiple sublineages largely structured by drainage basins, whereas nuclear data resolved four geographically concordant lineages. Population differentiation was strong (high F_ST), and SAMOVA/AMOVA supported major barriers restricting gene flow, including the Qiongzhou Strait, Gulf of Tonkin, Yunkai Mountains, and Nanling Mountains. Ancestral-area reconstruction inferred the Pearl River region as the most likely source area, followed by dispersal to northern Hainan and subsequent expansion to southern Hainan and the Red River, with additional northward expansion to the Zhejiang–Fujian region. Despite high haplotype diversity, within-population nucleotide diversity was low, consistent with long-term river isolation and complex demographic history. We propose six ESUs and four MUs for evolutionarily informed conservation and to guide stock enhancement in southern China. Full article

The Sharpchin Slickhead, Bajacalifornia burragei, is a rarely collected bathypelagic fish endemic to the eastern tropical Pacific Ocean, and its genetic diversity remains undocumented. This study characterizes mitochondrial diversity in a localized deep-basin collection from the Carmen Basin of the Gulf of California by sequencing complete mitochondrial genomes from four individuals collected simultaneously at 1300 m in a single Tucker trawl. A high-quality reference mitogenome was assembled using PacBio HiFi long reads, and three additional mitogenomes were generated from Illumina PE150 libraries mapped to this reference. The mitogenome of B. burragei exhibits the canonical 37 gene architecture and conserved gene order typical of teleost mitogenomes. Overall mitogenome divergence was low (Range: 0.21–0.29%), with most protein-coding and rRNA genes exceeding 99.5% identity. Slightly elevated variation occurred in atp8, nad6, and several tRNA genes. This study provides the first genetic characterization of B. burragei and establishes a baseline for evaluating mitochondrial diversity within a localized collection of individuals and provides a point of comparison for future studies assessing connectivity among deep basins. Full article

Echinoderms are marine invertebrates that play important roles in structuring marine benthic ecosystems. DNA barcoding has become a valuable tool for species identification; however, reference DNA barcode libraries for echinoderms remain incomplete. This study aims to: (i) develop a COI-5′ reference dataset for echinoderms from Vietnam by integrating DNA barcodes with morphological data; (ii) evaluate species resolution and barcode gaps using multiple analytical approaches; (iii) assess the consistency of species assignments from BOLD and GenBank for echinoderms collected in Vietnam; (iv) make barcode data publicly available to support global reference database development. Thirty-two echinoderm specimens representing 16 species were analyzed for COI-5′ sequences, and BLAST assignments were highly concordant with those from GenBank and BOLD. Integrative validation confirmed that all taxa were monophyletic in the Neighbor Joining Tree, formed single OTUs in Cluster Sequences, and exhibited clear barcode gaps greater than 3% to the nearest-neighbor species. These results provided species-level resolution for 75% and genus-level resolution for 90% of the records. The dataset, spanning four classes, eight orders, and eleven families, enhances barcode coverage and contributes records (ProcessIDs. BINs; GenBank accessions) to public repositories. This study delivers the first curated COI-5′ reference library, supporting regional baselines for taxonomy, conservation, and biodiversity assessment. Full article

Within the freshwater fish order Cypriniformes, loaches form a monophyletic lineage comprising nine families with more than 1400 species. Secondary sexual dimorphism is widespread among loach families, most notably in the form of enlarged pectoral fins and tubercles or other hard structures on the pectoral fin in adult males. To date, the family Botiidae, phylogenetically sister to all other loach families, was reported to lack such sexually dimorphic structures, leading to the hypothesis that the common ancestor of loaches did not exhibit sexual dimorphism. Here, we report the presence of sexual dimorphism in eight species of Botiidae: Leptobotia bellacauda, L. guilinensis, L. microphthalma, L. taeniops, L. tchangi, Parabotia fasciatus, Sinibotia pulchra, and S. robusta. In all species, adult males possess longer pectoral fins than females. Additionally, males of L. guilinensis and L. tchangi exhibit larger pelvic fins, while males of L. microphthalma have larger anal fins. In L. bellacauda, L. microphthalma, and L. tchangi, portions of the dorsal surface of the pectoral fin bear rows of tubercles. The three genera displaying sexual dimorphism belong to two different subfamilies, demonstrating that sexual dimorphism is widespread across Botiidae and not restricted to a single genus or subfamily. Our results show that sexual dimorphism is present in the most basal family of loaches, suggesting that it represents a synapomorphy of loach fishes. Full article

This study reports the first records of Sphyraena arabiansis in the Korean waters. The two specimens were collected from the coastal waters of Yeosu (1164 mm TL) and Jeju Island (1187 mm TL), Korea, on 31 July and 24 October 2025, respectively. This species is characterized by the posterior end of the upper jaw not extending vertically below the eye, the lateral line curving anterior to the first dorsal fin, the lower part of the branchiostegal membrane being whitish, dark transverse bands on the upper side of the body crossing the lateral line but not reaching the abdomen, no black spots on the body side, 118 and 121 lateral line scales, and 14 scales below the lateral line. To confirm the accuracy of species identification, the mitochondrial DNA cytochrome c oxidase subunit I sequences were obtained from the samples and compared with those of seven sphyraenid species recorded in the NCBI GenBank database. As a result, they matched well with S. arabiansis but differed from those of S. barracuda. The new Korean name, “Jjalb-eun-ip-keun-kko-chi-go-gi,” is proposed for the species. Full article

