Complete Mitochondrial Genome Sequence Research Articles

On the Species Identification of Korean Geoduck Clam (Panopea sp. 1) Based on the Morphological and Molecular Evidence

The geoduck clam is a high-value species in South Korea. However, the molecular and morphological characteristics of geoduck clams from the southern coast of South Korea remain unexamined. The accurate identification of native geoduck clams is crucial for their conservation and management. Therefore, this study used a combination of molecular and morphological analyses to characterize native geoduck clams from the southern coast of South Korea. Based on complete mitochondrial genome and morphological analyses, the native species of geoduck clam from this study area was identified as Panopea sp. 1. The complete mitochondrial genome sequencing of Panopea sp. 1 revealed a total of 16,225 bp in length with 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes). It was also shown that Panopea sp. 1 belongs to the family Hiatellidae based on a phylogenetic analysis tree with 11 bivalve species. In particular, Panopea sp. 1 is closely related to three other Panopea species (Panopea sp., Panopea abrupta, and Panopea japonica). The phylogenetic analysis correlated with the morphological analysis. Overall, this is the first reliable record of Panopea sp. 1 in South Korea. These findings provide a basis for accurate species identification based on morphological characteristics and complete mitochondrial genome sequencing.

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Auricularia villosula, an edible wild mushroom in China

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Auricularia villosula, an edible wild mushroom in China

Complete mitochondrial genome sequences and the phylogenetic relationship of the endangered species Acoptolabrus leechi yooni (Deuve, 1990) (Coleoptera: Carabidae), Korea

Carabid beetles, are one of the largest taxonomic groups with >40,000 recorded species. Acoptolabrus leechi yooni has been listed as an endangered species in the Republic of Korea. The whole mitochondrial genome of A. leechi yooni consisted of a16,825-bp encompassing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. The DNA sequence comprises 79.4% of A-T region and 20.6% of G-C region. Phylogenetic analysis revealed that A. leechi yooni is very close to A. mirabilissimus mirabilissimus and A. changeonleei. This study provides a complete mitochondrial genome sequence of A. leechi yooni and basic data for protecting the endangered species.

Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application.

Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases.

Complete mitochondrial genome and phylogenetic analysis of Kapsa arca and Alnetoidia dujuanensis (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) from the Karst region

Kapsa arca and Alnetoidia dujuanensis, which belong to erythroneurine leafhoppers (Cicadellidae and Typhlocybinae), are economic pests with the characteristics of a large number of small individuals and wide distribution. Analysis of the complete mitochondrial genome sequence and phylogenetic relationships of the leafhopper will help not only in its identification but also in its control. In this work, two mitochondrial gene sequences from K. arca and A. dujuanensis were sequenced, analyzed, and used to explore the phylogenetic relationships of the tribe. The lengths of the K. arca and A. dujuanensis genomes were 15,594 bp and 15,375 bp, respectively, and all contained a noncoding control region, two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and 13 PCGs. Most protein-coding genes end with TAA or TAG and start with ATN, with AT skew exhibiting a positive skew and GC skew exhibiting a negative skew. The mitotic genomes of K. arca and A. dujuanensis are similar in structure to those of other leafhoppers and are conserved. Phylogenetic analysis revealed that K. arca forms a sister group with Elbelus tripunctatus, and A. dujuanensis forms a sister group with Kaukania anser, but Zyginellini and Typhlocybini, which should branch separately, are interrelated and cannot form separate branches. The result differs from previous studies. The results indicated that the two species, K. arca and A. dujuanensis, should belong to the same tribe, the Erythroneurini leafhoppers, but should be grouped into different genera. A time-calibrated phylogeny estimated the earliest divergence time of Erythroneurini, Empoascini, Typhlocybini, and Zyginellini.

