The crescent perch, Terapon jarbua, is a medium-sized, euryhaline fish of ecological and economic importance, contributing to demersal fisheries and the marine ornamental fish trade in India. Genetic diversity and population structure of T. jarbua along the Indian coast were assessed using 145 partial sequences (506 bp) of the mitochondrial D-loop region. Populations exhibited high haplotype and nucleotide diversity. A total of 96 haplotypes were identified, with several shared among geographically distant populations. The results revealed high within-population variation and broad genetic connectivity of T. jarbua along the Indian coast, with evidence of partial genetic structuring and low-to-moderate differentiation in some pairwise comparisons. Neutrality tests and mismatch-distribution analyses provided suggestive evidence of historical demographic expansion. High genetic diversity and demographic patterns consistent with a possible historical expansion suggest a complex demographic history, including a possible population expansion during the Pleistocene epoch. These findings provide baseline information for future genetic assessments and the sustainable management of T. jarbua in Indian waters.
The complete mitochondrial genome of Plagiognathops microlepis was sequenced using Illumina NovaSeq and PacBio Sequel II platforms.The circular mitogenome is 16,632 bp in length and contains 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region (D-loop). The genome exhibits an AT content of 56.7%, with an AT skew of 0.104 and a GC skew of -0.255. COX1 initiates with GTG and CYTB with ATA, whereas the remaining 11 PCGs employ ATG; four PCGs (COX2, COX3, ND3, and ND4) terminate with incomplete stop codons (T or TA). Relative synonymous codon usage (RSCU) analysis revealed 27 preferred codons (RSCU > 1), with a strong bias toward A- and T-ending codons. All 22 tRNAs display conventional cloverleaf secondary structures. Maximum likelihood (ML), Bayesian inference (BI) and Neighbor joining (NJ) analyses consistently recovered P. microlepis as sister species to Xenocypris davidi (NJ bootstrap = 1, ML UFBoot = 67, BI posterior probability = 0.977), confirming its phylogenetic position within the genus Xenocypris. These findings provide molecular evidence for the taxonomic placement of P. microlepis and genomic resources for species delimitation, conservation genetics and evolutionary studies within Xenocyprinae.
To assess the genetic diversity and population structure of Palaemon modestus in the Three Gorges Reservoir (TGR), we analyzed mitochondrial COI sequences from five populations and further evaluated the two mitochondrial clades revealed by COI using Cyt b, D-loop, and nuclear 28S rDNA markers. The TGR populations showed high genetic diversity, with a haplotype diversity of 0.920 and a nucleotide diversity of 1.400%. Bayesian phylogenetic analysis and the COI haplotype network separated 54 haplotypes into TGR Clade A and TGR Clade B, with 11 mutational steps between them; Cyt b and D-loop phylogenies also supported the two-clade pattern. However, 28S rDNA sequences were identical between the clades, and ABGD assigned all COI haplotypes to a single molecular operational taxonomic unit. The overall FST among populations was 0.067; when analysis was restricted to Clade A individuals, the overall FST remained 0.064, indicating that population differentiation was not solely attributable to the uneven distribution of Clade B. Overall, P. modestus in the TGR maintains high genetic diversity and shows detectable population differentiation. The available evidence supports interpreting TGR Clades A and B as deeply divergent mitochondrial lineages within P. modestus.
This study presents the characterization of the complete mitochondrial genome of Pteronotus mexicanus, an endemic species from Mexico and a representative of the family Mormoopidae. The mitogenome was assembled de novo using the program GetOrganelle, and gene annotation was performed with the software MITOS2. The newly assembled mitogenome has a total length of 16,762 base pairs and exhibits the typical mammalian gene organization: 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding region commonly referred to as the control region. The nucleotide composition of the mitogenome was A = 33.10%, T = 25.29%, C = 27.89%, and G = 13.72%, with an overall A + T content of 58.39%. Codon usage analysis revealed preferences consistent with the adenine- and thymine-rich composition characteristic of vertebrate mitochondrial DNA. Ka/Ks ratio values estimated indicated purifying selective pressure on the protein-coding genes. Predicted secondary structures of tRNAs exhibited the typical cloverleaf configuration, except for trnS1, which lacks the DHU arm-a common feature among mammals. The phylogenetic position of the common Mexican mustached bat supports the monophyly of the genus within the superfamily Noctilionoidea. This study represents the first comprehensive description of the mitogenome of P. mexicanus and provides a valuable molecular resource for future research on the systematics, phylogeny, and population genetics of Neotropical bats.
