Complete Mitochondrial Genome Sequence Research Articles

The complete mitochondrial genome of Porodaedalea mongolica (Hymenochaetaceae, Basidiomycota)

Most Porodaedalea species are important phytopathogenic and medicinal fungi. Recently, several Porodaedalea species including P. mongolica were newly described. In the present study, the complete sequence of mitochondrial genome of P. mongolica was determined, with a size of 114,176 bp and a GC content of 28.98%, containing two ribosomal RNA subunit, 26 transfer RNA, and 54 protein-coding genes (PCGs). The comparative analyses indicated that the amino acids of 14 core PCGs were highly conserved in Porodaedalea. Phylogenetic analysis of Porodaedalea was performed based on mitogenomic data and provided a new insight to the phylogeny of the Porodaedalea. The complete mitogenome sequence provides important data for further study of Porodaedalea.

Molecular identification of the strains of the domestic silkworm, Bombyx mori (Lepidoptera: Bombycidae), which are endemic to Korea, based on single nucleotide polymorphisms in mitochondrial genome sequences

• We developed molecular identification methods for three endemic silkworm strains. • We found 15 SNP in mitogenomes of 5 endemic and 34 stock strains. • We applied the RFLP-PCR and the tetra-primer ARMS-PCR methods. • We distinguished three endemic strains using both methods in agarose gels. • These methods could be useful for distinguishing endemic strains preserved in Korea. The domestic silkworm, Bombyx mori (Lepidoptera: Bombycidae), has been diversified into various strains over a long period. However, methods to distinguish silkworm strains remain limited partially owing to the genetic similarity caused by the long history of domestication. In this study, we developed molecular identification methods to distinguish three domestic silkworm strains, which are endemic to Korea. By comparing publicly available complete mitochondrial genome (mitogenome) sequences of five endemic strains and 34 stock silkworm strains analyzed in a previous study, we detected 15 single nucleotide polymorphisms (SNPs; SNP1–SNP15), which distinguished the following three endemic strains: Sun7ho (SN7), Sandongsammyeon (SDS), and Sammyeonhonghoeback (SMH). We used two SNPs for each strain to identify the three endemic strains. To distinguish each SN7 and SDS from the remaining four endemic and 34 stock strains, the PCR-restriction fragment length polymorphism method was employed using Acu I and Hpa I restriction enzymes, which recognize SNP1 and SNP8, respectively. Additionally, the tetra-primer amplification refractory mutation system PCR method was used to determine the regions containing SNP3, SNP11, and both SNP14 and SNP15 to distinguish SN7, SDS, and SMH, respectively, from the remaining strains. A validation test with additional individuals showed that each target strain was clearly recognized, suggesting that mitogenome SNP-based methods can be used to identify three endemic silkworm strains during culture and breeding.

The First Isospora Species (Apicomplexa: Eimeriidae) Described from the Northern Yellow-Shafted Flicker (Colaptes auratus luteus) in Ontario, Canada.

Members of the genus Isospora commonly infect a wide variety of wild birds. By combining morphometric and genetic data, we are able to differentiate and describe a new apicomplexan parasite, Isospora picoflavae n. sp., from the Northern Yellow-shafted Flicker (Colaptes auratus luteus) in Ontario, Canada. Unsporulated oocysts were observed in intestinal contents obtained during necropsy; these oocysts completed exogenous sporulation within 7days at room temperature. Complete nuclear 18S rDNA and complete mitochondrial genome sequences were obtained from this previously undescribed Isospora sp. to compare with related coccidia. Sporulated oocysts were subspherical in shape measuring an average of 22.7 × 21.7μm (n = 53; mean shape index 1.05) containing a near-spherical polar granule. Sporocysts were ovoidal to ellipsoidal in shape, measuring an average size of 17.0 × 10.5μm (n = 9; mean shape index 1.62). Sporocyst residuum was concentrated in an irregular, spherical mass in the middle of each sporocyst. The isolated oocysts differed morphologically from other Isospora species reported to infect members of the family Picidae. Based on phylogenetic analyses using either combined nuclear 18S rDNA and mitochondrial cytochrome c oxidase I (COI) sequences or complete mitochondrial genome sequences, this Isospora sp. n. isolated from the Northern Flicker grouped within a clade containing Isospora species described from various passeriform hosts. Based on combined morphological and molecular data, the oocysts found in the gastrointestinal contents of Colaptes auratus luteus represent a new species of Isospora named herein as Isospora picoflavae n. sp.