Complete mitochondrial genome and the phylogenetic position of a new Annelida species belonging to the genus Syllis

The family Syllidae is the most taxonomically complex of the phylum Annelida. Although the gene order in the phylum Annelida's mitochondrial DNA (mtDNA) is well conserved, several exceptional cases have been reported. In this study, we describe the mitochondrial genome of a Syllis sp. that is 17,092 bp in length and contains 13 mitochondrial protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, including two tRNA-M, two ribosomal RNA (rRNA) genes, and a putative control region between tRNA-W and tRNA-G distinguished by a single short noncoding region. However, the gene order is not similar to those of other species in the family Syllidae. Phylogenetic analyses of 18S rRNA and 13 PCGs sequences demonstrated that this worm was clustered with other Syllis species in the family Syllidae. This is the first study to reveal the complete mitochondrial genome sequence of a previously unidentified Syllis sp. improving our understanding of the molecular biological characteristics of the poorly known genus Syllis.

Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences.

Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.

Genetic variation and population structure of brachiopods, Lingula anatina Lamarck, 1801 in the Northern Aceh shore, Indonesia

Abstract. Octavina C, Ramadhaniaty M, Daulay RE, Dewiyanti I, Ulfah M. 2023. Genetic variation and population structure of brachiopods, Lingula anatina Lamarck, 1801 in the Northern Aceh shore. Biodiversitas 24: 3951-3959. Lingula anatina is one of the brachiopods recognized as one of the most primitive groups with a fossil record from the early Cambrian period. Although L. anatina has been targeted as an object of biological studies, the information about the genetic variation within species is still limited. The purpose of this research is to identify the genetic variation and population structure of the species L. anatina found in the Aceh northern shore based on the mtDNA Cytochrome Oxidase I (COI) gene sequence. In this study, L. anatina specimens collected from five populations on Aceh's northern shore, namely Krueng Raya, Syiah Kuala, Ulee Lheue, and Ujong Pancu, with complete mitochondrial genome sequences were analyzed and compared with genebank sequences. The total nucleotide base of L. anatina is 657 bp, with 18 haplotypes. Based on the results of a comparison of the distribution of L. anatina in Asia shows that the Japanese population has the highest population structure value compared to the other five populations. The Fst value obtained from this study is 0.7, so it is classified as high and structured. Phylogenetic analysis showed that the correlation between geographic location and geographic distance affects the genetic distance between populations.

The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae).

Metopiellus Raffray, 1908 is a genus of South American rove beetles typically found in tropical humid forests. Here we describe a new cryptic species from Eastern Amazon, in northern Brazil, Metopiellus crypticus Asenjo sp. nov., and its major morphologic diagnostic features, which were photographed and illustrated. In addition, we bring the complete mitochondrial genome sequence of M. crypticus sp. nov., and its position within the phylogenetic context of the family, including previously available mitogenomes of Staphylinidae species.

Mitochondrial genome sequence characteristics and phylogenetic analysis of Schizothorax argentatus

Schizothorax argentatus that only distributes in the Ili River basin in Xinjiang is one of the rare and endangered species of schizothorax in China, thus has high scientific and economic values. In this study, the complete mitochondrial genome sequence of S. argenteus with a length of 16 580 bp was obtained by high-throughput sequencing. The gene compositions and arrangement were similar to those of typical vertebrates. It contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding region (D-loop). The nucleotide compositions were A (30.25%), G (17.28%), C (27.20%), and T (25.27%), respectively, showing obvious AT bias and anti-G bias. Among the tRNA genes, only tRNA-Ser(GCU) could not form a typical cloverleaf structure due to the lack of dihydrouracil arm. The AT-skew and GC-skew values of the ND6 gene were fluctuating the most, suggesting that the gene may experience different selection and mutation pressures from other genes. The mitochondrial control region of S. argenteus contained three different domains, i.e., termination sequence region (ETAS), central conserved region (CSB-F, CSB-E, CSB-D, and CSB-B), and conserved sequence region (CSB1, CSB2, and CSB3). The conserved sequence fragment TT (AT) nGTG, which was ubiquitous in Cypriniformes, was identified at about 50 bp downstream CSB3. Phylogenetic relationships based on the complete mitochondrial genome sequence of 28 Schizothorax species showed that S. argenteus had differentiated earlier and had a distant relationship with other species, which may be closely related to the geographical location and the hydrological environment where it lives.

