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.
