Complete mitochondrial genome of the diving beetle, Cybister brevis Aubé, 1838 (Coleoptera, Dytiscidae) from Jeju Island

The mitochondrial genome of Cybister brevis Aubé, 1838, is 16,198 bp long and includes 37 genes that are highly conserved in the family Dytiscidae. Phylogenetic analysis revealed that all genera in Dytiscidae, except Hydroporus and Oreodytes, are monophyletic. The Hydroporini tribe was found to be polyphyletic and closely associated with the Hygrotini, Bidessini, and Hyphydrini tribes. Dytiscinae was found to be a highly divergent polyphyletic group comprising three distinct clades. This study also revealed that C. brevis is closely related to Cybister japonicus and that the tribe Cybistrini diverged relatively early compared to other tribes in Hydroporinae. These findings are consistent with those of previous studies and provide new insights into the phylogeny of the Dytiscidae family, which has previously shown discrepancies between morphological characteristics and molecular data. The genome-level analyses conducted in this study serve as a valuable foundation for future investigations into the Dysticidae evolutionary history.

The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda

This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.

The complete mitochondrial genome of the bait worm, Marphysa victori (Annelida; Polychaeta; Eunicida; Eunicidae)

The complete mitochondrial genome of Marphysa victori Lavesque, Daffe, Bonifácio & Hutchings, 2017, was 15,891 bp in length with a GC content of 41%, comprising 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The maximum-likelihood tree showed the closest relationship between M. victori and M. sanguinea.

RNA editing events and expression profiles of mitochondrial protein-coding genes in the endemic and endangered medicinal plant, Corydalis saxicola

Corydalis saxicola, an endangered medicinal plant endemic to karst habitats, is widely used in Traditional Chinese Medicine to treat hepatitis, abdominal pain, bleeding hemorrhoids and other conditions. However, to date, the mitochondrial (mt) genome of C. saxicola has not been reported, which limits our understanding of the genetic and biological mechanisms of C. saxicola. Here, the mt genome of C. saxicola was assembled by combining the Nanopore and Illumina reads. The mt genome of C. saxicola is represented by a circular chromosome which is 587,939 bp in length, with an overall GC content of 46.50%. 40 unique protein-coding genes (PCGs), 22 tRNA genes and three rRNA genes were identified. Codon usage of the PCGs was investigated and 167 simple sequence repeats were identified. Twelve homologous fragments were identified between the mt and ct genomes of C. saxicola, accounting for 1.04% of the entire mt genome. Phylogenetic examination of the mt genomes of C. saxicola and 30 other taxa provided an understanding of their evolutionary relationships. We also predicted 779 RNA editing sites in 40 C. saxicola mt PCGs and successfully validated 506 (65%) of these using PCR amplification and Sanger sequencing. In addition, we transcriptionally profiled 24 core mt PCGs in C. saxicola roots treated with different concentrations of CaCl2, as well as in other organs. These investigations will be useful for effective utilization and molecular breeding, and will also provide a reference for further studies of the genus Corydalis.

Comprehensive Analysis of Phylogenetic Relationship and Optimal Codons in Mitochondrial Genomes of the Genus Pseudogastromyzon

As indicator organisms for water pollution detection, Pseudogasteromyzon species play a vital role in aquatic environment monitoring. We have successfully sequenced the mitogenomes of P. fasciatus jiulongjiangensis and P. myersi and downloaded the mitogenomes of nine other Pseudogastromyzon fish on GenBank to conduct a detailed comparative analysis of their phylogenetic relationships and evolutionary history. The findings revealed a conservation in both gene composition and gene order. Except for the trnS1 gene lacking dihydrouracil arms, the other 21 tRNAs showed the typical clover-leaf secondary structure. According to the ΔRSCU method, we identified the seven most abundant optimal codons: CUA, GUA, CCA, CAA, GAA, AGC, and GGC. The construction of maximum parsimony, maximum likelihood, and Bayes trees yielded congruent topologies, and the 11 Pseudogastromyzon species were clustered into two major clusters. Among them, one of which was composed of P. fangi, P. changtingensis changtingensis, and P. changtingensis tungpeiensis, while the remaining eight species formed another cluster, further subdivided into five smaller clusters. Distinct clusters formed between P. fasciatus jiulongjiangensis and P. meihuashanensis, P. cheni and P. peristictus, and P. laticeps and P. lianjiangensis, and the remaining two species were clustered separately, thereby enhancing our understanding of them. Furthermore, our analysis results of divergence times revealed that these 11 Pseudogasteromyzon species underwent rapid differentiation in the Pleistocene epochs. Overall, our study sheds light on the phylogenetic relationship and evolutionary history of Pseudogasteromyzon species, providing a necessary knowledge foundation for further understanding the intricacies of an ecosystem health assessment.