The complete mitochondrial genome of the Indian dammer bee, Tetragonula iridipennis, and the phylogenomics of Meliponini

The Indian stingless bee Tetragonula iridipennis (Hymenoptera: Apidae), popularly recognized as the Indian dammer bee, is an economically important and widely distributed non-Apis bee species in India. The taxonomic gaps, systematics, evolutionary puzzles, and structural motifs within the mitogenomes of this species have rarely been examined and are not fully understood. Next-generation sequencing was employed to decipher the complete mitochondrial genome of T. iridipennis (15,045 bp). De novo genome assembly revealed that it encompasses 34 genes: protein-coding genes (13), transfer RNA (tRNAs) genes (19), and ribosomal RNA (rRNA) genes (2). Additionally, genome organization, including gene content, nucleotide composition, codon usage, and gene rearrangement, was investigated to better comprehend, utilize, and conserve this germplasm resource. The average gene length was 400 bp; maximum and minimum lengths were 1,530 bp (cox1) and 57 bp (tRNA-S1), respectively. Phylogenetic analysis has suggested that T. iridipennis is mostly closely related to T. pagdeni and Lepidotrigona species. All the stingless bee species (Meliponini) formed a distinct clade that shared a closer relationship with bumble bees (Bombini) than honey bees (Apini). The nucleotide composition of T. iridipennis was biased toward A+T, which accounted for 75.95% of the whole mitogenome. Length and compositional differences between T. iridipennis and other bees were detected, and gene order was compared. The mitogenome of T. iridipennis showed the highest gene rearrangement score (78), suggesting this species has a hyperactive evolutionary history. The variations of gene positions and gene rearrangement in the mitogenome could also aid in resolving the phylogenetic relationships and evolutionary history in Meliponini. Additionally, this is the first report of a complete mitochondrial genome sequence of T. iridipennis.

Trichoderma koningiopsis (Hypocreaceae) has the smallest mitogenome of the genus Trichoderma.

Fungal mitogenomes exhibit remarkable variation in conformation, size, gene content, arrangement and expression, including their intergenic spacers and introns. The complete mitochondrial genome sequence of the mycoparasitic fungus Trichoderma koningiopsis was determined using the Illumina next-generation sequencing technology. We used data from our recent Illumina NGS-based project of T. koningiopsis genome sequencing to study its mitochondrial genome. The mitogenome was assembled, annotated, and compared with other fungal mitogenomes. T. koningiopsis strain POS7 mitogenome is a circular molecule of 27,560 bp long with a GC content of 27.80%. It harbors the whole complement of the 14 conserved mitochondrial protein-coding genes (PCG) such as atp6, atp8, atp9, cox1, cox2, cox3, cob, nad1, nad2, nad3, nad4, nad4L, nad5, and nad6, also found in the same gene order to other Hypocreales. The mitogenome also contains 26 transfer RNA genes (tRNAs), 5 of them with more than one copy. Other genes also present in the assembled mitochondrial genome are a small rRNA subunit and a large rRNA subunit containing ribosomal protein S3 gene. Despite the small genome size, two introns were detected in the T. koningiopsis POS7 mitogenome, one of them in cox3 gene and the other in rnl gene, accounting 7.34% of this mitogenome with a total size of 2,024 bp. A phylogenetic analysis was done using the 14 PCGs genes of T. koningiopsis strain POS7 mitogenome to compare them with those from other fungi of the Subphyla Pezizomycotina and Saccharomycotina. T. koningiopsis strain POS7 was clustered together with other representatives of Trichoderma lineage, within the Hypocreales group, which is also supported by previous phylogenetic studies based on nuclear markers. The mitochondrial genome of T. koningiopsis POS7 will allow further investigations into the taxonomy, phylogenetics, conservation genetics, and evolutionary biology of this important genus as well as other closely related species.