Mutations in mitochondrial tRNA (mt-tRNA) genes are associated with non-syndromic hearing loss (NSHL), though their detailed molecular mechanisms and pathogenic potential remain unclear. In this study, we reported three Han Chinese pedigrees exhibiting maternally transmitted NSHL. Mitochondrial genomes from probands were sequenced and compared to revised Cambridge reference sequence (rCRS), followed by phylogenetic analysis to assess pathogenicity. We further established cybrid cell lines to measure mtDNA copy number, ATP levels, mitochondrial membrane potential (MMP), reactive oxygen species (ROS), and 8-OHdG, we also screened mutations in nuclear deafness genes including GJB2, GJB3, GJB6, and TRMU. Affected individuals displayed a wide range of age at onset (mean 40.5 years) of deafness. A homoplasmic m.A10055G mutation was identified in the tRNAGly gene, which disrupted a conserved base pair. Compared to controls, mutant cybrids showed significantly reduced mtDNA copy number, ATP, and MMP, along with increased levels of 8-OHdG and ROS, whereas no pathogenic nuclear variants were detected. Collectively, these findings indicated that the m.A10055G mutation contributed to NSHL pathogenesis by impairing mitochondrial functions, most likely through defective tRNA metabolism and by increasing oxidative stress.
Billfishes (Xiphiidae and Istiophoridae) are economically important species. Unfortunately, these fish are part of the bycatch in many fisheries and are subject to unregulated trade. Another problem is inadequate identification, as diagnostic features are often removed when they are captured. This research aimed to design protocols based on PCR-RFLPs and PCR-Multiplex to carry out a relatively rapid and robust identification of billfish species of commercial interest in the Eastern Tropical Pacific. In silico PCR-RFLP analysis allowed the selection of six restriction enzymes; the enzyme HinfI was the most effective for species discrimination, while PvuII was the least effective. For the PCR-Multiplex, it was observed that the primers designed in silico amplify approximate sizes for their respective species and allow the identification of the species through the difference in band sizes in the agarose gels. These tools were tested on tissues from commercial sources, where it was possible to identify three species of billfishes (Kajikia audax, Makaira nigricans, and Xiphias gladius) and two species from other groups (Nematistius pectoralis and Thunnus albacares). The application of the protocols was successful in fresh tissue and processed (smoked) tissue. These protocols, implemented together, allow for greater support in the genetic identification of billfishes.
Though the family Ceratopogonidae is a species-rich group (6346 extant species in 2025) within the Diptera, the complete mitochondrial genomes (mitogenomes) have been characterized for a small number of species. In this study, we sequenced and characterized the complete mitogenomes of Dasyhelea ludingensis (15,687 bp) and Forcipomyia (Lasiohelea) taiwana (17,315 bp) to explore their genomic structure and phylogenetic relationships. Each mitogenome exhibited the typical insect structure: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region, maintaining the ancestral insect gene arrangement. All PCGs used typical ATN start codons, except for COX1 in D. ludingensis, which was putatively initiated by the atypical AAC codon. Both mitogenomes exhibited a strong A + T bias, with A + T contents of 78.29% in D. ludingensis and 78.89% in F. taiwana, respectively, which affects codon usage and amino acid (AA) composition. Regarding tRNA secondary structures, trnS1-GCU in F. taiwana lacked the dihydrouridine (DHU) arm and contained an unpaired adenine residue in the anticodon stem. Phylogenetic analyses confirmed the taxonomic status of D. ludingensis and F. taiwana at the molecular level. This study provides essential genomic resources for future studies in systematics, phylogenetics, and population genetics of biting midges.
Haplotype networks are widely used in population genetics, phylogeography, and molecular ecology to visualize relationships among DNA sequences and summarize patterns of population connectivity. Existing tools vary in interface, algorithmic approach, input requirements, and output format. Here, I introduce HapNet, an open-source Python command-line package for constructing population-aware, minimum-spanning-tree-based haplotype graphs from aligned FASTA files. HapNet collapses identical sequences into haplotypes, calculates Hamming distances among haplotypes, constructs an MST-based graph, and generates publication-ready visualizations in which node size reflects haplotype frequency and pie-chart sectors indicate population composition. HapNet also produces machine-readable tabular outputs documenting haplotype membership, shared and private haplotypes, individual assignments, summary statistics, and run metadata. This version adds optional metadata input, phased diploid sequence support, individual-level genotype summaries, and label-free figure export. Utility is demonstrated using a published Hydroides dianthus COI dataset and a simulated phased diploid dataset.