The overview of methods for assembling complex mitochondrial genomes in land plants

The large size and complex structural rearrangements inherent in mitochondrial genomes of land plants pose challenges for their sequencing. Originally, the assembly of these genomes required the cloning of mitochondrial DNA fragments, followed by Sanger sequencing. Subsequently, the advent of next-generation sequencing significantly expedited the process. This review highlights instances of plant mitochondrial genome assembly employing various technologies, including 454 sequencing, Illumina short sequencing reads, and Pacific Biosciences or Oxford Nanopore Technology long sequencing reads. The combination of short and long reads in hybrid assembly has proven to be the most efficient approach for achieving reliable assemblies of land plant mitochondrial genomes.

Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav

Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated the complete mt genome of C. pubescens. We investigated several aspects of its genome, including characteristics, codon usage, RNA editing sites, repeat sequences, selective pressure, gene clusters, and phylogenetic relationships. Furthermore, we compared it with other plant mt genomes. The data we obtained will provide valuable information for studying evolutionary processes in the Capsicum genus and will assist in the functional analysis of Capsicum mitogenomes.

Complete mitochondrial genome of an oleaginous microalga Vischeria punctata (Eustigmatophyceae: Chlorobotryaceae) and phylogenetic analysis

Vischeria punctata, as first described by Vischer in 1945, is a member of the family Chlorobotryaceae, within the order Eustigmatales. This species is recognized for its potential as a source of biofuels and other high-value products. In the present investigation, the whole genome of V. punctata was sequenced utilizing the Illumina HiSeq 4000 platform, enabling the assembly and annotation of its complete mitochondrial genome. The resulting circular genome spans 41,528 base pairs (bp) with a guanine-cytosine (GC) content of 27.3%. This genome encompasses 36 protein-coding genes, alongside 28 transfer RNA (tRNA), and three ribosomal RNA (rRNA) genes. The evolutionary trajectory of V. punctata was further explored by constructing a phylogenetic tree derived from the mitochondrial 33 gene dataset of 16 Ochrophyta species. Comparative analysis reveals that V. punctata bears closer ties to Vischeria sp. CAUP Q202 than to Vischeria stellata strain SAG 33.83, suggesting shared evolutionary pathways and phenotypic traits. This investigation constitutes the inaugural study into the mitochondrial evolution and phylogenetic patterning of the mitogenome in V. punctata. The outcomes from this research bolster our understanding of the genetic diversity and evolutionary processes within the class Eustigmatophyceae. In particular, the mitochondrial genome of V. punctata serves as a valuable resource in elucidating these aspects.

The complete mitochondrial genome of Bauhinia variegata (Leguminosae)

The mitogenome of Bauhinia variegate was assembled and characterized in this study. The mitogenome size was 437,271 bp, and its GC content was 45.5%. 36 protein-coding genes, 17 tRNAs and 3 rRNAs were annotated in the mitogenome. A total of 12 MTPTs, ranging from 71 bp to 3562 bp, were identified in the mitogenome and covered 1.46% (6373 bp) of the mitogenome. Phylogenetic analysis of 15 species of Leguminosae based on 23 core protein-coding genes showed that B. variegata was sister to Tylosema esculentum, another member from the subfamily Cercidoideae. The mitogenome of B. variegata provides a valuable genetic resource for further phylogenetic studies of this family.

The Mitogenomic Characterization and Phylogenetic Analysis of the Plant Pathogen Phyllosticta yuccae