The complete mitochondrial genome of Hemiclepsis yangtzenensis (Clitellata: Glossiphoniidae)

We present the complete mitochondrial genome sequence of a recently described new leech species named Hemiclepsis yangtzenensis Yang & Bolotov 2021 collected in central China. The mitochondrial genome is 14,984 bp in length and consists of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, all of which are encoded on a single strand. It exhibited a strong A + T bias of 72.87%. There is a large non-coding region (614 bp) located between the tRNA-Arg and tRNA-His genes, wherein we identified 40 short dispersed repeats, 13–22 bp long, 8 of which were direct, 20 inverted, and 12 palindromic. Phylogenetic analysis of 20 Hirudinea mitogenome sequences resolved monophyletic Glossiphoniidae, and H. yangtzenensis formed a sister lineage with Glossiphonia concolor.

The mitochondrial genome of Lamellomphalus manusensis Zhang & Zhang, 2017 (Gastropoda: Neomphalida) from deep-sea hydrothermal vent

We report the nearly complete mitochondrial genome sequence of Lamellomphalus manusensis Zhang and Zhang 2017, a deep-sea snail inhabiting hydrothermal vent. The mitogenome is 15,990 bp in length, has a base composition of A (35.7%), T (33.5%), C (15.4%) and G (15.4%), and contains 13 protein-coding genes, 2 ribosomal RNA genes, and 22 tRNA genes. Phylogenetic analyses show that the family Peltospiridae is not monophyletic, suggesting that its genera need to be redefined.

The complete mitochondrial genome sequencing of the Asian lesser white-toothed shrew (Crocidura shantungensis Miller, 1901; Eulipotyphla: Soricidae) from Jeju of Korea

We report the complete mitochondrial genome of Crocidura shantungensis (Asian Lesser White-toothed Shrew). The complete mitochondrial genome is 17,160bp in length and contains 13 protein coding genes, one replication origin region, 22 transfer RNA, two ribosomal RNA, and one D-loop (control region). The mitogenome is A+T rich, with a composition of A: 32.5%, T: 32.6%, C: 21.7%, and G: 13.1%. In the phylogenetic tree, the Crocidura genus species formed a solid monophyletic group in the family Soricidae, C. shantungensis was well grouped with sister group to C. sibicica within the Genus Crocidura clade, and each species noted against each other well.

Characterization of the complete mitochondrial genome and phylogenetic analysis of Opsarius pulchellus (Cypriniformes, Danionidae, Chedrinae)

This study aimed to sequence and annotate the complete mitochondrial DNA genome sequence of Opsarius pulchellus. Complete mitochondrial genome is a circular molecule of 16,552 bp in length, including 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a displacement loop region. Proportion of nucleotides in mitochondrial genome is 26.8% T, 26.9% C, 27.6% A, and 18.8% G, with an AT bias of 54.4%. Maximum-likelihood phylogenetic tree was reconstructed using the connected protein sequences of 13 PCGs of O. pulchellus and other 18 fishes. Result of phylogenetic analysis supports a close relationship between O. pulchellus and Barilius bendelisis (Hamilton, 1807). Fundamental genetic data of O. pulchellus would be beneficial for further studies on genetic diversity and phylogeny.

The complete mitochondrial genome sequence of the fairy ring-forming fungus Lepista sordida

Lepista sordida is a fairy ring-forming fungus that belongs to the family Tricholomataceae and is widely distributed in the Northern Hemisphere. Here, we report the complete mitochondrial genome sequence of L. sordida. The mitochondrial genome (57,375 bp) contained 20 protein-coding genes, 2 ribosomal RNA genes, and 26 transfer RNA genes. Phylogenetic analysis based on 14 conserved protein sequences from L. sordida and 15 related basidiomycetes showed that L. sordida was located on the outermost branch of the Tricholomataceae clade. This study is the first to report the complete mitochondrial genome sequence of a fairy ring-forming fungus belonging to the genus Lepista.

