Complete Mitochondrial Genome Sequence Research Articles

The complete mitochondrial genome of the tropical sea urchin Tripneustes gratilla (Linnaeus, 1758) with two spine colors

The complete mitochondrial genomes of two spine-color individuals, red and white, of the tropical sea urchin species Tripneustes gratilla (Linnaeus, 1758) were sequenced on Illumina system platform. The red-spined species had a genome size of 15,774 bp, while the white-spined species had a genome size of 15,723 bp. Both genomes contained 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The GC composition in both species was above 40%. In order to investigate the phylogenetic relationships of two different spine-color individuals, a comprehensive analysis was conducted using eight complete mitochondrial genomic sequences of the genus Tripneustes on the software MEGA X. It was observed that the two spine color types of T. gratilla species showed a high similarity of 98.91%. However, different color-spined species of T. gratilla were found in separate branches of the phylogenetic tree of the same sea urchin species.

Structural Analysis and Phylogenetic Relationship of a Lepidopteran Scopelodes kwangtungensis Based on its Complete Mitochondrial Genome Sequence

Structural Analysis and Phylogenetic Relationship of a Lepidopteran Scopelodes kwangtungensis Based on its Complete Mitochondrial Genome Sequence

The complete mitochondrial genome and phylogenetic analysis of hydrozoan jellyfish Eirene ceylonensis (Cnidaria, Hydrozoa, Eirenidae) in the coastal sea of Qinhuangdao, China

Eirene ceylonensis, a hydrozoan jellyfish species with a complex polymorphic life cycle, is widely distributed in the Chinese coastal sea. In this study, we conducted sequencing and analysis of the first complete mitochondrial genome of E. ceylonensis, obtained from the coastal sea of Qinhuangdao, China. The linear mitochondrial genome is 14,997 bp in length with the overall AT content being 72.8%, encoding 13 protein-coding genes (PCGs), two transfer RNA (tRNA) genes (tRNA-Met and tRNA-Trp) and two ribosomal RNA (rRNA) genes (rrnS and rrnL). Phylogenetic analysis of 13 PCGs suggests that the E. ceylonensis is closely related to Laomedea flexuosa. The availability of the complete mitochondrial genome of E. ceylonensis will be useful for studying the evolutionary relationships of hydrozoan jellyfish species.

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.

Anopheles gambiae on remote islands in the Indian Ocean: origins and prospects for malaria elimination by genetic modification of extant populations

The mosquito Anopheles gambiae s.s. is a primary malaria vector throughout sub-Saharan Africa including the islands of the Comoros archipelago (Anjouan, Grande Comore, Mayotte and Mohéli). These islands are located at the northern end of the Mozambique Channel in eastern Africa. Previous studies have shown a relatively high degree of genetic isolation between the Comoros islands and mainland populations of A. gambiae, but the origin of the island populations remains unclear. Here, we analyzed phylogenetic relationships among island and mainland populations using complete mitochondrial genome sequences of individual A. gambiae specimens. This work augments earlier studies based on analysis of the nuclear genome. We investigated the source population of A. gambiae for each island, estimated the number of introductions, when they occurred and explored evidence for contemporary gene flow between island and mainland populations. These studies are relevant to understanding historical patterns in the dispersal of this important malaria vector and provide information critical to assessing their potential for the exploration of genetic-based vector control methods to eliminate this disease. Phylogenetic analysis and haplotype networks were constructed from mitogenome sequences of 258 A. gambiae from the four islands. In addition, 112 individuals from seven countries across sub-Saharan Africa and Madagascar were included to identify potential source populations. Our results suggest that introduction events of A. gambiae into the Comoros archipelago were rare and recent events and support earlier claims that gene flow between the mainland and these islands is limited. This study is concordant with earlier work suggesting the suitability of these oceanic islands as appropriate sites for conducting field trial releases of genetically engineered mosquitoes (GEMs).

Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl

BackgroundForsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated.ResultThe F. suspensa mitochondrial genome was obtained in the length of 535,692 bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea.ConclusionIn this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.

The New Mitochondrial Genome of Hemiculterella wui (Cypriniformes, Xenocyprididae): Sequence, Structure, and Phylogenetic Analyses.