Phyllosticta yuccae is an important plant pathogen causing leaf spot disease in Yucca gigantea Lem. It is imperative to note that the amount of information available about the mitogenome of this subject is severely limited. This must be addressed immediately, as it is crucial to our understanding and progress in this field. To better understand the mitogenomic characteristics of P. yuccae, we conducted its sequencing by MGISEQ. Afterwards, the mitogenome was assembled and annotated. The mitogenomic characteristics and phylogenetic placement of the P. yuccae strain KUMCC 6213 were analyzed. The study revealed that the mitogenome of P. yuccae is a circular DNA molecule, consisting of 178,540 base pairs. It contains a total of 64 genes, including 14 protein-coding genes (PCGs), 26 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 22 open reading frame genes (ORF), accounting for 80.98% of the total size. Repetitive sequences accounted for 15.42% of the mitogenome. The analysis of codon usage indicated that the codon UUA was the most commonly utilized, whereas the amino acid Leu was the most frequently employed. A comparative analysis of mitogenomes between P. yuccae and Macrophomina phaseolina (Tassi) Goid. showed notable variations in the position and size of gene clusters, with cox1, nad4, and nad4L genes exhibiting relatively low conservation. Phylogenetic analysis based on the 14 PCGs revealed that P. yuccae has the closest genetic relationship with M. phaseolina (Botryosphaeriaceae, Botryosphaeriales). This study first reports the mitogenome of P. yuccae and validates its phylogenetic placement. The findings enhance the knowledge of mitogenomes in Botryosphaeriales, offering novel perspectives on the genetics and evolution of the plant pathogen P. yuccae. This is crucial for the accurate prevention and management of leaf spot disease in Y. gigantea.

Assembly and analysis of the complete mitochondrial genome of the Chinese wild dwarf almond (Prunus tenella)

Background: The wild dwarf almond (Prunus tenella) is one of the national key grade II-protected wild plants in China. It is a relic deciduous forest species from the middle Eocene of the ancient Mediterranean Sea and is also known as a "living fossil of plants." It is distributed in Southeast Europe, West Asia, Central Asia, Siberia, and Xinjiang (Tacheng) and other areas of China. The plant grows on arid slopes, steppes, depressions, and valleys at an altitude of 1,200 m. The seeds of wild dwarf almonds are frost resistant and contain oil and bitter lentil glycosides, which possess medicinal value. Additionally, the seeds of wild dwarf almonds can be used as the original material for breeding new varieties of almonds and obtain ornamental flowers and trees. Results: The complete mitochondrial genome of P. tenella was sequenced and assembled using two sequencing platforms, namely, Illumina Novaseq6000 and Oxford Nanopore PromethION. The assembled genome was 452,158-bp long with a typical loop structure. The total number of A, T, C, and G bases in the genome was 122,066 (26.99%), 124,114 (27.45%), 103,285 (22.84%), and 102,693 (22.71%), respectively, with a GC content of 45.55%. A total of 63 unique genes, including 36 protein-coding genes, 24 tRNA genes, and 3 rRNA genes, were identified in the genome. Furthermore, codon usage, sequence duplication, RNA editing, and mitochondrial and chloroplast DNA fragment transfer events in the genome were analyzed. A phylogenetic tree was also constructed using 30 protein-coding genes that are common to the mitochondrial genomes of 24 species, which indicated that the genome of wild lentils is highly conserved with those of apples and pears belonging to Rosaceae. Conclusion: Assembly and annotation of the P. tenella mitochondrial genome provided comprehensive information about the mitochondrial genome of wild dwarf almonds, This study provides information on the mitochondrial genome of Prunus species and serves as a reference for further evolutionary studies on wild dwarf almonds.

Characterization of Four Complete Mitogenomes of Monolepta Species and Their Related Phylogenetic Implications

Monolepta is one of the diverse genera in the subfamily Galerucinae, including 708 species and 6 sub-species worldwide. To explore the information on the mitogenome characteristics and phylogeny of the section "Monoleptites", especially the genus Monolepta, we obtained the newly completed mitochondrial genomes (mitogenomes) of four Monolepta species using high-throughput sequencing technology. The lengths of these four new mitochondrial genomes are 16,672 bp, 16,965 bp, 16,012 bp, and 15,866 bp in size, respectively. All four mitochondrial genomes include 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and one control region, which is consistent with other Coleoptera. The results of the nonsynonymous with synonymous substitution rates showed that ND6 had the highest evolution rate, while COI displayed the lowest evolution rate. The substitution saturation of three datasets (13 PCGs_codon1, 13 PCGs_codon2, 13 PCGs_codon3) showed that there was no saturation across all datasets. Phylogenetic analyses based on three datasets (ND1, 15 genes of mitogenomes, and 13 PCGs_AA) were carried out using maximum likelihood (ML) and Bayesian inference (BI) methods. The results showed that mitogenomes had a greater capacity to resolve the main clades than the ND1 gene at the suprageneric and species levels. The section "Monoleptites" was proven to be a monophyletic group, while Monolepta was a non-monophyletic group. Based on ND1 data, the newly sequenced species whose antennal segment 2 was shorter than 3 were split into several clades, while, based on the mitogenomic dataset, the four newly sequenced species had close relationships with Paleosepharia. The species whose antennal segment 2 was as long as 3 were split into two clades, which indicated that the characteristic of "antennal segment 2 as long as 3" of the true "Monolepta" evolved multiple times in several subgroups. Therefore, to explore the relationships among the true Monolepta, the most important thing is to perform a thorough revision of Monolepta and related genera in the future.