Seven fish complete mitochondrial genomes of the Gastromyzontidae in Southern China (Teleostei: Cypriniformes)

Family of Gastromyzontidae originates from China and Southeast Asia, which is widely distributed in the southern part of the Yangtze River. In this study, we sequenced seven fish complete mitogenomes from three of all 18 genera in the Gastromyzontidae on the Illumina HiSeq platform. Lengths of seven complete mitochondrial genome sequences varied from 16,554 to 16,574 bp, with an AT bias of 53.6–54.9%. Maximum-likelihood phylogenetic tree was reconstructed using the connected protein sequences of 13 protein-coding genes of 34 species of fish. The phylogeny revealed that the genera Gastromyzon, Sewellia, and Erromyzon were monophyletic, and other genera Beaufortia, Vanmanenia, Formosania, and Pseudogastromyzon were paraphyletic or polyphyletic. Phylogeny corrected the taxonomic status of Metahomaloptera omeiensis, which should be categorized under the family of Gastromyzontidae rather than Balitoridae, denoting the significance of this study to the overall fisheries research.

The complete mitochondrial genome of Turbo cornutus (Trochida: Turbinidae) and its phylogeny analysis

The complete mitochondrial genome sequence of Turbo cornutus, a species of the Turbinidae family, was characterized from the de novo assembly of Illumina paired-end sequencing data. The complete mitochondrial genome of T. cornutus was 17,297 bp in length and comprised of 13 protein-coding genes, 25 tRNAs, and two rRNAs. The base composition of T. cornutus exhibited a high A + T content of 71.17%. The phylogenetic analysis of T. cornutus with 14 species from GenBank revealed that the ancestor of Astralium haematragum and Bolma rugosa was diverged from T. cornutus.

The complete mitochondrial genome sequence of the hawkmoth, Ambulyx tobii (Lepidoptera: Sphingidae) and phylogenetic analysis

In this study, we sequenced and analyzed the complete mitochondrial genome of Ambulyx tobii to compare mitochondrial genome structures and reconstruct phylogenetic relationships. The complete mitochondrial genome sequence of A. tobii is circular, 15,343 bp in size and encodes 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region (CR). Nucleotide composition is highly biased toward A + T nucleotides (81.2%). Most PCGs initiate with the standard start codon of ATN and terminate with the typical stop codon TAA/TAG. Phylogenetic analyses were performed using both 13 PCGs and whole mitochondrial genomes showed that A. tobii is closely related to A. substrigilis.

A chromosome-level genome of the human blood fluke Schistosoma japonicum identifies the genomic basis of host-switching.

The evolution and adaptation of S.japonicum, a zoonotic parasite that causes human schistosomiasis, remain unclear because of the lack of whole-genome data. We construct a chromosome-level S.japonicum genome and analyze it together with 72 samples representing six populations of the entire endemic region. We observe a Taiwan zoophilic lineage splitting from zoonotic populations ∼45,000 years ago, consistent with the divergent history of their intermediate hosts. Interestingly, we detect a severe population bottleneck in S.japonicum, largely coinciding with human history in Asia during the last glacial maximum. We identify several genomic regions underlying natural selection, including GATAD2A and Lmln, both showing remarkable differentiation among different areas. RNAi knockdown suggests association of GATAD2A with parasite development and infection in definitive hosts, while Lmln relates to the specificity of the intermediate hosts. Our study provides insights into the evolution of S.japonicum and serves as a resource for further studies.