The sun anemone shrimp, Periclimenes rathbunae (Decapoda: Palaemonidae), is a small, translucent shrimp broadly distributed across the tropical Western Atlantic that typically inhabits sea anemones in shallow waters. Recent trading of the host sea anemones in the ornamental industry has likely increased stress on the population health of this shrimp. To aid in conservation efforts, the complete mitochondrial genome of P. rathbunae has been assembled and characterized in detail. The mitochondrial genome of P. rathbunae is 15,809 bp long and includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S and 16S rRNA), and a 976 bp control region. The gene order is identical to that reported for two other species in family Palaemonidae, but different from the ancestral decapod ground pattern. The overall A + T content is 67.8%, and the codon usage of PCGs exhibits a strong preference for A + T-rich codons. All 13 PCGs exhibited purifying selection, with the strongest selection exhibited in cox1 and the weakest exhibited in atp8. All tRNA genes exhibited the typical cloverleaf secondary structures except for trnT and trnL2, which were missing the TC-loop, trnR missing the D-loop, and trnS1 missing the dihydroxyuridine (DHU) arm. The control region exhibited a high A + T content (74.2%), four dinucleotide microsatellite repeats, a single tandem repeat, and multiple hairpin loops in the predicted Minimum Free Energy (MFE) and Centroid secondary structures. The newly assembled mitochondrial genome will aid in the identification of P. rathbunae and support programs based on environmental DNA (eDNA).
Anthopleura xanthogrammica and Diadumene lineata have considerable pharmaceutical potential, but their distribution and population genetics along the Chinese coastline remain poorly understood. We collected 162 samples of the two species based on external morphology from nine intertidal sites. Subsequent analyses of the mitochondrial COI segment (607 bp) confirmed 143 A. xanthogrammica individuals across all nine localities, and only 19 D. lineata individuals restricted to three localities. For A. xanthogrammica, genetic diversity, phylogenetic relationships, population structure and demographic history were analyzed using combined mitochondrial segments (COI + 16S rRNA: 1,055 bp) and nuclear segments (28S rRNA: 316 bp; ITS: 658 bp). This species showed high genetic polymorphism. Mitochondrial DNA data (neutrality tests, mismatch distributions, haplotype network) suggested a historical and mild population expansion, while phylogenetic and molecular variance analyses indicated limited gene flow and high genetic differentiation among geographic populations. Population structure supported three management units for the conservation of this species. For D. lineata, we attempted genetic diversity and neutrality tests using the same molecular markers, but the results were unreliable due to the small sample size. Future studies should identify more suitable sampling sites and use a larger sample size to assess its genetic polymorphism and population structure.
Non-invasive genetic approaches provide reliable tools for species identification, particularly in cases where morphological traits are ambiguous. This study investigated the potential presence of Rüppell's fox (Vulpes rueppellii) in Southeastern Anatolia (Türkiye), prompted by camera trap images showing features that could be attributed to either V. rueppellii or the red fox (V. vulpes). Mitochondrial cytochrome b (Cytb) sequences were obtained from fecal samples and analyzed using Maximum Likelihood phylogenetic methods, complemented by haplotype network analysis. All sequences showed high similarity (99-100%) to V. vulpes and clustered within the V. vulpes reference sequences. No genetic evidence supporting the presence of V. rueppellii was detected. The haplotype network further confirmed the placement of all samples within the Holarctic lineage of V. vulpes. These findings demonstrate that the individuals observed in the study area belong to V. vulpes, despite morphological variation that could suggest otherwise. The results highlight the importance of mitochondrial DNA-based methods for accurate species identification in non-invasive studies, particularly in regions where closely related taxa may occur.
The complete mitogenome of Hoplia bomiensis Zeng (H. bomiensis) was sequenced and characterized. It was 16,311 bp in length and exhibited conserved gene order, content, and orientation typical of Scarabaeidae. All protein-coding genes (PCGs) began with ATN start codons. The COX1, COX2, and COX3 genes terminated with incomplete stop codon T, while the remaining PCGs ended with TAA or TAG. The non-synonymous (Ka) to synonymous (Ks) substitution ratios for all 13 PCGs were less than 1, suggesting purifying selection. ATP8 displayed the highest Ka/Ks ratio (0.48) and the largest genetic distance compared to the other PCGs. Sliding window analysis identified ND2 as the most variable gene and COX1 as the most conserved. This mitogenome contained 22 tRNA genes, all exhibiting typical cloverleaf structure except trnS1, which lacked the dihydrouracil (DHU) arm. Codon usage was strongly biased toward A/U-ending codons, particularly UUA, AUU, and UUU. Phylogenetic analysis indicated two clades in the family Scarabaeidae. The first clade contained Aphodiinae and Scarabaeinae. Within the second clade, Sericinae diverged first. Melolonthinae was recovered as a non-monophyletic group with three distinct clades, where H. bomiensis formed a highly divergent lineage and exhibited unstable phylogenetic positions between nucleotide- and amino acid-based trees.