The first complete mitochondrial genome of the agricultural pest Micromelalopha sieversi (Staudinger, 1892) (Lepidoptera: Notodontidae)

Micromelalopha sieversi (Staudinger, 1892) is a significant pest of Poplar trees in China. In this study, we used high-throughput sequencing to sequence the whole mitochondrial genome of M. sieversi. The length of the genome was 15,373 base pairs. The nucleotide composition was 39.8%, 11.5%, 8.0%, and 40.7% for A, C, G, and T, respectively. We used the maximum-likelihood method to construct a molecular phylogenetic tree based on complete mitogenome sequences of 19 Noctuoidea species as ingroups and five Geometroidea species as outgroups. The results indicate that the genus Micromelalopha is closely related to the genus Clostera in family Notodontidae.

Complete mitochondrial genome sequence of Butyriboletus hainanensis (Boletales, Basidiomycota)

Butyriboletus hainanensis, a macrofungus belonging to the Boletaceae family, is named after its collection location on Hainan Island, China. However, little is known about its mitochondrial genome and its phylogenetic relationship with other boletes. In this study, we utilized next-generation sequencing technology to sequence the mitochondrial genome of Bu. hainanensis. Our findings revealed that the mitochondrial genome of this species is presumably a circular DNA molecule spanning 36,592 bp. It consists of 15 protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The base composition of the mitochondrial genome is as follows: A (36.64%), C (12.22%), G (11.73%), and T (39.41%), with a GC content of 23.95%. Additionally, a phylogenetic tree was constructed based on 22 mitochondrial genomes, which provided valuable insights into the phylogenetic relationships of Bu. hainanensis with other boletes for the first time.

The Mitochondrial Genomes of Siboglinum plumosum and Oligobrachia dogieli (Annelida: Siboglinidae) and Their Phylogenetic Analysis

Frenulates are a group of sedentary Annelida within the family Siboglinidae that inhabit the ocean floor and present a unique challenge for comprehensive molecular and phylogenetic investigations. In this study, we focused on the frenulates, specifically assembling the mitochondrial genomes of Siboglinum plumosum and Oligobrachia dogieli. The phylogenetic reconstruction placed S. plumosum as a sister taxon to S. ekmani, and O. dogieli as a sister taxon to S. fiordicum, supporting the non-monophyletic nature of the genus Siboglinum. Overall, this study supports the phylogeny of the family Siboglinidae while highlighting the need for additional molecular data within frenulates.

An Overview of Aquatica Fu et al., a Phylogeny of Aquatic Fireflies Using Mitochondrial Genomes, a Description of Two New Species, and a New Record of Aquatic Fireflies in China (Coleoptera: Lampyridae: Luciolinae)

There are now seven species in the genus Aquatica Fu & Ballantyne, with all but one known from the characteristics of males, females, and larvae. Molecular information is combined with morphological taxonomy for the delimitation of both genus and species. The monophyly of the genus Aquatica is strongly supported in six trees, and its position as sister to the genus Nipponoluciola Ballantyne Kawashima Jusoh et Suzuki is stable across maximum likelihood and Bayesian inference results. Two new species of Aquatica Fu & Ballantyne, A. qingshen sp. nov. and A. xianning sp. nov., described from the features of males, females, and larvae, are closely related within a single clade within the genus Aquatica. Females have distinctively shaped median oviduct plates. A Chinese population identified as A. lateralis was found to be morphologically similar to the Japanese population, but genetic distances suggest that it is a distinctive species. No larvae are associated with this species. Definitions of the aquatic status of Luciolinae fireflies are expanded.

Complete mitochondrial genome sequence of Aureoboletus raphanaceus (Boletales, Basidiomycota)

Aureoboletus raphanaceus is a member of boletoid mushroom, which is named after its distinctive radish smell. The mitochondrial genome and phylogenetic relationships with other boletes need to be investigated to gain a comprehensive understanding of it. In this study, we sequenced the mitochondrial genome of A. raphanaceus using next-generation sequencing technology and found that its mitochondrial genome is a circular DNA molecule measuring 42,157 bp. It consists of 15 core protein-coding genes, 27 transfer RNA genes, and two ribosomal RNA genes. The mitochondrial genome had a base composition of A (39.89%), C (11.06%), G (11.67%), and T (37.38%), with a GC content of 22.73%. A phylogenetic tree based on 22 mitochondrial genomes was constructed, which provided the first insights into the phylogenetic relationships of this species with related boletes.

