Nucleotide diversity and evolutionary rate analyses across mitogenomes of Oedipodinae revealed pervasive purifying selection acting on all 13 PCGs, which strongly supported M. wagneri as a monophyletic lineage within the subfamily Oedipodinae.
Abstract
We employed second-generation sequencing technology to determine the complete mitochondrial genome of Mioscirtus w. wagneri (Eversmann, 1859), which is the first species reported in the genus Mioscirtus. The mitochondrial genome spans 15,632 base pairs and encodes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and an AT-rich control region (D-loop region). The nucleotide composition exhibits a strongly A+T bias (75.6%). Among the 13 PCGs, 27 codons exhibited higher usage frequencies, predominantly with A/U endings. All tRNA genes adopt the canonical cloverleaf secondary structure, except for tRNASer(AGN), which lacks the dihydrouridine (DHU) arm. Nucleotide diversity and evolutionary rate analyses across mitogenomes of Oedipodinae revealed pervasive purifying selection acting on all 13 PCGs (Ka/Ks < 1). Among these, ND2 exhibited the highest nucleotide diversity, whereas ND4L exhibited the lowest. Phylogenetic analyses were conducted based on the concatenated nucleotide sequences of all 13 PCGs, using both Maximum likelihood (ML) and Bayesian inference (BI) frameworks, which produced an identical topology strongly supported M. w. wagneri as a monophyletic lineage within the subfamily Oedipodinae. This lineage formed a sister group relationship with species of the genus Celes and shared a most recent common ancestor with species of the genus Oedipoda, together constituting the tribe Oedipodini. This phylogenetic relationship is consistent with traditional morphology-based classifications. These findings expand the currently sparse mitogenomic resource for the subfamily Oedipodinae and provide a robust genetic foundation for future studies on the population genetics and evolutionary history of M. w. wagneri.
Background: Leptobotia tchangi is a loach species endemic to South China, but its mitochondrial genome has not yet been characterized, limiting understanding of its evolutionary relationships and conservation genetics. Methods: Here, we report the first complete mitochondrial genome of L. tchangi, using next-generation sequencing, assembly and bioinformatics analyses. Results: The double-stranded circular mitogenome has 16,590 bp and contains: 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (D-loop) containing conserved ETAS and CSB motifs. The overall base composition is 25.0% thymine (T), 27.9% cytosine (C), 31.1% adenine (A), and 16.0% guanine (G), showing a clear A + T bias (56.1%) which is consistent with other Botiidae mitogenomes. To infer the phylogenetic placement of L. tchangi within Botiidae, we conducted both Bayesian inference and maximum-likelihood phylogenetic analyses based on the concatenated PCG sequences. Our results strongly support (1) the monophyly of the subfamilies Leptobotiinae and Botiinae, as well as the monophyly of each genus within the family Botiidae; (2) three sister-group relationships within Botiinae: (Botia + Chromobotia), (Ambastaia + Sinibotia), and (Syncrossus + Yasuhikotakia), with the latter two species groups also being sister groups; (3) L. tchangi being most closely related to Leptobotia taeniops. Conclusions: These findings not only provide essential molecular markers for the species identification and conservation genetics of L. tchangi, but also clarify the taxonomic status of L. tchangi within Botiidae.
Overall, this study uncovers inversion-driven mitochondrial gene rearrangements as a major evolutionary force in Littorinimorpha, expanding genomic resources for Naticidae and refining phylogenetic relationships within this diverse clade.
Xiaoxu Zheng, Ying-Ying Ye, Ji-Ji Li et al.· Genetica· 0 citations
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.
Huiming Zhou, Guo-Yong Xiong, Jiaxin Yuan et al.· Mitochondrial DNA. Part A, D...· 0 citations
The family Uzelothripidae is represented by a single genus Uzelothrips and can be distinguished from others by the presence of whip-like antennae, a circular ventral sensorium on antennal segment III, a well-developed tentorium, and a membranous ovipositor. Here, we generated the first complete mitochondrial genome of Uzelothrips scabrosus (15,674 bp) using next-generation sequencing to explore the gene rearrangements and phylogenetic relationships. It consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two putative control regions. The genome exhibits strong AT bias (71.35%) with negative AT and GC skew. Codon usage analyses indicate a strong bias towards A/U-ending codons and influenced by both natural selection and mutation pressure. All PCGs were under purifying selection, with cox1 being the most conserved and nad4L the most variable. The gene order of the family Uzelothripidae is highly rearranged compared to the ancestral insect gene order. Comparative analysis revealed that gene block B was the most widely conserved, whereas the remaining gene blocks exhibited family or lineage-specific conservation patterns, reflecting extensive mitochondrial gene rearrangements during the evolution of the Thysanoptera. Moreover, 228 synapomorphic and 68 autapomorphic gene boundaries were identified across thysanopteran mitogenomes. Phylogenies indicated that the family Uzelothripidae is in a sister relationship with Stenurothripidae, and the Uzelothripidae + Stenurothripidae clade is sister to Thripidae. This study provides the first mitogenomic insights into Uzelothripidae and highlights the need for broader taxon sampling and nuclear genomic data to resolve deep evolutionary relationships within Thysanoptera.
The mitogenome of the decorator crab Hyastens ducator is sequenced for the first time, clarifies its phylogenetic position, enriches the molecular dataset for the family Epialtidae and provides an important reference for future taxonomic and evolutionary studies of Majoidea.
Chenfang Niu, Ji-Chun Li, Ying-Xuan Bao et al.· Crustaceana· 0 citations
The first complete mitogenome of Eurostus validus is reported and indicates that both mutation pressure and natural selection shape codon usage bias, with natural selection playing a dominant role.
Dong-Kai Liu, Chao Xue, Yingyin Gao· Journal of the Entomological...· 0 citations
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