Toxospathius auriventris Bates and Maladera orientalis Motschulsky, are soil-dwelling insects that are mainly distributed in Xizang, China, and considered to be agricultural pests. This study sequenced and characterized the mitogenomes of T. auriventris and M. orientalis, which were 16,837 bp and 16,972 bp in-length. Both mitogenomes exhibited highly conserved gene order of Scarabaeidae. Most protein-coding genes (PCGs) initiated with typical ATN start codon. The incomplete stop codon T was used in COX1, COX2 (only in T. auriventris) and COX3 genes, whereas typical stop codon TAN was used in other PCGs. The Ka/Ks ratios for each PCG among 18 species from subfamily Melolonthinae were less than 1 (0.078 to 0.69). The genetic distances of PCGs indicated ATP8 (0.47) evolved relatively fast, while COX1 (0.23) and ND4L (0.24) were more conserved. The nucleotide diversity analysis (Pi values) across the 13 PCGs in subfamily Melolonthinae indicated that ND2 gene exhibited the greatest variability. While, COX1 and ND5 presented lower diversity. Phylogenetic trees reconstructed via maximum likelihood (ML) and Bayesian inference (BI) methods suggested that the subfamily Melolonthinae is non-monophyletic, in contrast to the monophyletic Cetoniinae, Rutelinae, and Dynastinae. T. auriventris and M. orientalis were clustered in different clades within the subfamily Melolonthinae.
Vischeria sp. WL1, an oleaginous microalga isolated from biocrusts, is a promising candidate for biofuel production due to its high lipid accumulation and tolerance to moderate salt stress. In this study, we sequenced and assembled the complete plastid genome of Vischeria sp. WL1. The circular genome is 126,330 bp in length with a GC content of 32.5%, and contains 142 protein-coding genes, 29 transfer RNA (tRNA) genes, and six ribosomal RNA (rRNA) genes. Comparative plastid genome analysis identified a conserved six-gene operon shared by all five Vischeria strains and uncovered specific molecular markers for distinguishing eustigmatophyte species. Phylogenetic analysis based on 64 genes from Ochrophyta species confirmed the placement of Vischeria sp. WL1 within the Vischeria clade. Our work on the plastid genomes of Vischeria strains provides a foundational resource for understanding genetic diversity and conservation in the Eustigmatophyceae.
The present study established the first molecular-based inventory of nine freshwater fish species from Pantabangan Dam, a genetically unexplored fishery resource in Nueva Ecija, Central Luzon region of the Philippines. Forty mitochondrial cytochrome c oxidase I (COI) sequences were generated representing nine species, eight families and six orders of fishes, providing potential application in biodiversity assesment and management. In all cases, sequence analysis yielded low intraspecific divergence and a high interspecific genetic distance was observed in the Nearest Neighbor Distance analysis. Neighbor-Joining and Maximum Likelihood phylogenetic trees recovered a monophyletic species-level clades supported by high bootstrap values. Out of the nine species identified, three were native species in the Philippines (Leiopotherapon plumbeus, Glossogobius aureus and Clarias batrachus). Two species (Micropterus floridanus and Coptodon zillii) have been recorded for the first time in the dam, indicating the need to review how monitoring protocols can be enhanced by combining morphological assessment and molecular identification. The generated sequences can be used as a baseline data for the conservation of endemic species and formulation of management decisions on the invasive fishes. Overall, our study confirmed the efficiency of DNA barcoding in species delineation and offered a new framework for fish management in the dam.
The genus Himantura, Müller and Henle 1837 (Myliobatiformes: Dasyatidae) comprises benthic stingrays inhabiting tropical and subtropical waters, including the biodiversity-rich Southwest Indian Ocean (SWIO). Despite their ecological significance and susceptibility to anthropogenic pressures, the genetic diversity and evolutionary relationships of Himantura species remain poorly understood. This study sequenced and characterised the complete mitochondrial genomes of the SWIO variants of Himantura leoparda (17,682 bp) and Himantura uarnak (17,670 bp), the latter representing the first mitogenome for this species. Each mitogenome exhibited the typical vertebrate structure: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Codon usage was strongly AT-biased, with leucine (CTA) and isoleucine (ATC) predominating. Elevated single nucleotide polymorphism diversity in ND4 suggests ongoing divergence with adaptive implications. Phylogenetic analysis of concatenated PCGs confirmed the monophyly of Himantura within Dasyatidae, with distinct separation between the two SWIO mitogenomes supporting recognition of two separate species. The SWIO H. leoparda variant was most closely related to the Indo-Pacific H. leoparda variant. These findings address taxonomic ambiguities within the genus and highlight the need for species-specific conservation strategies, providing essential mitogenomic data to support future Himantura research in the SWIO.