Epicrates crassus SNAKE: COMPLETE MITOCHONDRIAL GENOME SEQUENCE

Epicrates crassus Cope, 1862 is a snake distributed in South America and a target species for illegal animal trafficking. In this work, we sequenced and described this species complete mitochondrial genome sequence. The mtDNA of E. crassus has 17,379 bp, with 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes, and two non-coding control regions. Phylogenetic reconstruction, based on the complete mitogenome sequence of E. crassus and 18 other mitogenomes, confirmed the best grouping of this species with other members of the Boidae family. These new data can contribute to correctly identifying E. crassus, which would represent one more tool in the fight against the illegal trafficking of this species.

The Complete Mitochondrial Genome and Phylogenetic Analyses of To Chicken in Vietnam.

Indigenous chicken breeds have both cultural significance and economic value since they possess unique genetic characteristics that enable them to adapt to the local environment and contribute to biodiversity, food security, and sustainable agriculture in Vietnam. To (Tò in Vietnamese) chicken, a Vietnamese indigenous chicken breed, is popularly raised in Thai Binh province; however, little known is about the genetic diversity of this breed. In this study, we sequenced the complete mitochondrial genome of To chicken for a better understanding of the diversity and origin of the breed. The results of sequencing showed that the mitochondrial genome of To chicken spans a total length of 16,784 base pairs and comprises one non-coding control region (known as the displacement-loop (D-loop) region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. The phylogenetic tree analyses and estimated genetic distances based on 31 complete mitochondrial genome sequences indicated that To chicken has a close genetic distance with the Laotian native chicken breed, Lv'erwu breed in China, and Nicobari black and Kadaknath breeds in India. The result of the current study might be important for conservation, breeding, and further genetic studies of To chicken.

Characterization and Phylogenetic Analysis of the First Complete Mitochondrial Genome of Gnathophyllum americanum (Guérin-Méneville, 1855) (Malacostraca: Decapoda: Palaemonidae)

Complete mitochondrial genome (mitogenome) sequences can provide useful and varied information for evolutionary and phylogenetic studies. We report the first complete mitogenome sequence of the bumblebee shrimp (Gnathophyllum americanum). The mitogenome is 15,842 bp in length and contains 13 protein-encoding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The nucleotide composition of the mitogenome was as follows: A,36.72%; T,29.62%; C,21.0%; and G,12.66%. The most common start and stop codons are ATG and TAA, respectively. The MGO (mitochondrial gene order) of G. americanum and Hymenocera picta is unique in Decapoda. Both the phylogeny based on mitochondrial genomic DNA data and the unique MGO pattern indicate that the genus Gnathophyllum might be a sister genus to the genus Hymenocera. The mitogenomic sequence data obtained in this study will provide more information on G. americanum for species identification, population genetics, and biogeography.

Complete mitochondrial genomes of the “Acmaeidae” limpets provide new insights into the internal phylogeny of the Patellogastropoda (Mollusca: Gastropoda)

The subclass Patellogastropoda (called “true limpets”) is one of the most primitive groups of the Gastropoda and contains approximately 350 species worldwide. Within this subclass, internal phylogeny among family members, including relationships of the “Acmaeidae” with other patellogastropod families, remains incompletely clarified. Here, we newly determined two complete mitochondrial genome sequences of “Acmaeidae” (Acmaea mitra and Niveotectura pallida) and one sequence from Lottiidae species (Discurria insessa) and combined them with mitochondrial genome sequences of 20 other published limpet species for phylogenetic analysis of the sequence dataset (nucleotides and amino acids) of 13 protein-coding genes using maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed monophyly of Patellogastropoda species that were subsequently subdivided into two clades [clade I (Nacellidae, Pectinodontidae, Acmaeidae, and Patellidae) and clade II (Eoacmaeidae and Lottiidae)]. The sister relationship between the Acmaeidae and Pectinodontidae species revealed by phylogenetic analysis was also supported by sharing their similar gene arrangement patterns, which differ substantially from those of clade II members including the Lottiidae species. The polyphyletic relationship between Acmaeidae (grouped with Pectinodontidae as a sister taxon in clade I) and Lottiidae species (grouped with Eoacmaeidae in clade II) corroborates that they are phylogenetically distinct from each other. This mitochondrial genome phylogeny contradicts previous morphology-based hypotheses, yet highlights that Acmaeidae and Pectinodontidae are the most closely related. Further in-depth analysis of the complete mitochondrial genome sequences based on a broad range of samples including those from relatively unstudied and/or underrepresented taxa is required to fully understand the mitochondrial genome evolution and a more comprehensive phylogeny among the major groups of the Patellogastropoda.