Hemiculterella wui is an endemic small freshwater fish, distributed in the Pearl River system and Qiantang River, China. In this study, we identified and annotated the complete mitochondrial genome sequence of H. wui. The mitochondrial genome was 16,619 bp in length and contained 13 protein coding genes (PCGs), two rRNA genes, 22 tRNA genes, and one control region. The nucleotide composition of the mitochondrial genome was 29.9% A, 25.3% T, 27.4% C, and 17.5% G, respectively. Most PCGs used the ATG start codon, except COI and ATPase 8 started with the GTG start codon. Five PCGs used the TAA termination codon and ATPase 8 ended with the TAG stop codon, and the remaining seven genes used two incomplete stop codons (T and TA). Most of the tRNA genes showed classical cloverleaf secondary structures, except that tRNASer(AGY) lacked the dihydrouracil loop. The average Ka/Ks value of the ATPase 8 gene was the highest, while the average Ka/Ks value of the COI gene was the lowest. Phylogenetic analyses showed that H. wui has a very close relationship with Pseudohemiculter dispar and H. sauvagei. This study will provide a valuable basis for further studies of taxonomy and phylogenetic analyses in H. wui and Xenocyprididae.

Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

In recent phylogenetic studies, bat Polychromophilus and ungulate Plasmodium, two relatively understudied haemosporidian parasites within the Apicomplexa phylum, have often been overlooked. Instead, the focus has been primarily on haemosporidian parasites in primates, rodents, and birds. Several phylogenetic analyses of bat Polychromophilus have relied on limited datasets and short informative DNA sequences. As a result of these inherent limitations, the substantiation of their evolutionary stance has encountered a diminished degree of robust validation. This study successfully obtained complete mitochondrial genome sequences from 11 Polychromophilus parasites originating from Hipposideros gentilis and Myotis siligoensis bats for the first time. Additionally, the authors have sequenced the apicoplast caseinolytic protease C genes from Polychromophilus murinus and a potentially new Polychromophilus species. These mitochondrial genomes range in length from 5994 to 6001 bp and consist of three protein-coding genes (PCGs), seven small subunit ribosomal RNA genes (SSU rRNA), 12 large subunit ribosomal RNA genes (LSU rRNA), and seven miscellaneous RNA genes. Phylogenetic analyses using Bayesian Inference and Maximum Likelihood methods indicated robust support for the grouping of ungulate Plasmodium and bat Polychromophilus in a single clade separate from other Plasmodium spp., confirming previous reports, albeit with stronger evidence in this study. The divergence between Polychromophilus in bats and Plasmodium in ungulates occurred approximately 29.61 to 55.77 million years ago (Mya), with a node age estimated at 40.63 Mya. These findings highlight that the genus Plasmodium, which includes species found in ungulates, birds, reptiles, and other mammals, does not form a monophyletic group. By incorporating Polychromophilus in bats and Plasmodium in ungulates, this study contributes significantly to understanding the phylogenetic relationships within the Haemosporida order. It provides valuable insights into the evolutionary history and interconnections among these diverse parasites, thereby expanding knowledge in this field.

Characterization of the CMS genetic regulation through comparative complete mitochondrial genome sequencing in Nicotiana tabacum.

Mitochondrial genomes (mitogenomes) of flowering plants vary greatly in structure and size, which can lead to frequent gene mutation, rearrangement, or recombination, then result in the cytoplasmic male sterile (CMS) mutants. In tobacco (Nicotiana tabacum), suaCMS lines are widely used in heterosis breeding; however, the related genetic regulations are not very clear. In this study, the cytological observation indicated that the pollen abortion of tobacco suaCMS(HD) occurred at the very early stage of the stamen primordia differentiation. In this study, the complete mitochondrial genomes of suaCMS(HD) and its maintainer HD were sequenced using the PacBio and Illumina Hiseq technology. The total length of the assembled mitogenomes of suaCMS(HD) and HD was 494,317bp and 430,694bp, respectively. Comparative analysis indicated that the expanded 64 K bases in suaCMS(HD) were mainly located in noncoding regions, and 23 and 21 big syntenic blocks (>5000bp) were found in suaCMS(HD) and HD with a series of repeats. Electron transport chain-related genes were highly conserved in two mitogenomes, except five genes (ATP4, ATP6, COX2, CcmFC, and SDH3) with substantial substitutions. Three suaCMS(HD)-specific genes, orf261, orf291, and orf433, were screened. Sequence analysis and RT-PCR verification showed that they were unique to suaCMS(HD). Further gene location analysis and protein property prediction indicated that all the three genes were likely candidates for suaCMS(HD). This study provides new insight into understanding the suaCMS mechanism and is useful for improving tobacco breeding.

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.