Characterization of the complete mitochondrial genomes of the zoonotic parasites Bolbosoma nipponicum and Corynosoma villosum (Acanthocephala: Polymorphida) and the molecular phylogeny of the order Polymorphida

Acanthocephalans of the order Polymorphida mainly parasitic in birds and mammals, are of veterinary, medical and economic importance. However, the evolutionary relationships of its 3 families (Centrorhynchidae, Polymorphidae and Plagiorhynchidae) remain under debate. Additionally, some species of Polymorphida (i.e. Bolbosoma spp. and Corynosoma spp.) are recognized as zoonotic parasites, associated with human acanthocephaliasis, but the mitochondrial genomes for representatives of Bolbosoma and Corynosoma have not been reported so far. In the present study, the complete mitochondrial genomes B. nipponicum and C. villosum (Acanthocephala: Polymorphidae) are reported for the first time, which are 14 296 and 14 241 bp in length, respectively, and both contain 36 genes [including 12 PCGs, 22 tRNA genes and 2 rRNA genes] and 2 non-coding regions (NCR1 and NCR2). The gene arrangement of some tRNAs in the mitogenomes of B. nipponicum and C. villosum differs from that found in all other acanthocephalans, except Polymorphus minutus. Phylogenetic results based on concatenated amino acid (AA) sequences of the 12 protein-coding genes (PCGs) strongly supported that the family Polymorphidae is a sister to the Centrorhynchidae rather than the Plagiorhynchidae, and also confirmed the sister relationship of the genera Bolbosoma and Corynosoma in the Polymorphidae based on the mitogenomic data for the first time. Our present findings further clarified the phylogenetic relationships of the 3 families Plagiorhynchidae, Centrorhynchidae and Polymorphidae, enriched the mitogenome data of the phylum Acanthocephala (especially the order Polymorphida), and provided the resource of genetic data for diagnosing these 2 pathogenic parasites of human acanthocephaliasis.

Application of noninvasive sampling technique in mitochondrial genome intraspecific phylogeny of the endangered butterfly, Teinopalpus aureus (Lepidoptera: Papilionidae)

The butterfly genus of Teinopalpus, endemic to Asia, embodies a distinct species of mountain-dwelling butterflies with specific habitat requirements. These species are rare in the wild and hold high conservation and research value. Similar to other protected species, the genetic analysis of the rare Teinopalpus aureus poses challenges due to the complexity of sampling. In this study, we successfully extracted DNA and amplified mitochondrial genomic DNA from various noninvasive sources such as larval feces, larval exuviae, larval head capsules, pupal exuviaes, and filamentous gland secretions, all integral parts of butterfly metamorphosis. This was conducted as part of a research initiative focused on the artificial conservation of T. aureus population in Jinggang Shan Nature Reserve. Our findings illustrated the successful extraction of DNA from multiple noninvasive sources, achieved through modified DNA extraction methodologies. Although the DNA concentration obtained from noninvasive samples was lower than that from muscle tissues of newly dead larvae during rearing, all samples met the requirements for PCR amplification and sequencing, yielding complete circular sequences. These sequences are pivotal for both interspecific and intraspecific genetic relationship analysis. Our methods can be extended to other insects, especially scarce species.

Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta)

The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.

Cytochrome c oxidase subunit I gene in Thalassiosira nordenskioeldii strains inhabiting in cold and warm sea waters

From the biota beneath the sea ice in Lake Saroma, which is adjacent to Sea of Okhotsk, a diatom culture of Saroma 16 was isolated. Strutted processes and a labiate process in Saroma 16 were characteristic of those in Thalassiosira nordenskioeldii. Similarity search analysis showed that the 826-bp rbcL-3P region sequence of this strain was 100% identical to multiple sequences registered as T. nordenskioeldii in a public database. The 4305-bp PCR-amplified mitochondrial cytochrome c oxidase subunit I (COI) gene (COI)-5P region of Saroma 16 included a 1060-bp open reading frame (ORF), which was interrupted by 934-bp and 2311-bp introns that included frame-shifted ORFs encoding reverse-transcriptase (RTase)-like proteins. Previous reports showed that a strain of the same species, CNS00052, originating from the East China Sea included no introns in the COI, whereas North Atlantic Ocean strains of the same species, such as CCMP992, CCMP993, and CCMP997, included a 2.3-kb intron in the same position as Saroma 16.