The shortfin lizardfish Saurida micropectoralis is recorded here for the first time from Jizan, Southern Red Sea, based on morphological and molecular analyses. This species closely resembles both S. tumbil and S. lessepsianus. However, S. micropectoralis is characterized by translucent whitish pelvic fins (vs. dusky in S. tumbil), indistinct blackish spots on the upper margin of the caudal fin (vs. distinct black spots (6–8) in S. lessepsianus), a short pectoral fin that never reaches the origin of the pelvic fin (vs. reaching a little beyond the base of the pelvic fin in S. lessepsianus), three rows of teeth on the outer palatines (vs. two rows in S. lessepsianus) and a pale whitish stomach and intestine (vs. greyish or black anteriorly in S. lessepsianus). Molecular analyses based on COI haplotypes confirmed the species-level identification but also revealed the existence of four distinct lineages across the species distribution range. The COI data revealed a clear geographic partitioning of haplotypes, indicating restricted gene flow and suggesting the presence of four cryptic species or, at minimum, independent evolving evolutionary units within Saurida micropectoralis. Populations of the shortfin lizardfish are well established in the Southern Red Sea and belong to a genetic lineage reported along the East African coast (Madagascar, Mozambique and Tanzania) and India. Full article

In this paper, we use molecular phylogenetics, micro-CT scanning, and morphological analyses to describe a new species of goby, Pascua marecoralliensis, and demonstrate that the genus Pascua is distinct from Hetereleotris, as supported by five diagnostic characters, including modified basicaudal scales and reduced sensory papillae patterns. Phylogenetic analysis places Pascua as sister to the Gobiodon group, while Hetereleotris forms a separate clade. The new species, P. marecoralliensis, differs from congeners in fin ray counts, cephalic pore patterns, and head morphology and exhibits unique live colouration. Additionally, we reclassify Hetereleotris readerae and H. sticta as Pascua readerae and P. sticta based on shared genus-specific traits. The distribution of Pascua spans the southern Pacific, suggesting a relict lineage or undiscovered diversity in the genus. This work underscores the importance of integrative taxonomic approaches for resolving cryptic diversity in gobioid fishes and highlights the need for further sampling in understudied regions. Full article

Hybridization is common among minnows and shiners in the family Leuciscidae, and mitonuclear discordance can reveal evidence of historical hybridization and introgression events that have shaped extant species and populations. We have identified a notable case of serial mitogenome replacement in populations of two shiner species, Luxilus zonatus and L. chrysocephalus, which are syntopic in drainages throughout the northern and eastern Ozark Interior Highlands of North America. These mitogenome replacement events involved L. zonatus acquiring the mitogenome of L. chrysocephalus, and populations of L. chrysocephalus acquiring the mitogenome of an allopatric congeneric species, L. cornutus. The latter species has a more northern distribution that was likely shifted southward by glacial advances during the Pleistocene. The geographic extent of mitogenome replacements in both species spans multiple separate drainages encompassing most of the major river systems that comprise the northern and eastern Ozark Highlands. We attribute these patterns to shifting species distributions, which were impacted by multiple glacial advances and coincident geomorphological changes to Ozark Highland drainages throughout the Pleistocene. The serial nature of mitogenome replacements in L. zonatus and L. chrysocephalus may exclude a role for natural selection in these introgression events, but the dynamic shifts in species distributions and gene flow connections throughout the Pleistocene may have favored an invasion-with-hybridization model that predicts massive asymmetric introgression between invading and resident species. These results have applied significance for eDNA metabarcoding methods of biodiversity assessment in Ozark streams, as they are dependent on mitogenome detections. Full article

This study reports the first record of Lyconus brachycolus in Spanish waters. A single specimen measuring 216 mm in total length was captured on 13 October 2024 in the Cantabrian Sea (north of Spain, 43.8467 N, −6.2109 W) by bottom trawl at a depth of 412 m. A detailed morphological description, updated characteristics, and illustrations are provided. For comparative purposes, an update of the species’ morphological characteristics was carried out. In an integrative taxonomic approach, the DNA barcode was obtained, which confirmed the morphological identification of the specimen as Lyconus brachycolus. A molecular taxonomic analysis using this marker showed the existence of two clades separated by 5.1%, corresponding to Lyconus brachycolus and Lyconus pinnatus, the two currently valid species of the genus. Full article

In this study, we sequenced and characterized the complete mitochondrial genome of Acorssocheilus spinifer, an endemic stream-dwelling cyprinid species from South China first described in 2006. The mitogenome is 16,591 bp in length and contains the standard set of 37 genes (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes) plus a control region. The genome exhibits typical cyprinid characteristics, with most genes encoded on the H-strand and a nucleotide composition biased toward A + T (55.9%). All tRNA genes display the typical cloverleaf secondary structure, except for tRNA^Ser (GCU), which lacks the dihydrouridine (DHU) arm. Phylogenetic analysis using complete mitogenomes from 14 Acrossocheilus species revealed that 12 species form a monophyletic assemblage with three distinct clades. Within this framework, A. spinifer clusters closely with A. beijiangensis, supporting previous morphological observations. Our findings provide valuable genetic data for further taxonomic refinement and conservation efforts for Chinese barred species of Cyprinidae. Full article