Complete Mitochondrial Genome Sequence of an Australian Little Crow (Corvus bennetti)

This study reports the complete mitochondrial genome sequence of an Australian little crow (Corvus bennetti). The circular genome has a size of 16,895 bp and contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The study provides a reference mitochondrial genome of a little crow for further molecular studies.

New Record of Geoduck Clam Collected from the East Coast of South Korea and Its Reproductive Characteristics

Geoduck clams are important commercial marine resources in Southeast Asia. However, the complete mitochondrial genome of the native geoduck clam in South Korea has not been reported yet. This study reports a geoduck clam collected from the east coast of South Korea. Based on its morphological characteristics and molecular data, the geoduck clam was identified as Panopea sp. belonging to the bivalve family Hiatellidae. We determined the complete mitochondrial genome of this species and investigated the seasonal reproductive pattern for monthly changes in sex ratio, gametogenesis, and reproductive cycle from September 2019 to August 2020. The total length of the complete mitochondrial genome sequence is 16,006 bp, containing 13 protein-coding, 22 transfer RNA, 2 ribosomal RNA, and a control region (D-loop). A molecular phylogenetic comparison with 10 bivalve species showed that the geoduck clam specimen belongs to the family Hiatellidae, clustering with Panopea abrupta Chinese strain, P. generosa, and P. globosa. The gametogenesis of the geoduck clam was identified in six stages by histological analysis. The sex ratio was biased towards males from May 2019 to July 2019, the main spawning activity from the frequency of the gonads with ripe and spent stages occurred from October 2018 to April 2019, and there was no clear pattern of spawning peaks from May to August 2019 with gonads developed asynchronously between both sexes. This is the first study to report new records of the genus Panopea based on the complete mitochondrial genome and to examine the seasonal reproductive pattern of the native geoduck clam Panopea sp. in South Korea, providing valuable information for its sustainable management in South Korea.

First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages.

The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.

First record of the complete mitochondrial genome of Culex pipiens (Diptera: Culicidae) in Iraq and its phylogenetic analysis

The common house mosquito, Culex pipiens, is a worldwide insect that is known as a vector of several human and animals’ pathogens that cause critical diseases, such as malaria, yellow fever and encephalitis. The mitochondrial genome knowledge can supply a foresight for evolutionary biology and phylogenetic analysis. Thus, in the current study, the complete mitochondrial genomes of the Iraqi C. pipiens were first sequenced, assembled, annotated, and analyzed using high throughput sequencing techniques. The results revealed that the length of the complete mitochondrial genome is 14,856 bp, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. The A + T content was 77.09%, while the G+C content was only 22.1%. All PCGs open with the start codon ATN, except the cox1 gene and end with the stop codon TAA. A phylogenetic relatedness with other different species of Culex spp. was achieved by operating the molecular evolutionary genetic analysis based on the whole mitochondrial genome sequences. The results showed that C. pipiens from Iraq shares a close ancestry with C. pipiens from Tunisia and France. To our knowledge, this is the first report of the complete mitochondrial genome sequence of the Iraqi C. pipiens. As a consequence, this conclusion may provide a new profound insight into the evolution of C. pipiens in Iraq.