Recent advances in sequencing technology have enabled rapid and cost-effective recovery of mitochondrial genomes (mitogenomes), which are used in phylogenetic and evolutionary studies. Among cnidarians, the order Zoantharia possesses one of the largest mitogenomes on average 20,976 bp. Palythoa tuberculosa (Hexacorallia: Zoantharia: Sphenopidae) has the largest reported mitogenome in this order (23,044 bp), approximately 2,000 bp larger than the zoantharian average. In this study, to determine the basis of this expansion, we generated and annotated the complete mitogenome of P. tuberculosa. Synteny analysis revealed that this increased genome size is attributed to the insertion of a novel open reading frame (ORF) located between trnW and cox2, encoding 665 amino acids, initiated with the codon ATG and terminated with TAA. This ORF was also present in the closely related species P. caribaeorum, suggesting its origin in their common ancestor. This represents the first case of a novel ORF insertion in zoantharians and demonstrates that mitogenome expansion in zoantharians can result from lineage-specific protein-coding insertions, revealing greater structural dynamism in anthozoan mitogenomes than previously recognized.
The Madras hedgehog (Paraechinus nudiventris) is an understudied species endemic to southern India, with limited genetic data available for understanding its evolutionary history. Here, we present the complete mitochondrial genome (17,232 bp), annotated and analysed in comparison with other Erinaceidae species. The mitogenome retains the typical vertebrate structure, comprising 13 protein-coding genes, 22 tRNAs, two rRNAs, and a non-coding control region, with an A + T rich nucleotide composition. Phylogenetic analyses using Bayesian and maximum-likelihood approaches confirmed the species' placement within Paraechinus, with divergence from P. micropus estimated during the Pleistocene. Molecular evolutionary analyses revealed selective constraints on oxidative phosphorylation genes, with atp8 showing the highest variability. Our divergence time estimates, incorporating fossil calibrations, refine the evolutionary timeline of Erinaceidae, providing insights into the diversification of hedgehogs in South Asia. By making this annotated mitochondrial genome publicly available, we provide a foundational resource for future studies on the genetic diversity, phylogeography, and conservation of P. nudiventris and its relatives.
An analysis of partial sequences of the cytochrome c oxidase subunit I (COI) gene from 39 specimens of Emplectonema ex gr. gracile from the Sea of Okhotsk, Sea of Japan, and Yellow Sea has shown that almost all the studied specimens from the first two seas belong to Emplectonema viride, which is also distributed along the Pacific coast of North America. In the Sea of Okhotsk and Sea of Japan, only three haplotypes for this species have been identified, all differing from the haplotypes sampled from off the North American coast. One specimen from the Sea of Japan (Spokoinaya Bay, southern Primorsky Krai, Russia) and all the specimens from the Yellow Sea belong to E. gracile. Of the six haplotypes of Pacific E. gracile, four are also found in the Atlantic Ocean. It has been suggested that E. gracile is an invasive species to the Pacific Ocean.
Mitochondrial DNA has unique biological characteristics, such as a high mutation rate and clonal inheritance, which make it an appropriate marker in molecular biology. However, exceptionally high mitochondrial divergences have been reported in terrestrial and marine invertebrates, plants, and certain vertebrate lineages, which complicates the interpretation of the results in DNA barcoding and evolutionary studies. The freshwater snails in the genus Semisulcospira have two mitochondrial DNA lineages: a normal mitochondrial lineage (mt-A type) and a highly divergent 'enigmatic' lineage (mt-B type). We assembled thirty-two mitogenomes of Semisulcospira to understand the molecular evolution of the mt-B type. We found that the mt-B type evolves faster than the mt-A type, has more non-synonymous mutations, and exhibits structural variations with truncated cob and cox3 genes. Our results showed that the observed molecular evolution of the mt-B type could result from a decreased efficiency of natural selection due to small population size and/or the accumulation of slightly deleterious mutations caused by mitochondrial sex ratio distortion.