Characterization of the Complete Mitochondrial Genome of Agelas nakamurai from the South China Sea

The Agelas genus sponges are widely distributed and provide shelter for organisms that inhabit reefs. However, there is a lack of research on the genetic diversity of the Agelas sponges. Additionally, only one Agelas mitochondrial genome has been documented, leaving the characteristics of the Agelas genus's mitogenome in need of further clarification. To address this research gap, we utilized Illumina HiSeq4000 sequencing and de novo assembly to ascertain the complete mitochondrial genome of Agelas sp. specimens, sourced from the South China Sea. Our analysis of the cox1 barcoding similarity and phylogenetic relationship reveals that taxonomically, the Agelas sp. corresponds to Agelas nakamurai. The mitogenome of Agelas nakamurai is 20,885 bp in length, encoding 14 protein-coding genes, 24 transfer RNA genes, and 2 ribosomal RNA genes. Through a comparison of the mitochondrial genes, we discovered that both Agelas nakamurai and Agelas schmidti have an identical gene arrangement. Furthermore, we observed a deletion in the trnD gene and duplication and remodeling of the trnL gene in the Agelas nakamurai's mitogenome. Our evolutionary analysis also identified lineage-specific positive selection sites in the nad3 and nad5 genes of the Agelas sponges' mitogenome. These findings shed light on the gene rearrangement events and positive selection sites in the mitogenome of Agelas nakamurai, providing valuable molecular insights into the evolutionary processes of this genus.

The complete mitochondrial genome of the Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong (Rhizophoraceae)

Kandelia obovata Sheue, H.Y.Liu & J.W.H.Yong is one of the most cold-resistant true mangrove species, and it is widely distributed from the South China Sea to southern Japan. In the current study, the complete mitochondrial genome sequence of K. obovata was assembled using Illumina reads. It is the first mitochondrial genome of the Kandelia genus within the family Rhizophoraceae to be sequenced. The mitochondrial genome size is 312,146 bp with a total of 49 predicted genes, including 29 protein-coding genes, 17 transfer RNA genes, and 3 ribosomal RNA genes. The overall GC content of the genome is 41.87%. A phylogenetic tree constructed using nine complete mitochondrial genomes revealed that K. obovata is more closely related to Bruguiera species. This study enriches the plastid genome of Kandelia, furnishing valuable genetic insights for the investigation of evolutionary and population genetics in Kandelia and other mangrove species.

The complete mitochondrial genome of the spotted knifejaw Oplegnathus punctatus

In this study, the mitochondrial genome was sequenced in a new commercial species, spotted knifejaw (O. punctatus), using next-generation sequencing and PCR-based methods. The overall length of the female O. punctatus mitochondrial genome was 16,508 bp. It contained 13 PCGs, 2 r-RNA genes, 22 t-RNA genes, and a displacement loop locus (a control region). The total nucleotide composition was 28.75% A, 25.69% T, 29.70% C, and 15.86% G, with a total A + T content of 54.44%. The results demonstrated that the mitochondrial genome of O. punctatus has a high sequence identity with that of another species of Perciformes. This finding provides a deeper understanding of mitogenomic diversity and evolution in marine fish.

Complete mitochondrial genome of the razor-backed musk turtle (Sternotherus carinatus, testudines: emydidae) in Korea

Sternotherus carinatus has been considered as a potential invasive species in Korea. However, the mitochondrial genome information of S. carinatus which can be used to control its effect on ecosystem is lacking. In this study, the complete mitochondrial genome of S. carinatus in Korea was sequenced and characterized. The mitochondrial genome consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and a noncoding region. Phylogenetic analysis based on the mitochondrial genome sequences showed that S. carinatus from Korea is separated from other turtles which are the invasive species in Korea. Sequence divergence calculations indicated near-zero divergence between S. carinatus populations in Korea, the USA, and China, suggesting limited genetic differentiation. In the context of the broader issue of invasive species disrupting ecosystems, this research contributes to the identification of mitochondrial genomes for various freshwater turtle species, emphasizing the need for extended data collection to discern genetic mixing trends between native and non-native species. This study is a significant step toward managing S. carinatus as a potential invasive species in Korea.