The cotton mitochondrial chimeric gene orf610a causes male sterility by disturbing the dynamic balance of ATP synthesis and ROS burst

Plant cytoplasmic male sterility (CMS) is maternally inherited and often manifested as aborted pollen development, but the molecular basis of abortion remains to be identified. To facilitate an investigation of CMS in cotton, the complete sequence of cotton mitochondrial (mt) genome for CMS-D2 line ZBA was determined. The mt genome was assembled as a single circular molecule with 634,036 bp in length. A total of 194 ORFs, 36 protein‐coding genes, six rRNAs, and 24 tRNAs were identified. Several chimeric genes encoding hypothetical proteins with transmembrane domains were identified. Among them, a previously unknown chimeric gene, orf610a, which is composed of atp1 and a 485-bp downstream sequence of unknown nature, was identified. RT-PCR and qRT-PCR validation indicated that orf610a was expressed specifically in a sterile line. Ectopic expression of orf610a in yeast resulted in excessive accumulation of reactive oxygen species and reduction in ATP content, in addition to inhibition of cellular growth. Transgenic A. thaliana overexpressing orf610a fused with a mitochondrial targeting peptide displayed partial male sterility. Interaction between ORF610a and the nuclear-encoded protein RD22 indicated an association between ORF610a and pollen abortion. Positive feedback during transcriptional regulation between nuclear regulatory factors and the mt CMS gene may account for the male sterility of ZBA.

Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa.

Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.

The complete mitochondrial genome of the moss Neckeropsis nitidula (Mitt.) M. Fleisch.

In this study, the complete mitochondrial genome of Neckeropsis nitidula (Mitt.) M. Fleisch. in the family Neckeraceae was determined. This mitogenome was 104,716 base pairs in length and contained 40 protein-coding genes, three ribosomal RNA genes, and 24 transfer RNA genes. The overall nucleotide composition was asymmetric (29.5% A, 29.3% T, 21.3% G, and 19.9% C), with a 41.2% G + C content. The gene arrangement was identical to that of most Hypnales genomes. A phylogenetic tree was constructed using the N. nitidula mitogenome obtained in this study and the complete mitochondrial genome sequences of 23 bryophytes and 3 Marchantiophyta that were publicly available in GenBank. Our phylogenetic analysis revealed that N. nitidula was clustered in a clade with other Hypnalean taxa.

Complete Mitochondrial Genome Sequence of a Seabird, Wedge-Tailed Shearwater (Ardenna pacifica).

ABSTRACTHere, we report the complete mitochondrial genome sequence of a seabird, wedge-tailed shearwater (Ardenna pacifica). The circular genome has a size of 16,434 bp and contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The study provides a reference mitochondrial genome of wedge-tailed shearwater for further molecular studies.

Complete mitochondrial genome of Rhodeuscyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis.

Rhodeuscyanorostris Li, Liao & Arai, 2020 is a freshwater fish that is endemic to China and restricted to Chengdu City in Sichuan Province. This study is the first to sequence and characterize the complete mitochondrial genome of R.cyanorostris. The mitogenome of R.cyanorostris is 16580 bp in length, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region (D-loop). The base composition of the sequence is 28.5% A, 27.6% C, 26.4% T, and 17.5% G, with a bias toward A+T. The genome structure, nucleotide composition, and codon usage of the mitogenome of R.cyanorostris are consistent with those of other species of Rhodeus. To verify the molecular phylogeny of the genus Rhodeus, we provide new insights to better understand the taxonomic status of R.cyanorostris. The phylogenetic trees present four major clades based on 19 mitogenomic sequences from 16 Rhodeus species. Rhodeuscyanorostris exhibits the closest phylogenetic relationship with R.pseudosericeus, R.amarus, and R.sericeus. This study discloses the complete mitochondrial genome sequence of R.cyanorostris for the first time and provides the most comprehensive phylogenetic reconstruction of the genus Rhodeus based on whole mitochondrial genome sequences. The information obtained in this study will provide new insights for conservation, phylogenetic analysis, and evolutionary biology research.

The first de novo genome assembly and sex marker identification of Pluang Chomphu fish (Tor tambra) from Southern Thailand

The Tor genus belongs to the group of cyprinid fish commonly known as mahseer. Although Tor species are rapidly declining in the wild, and some face extinction, ambiguities in species identification hinder their collection and conservation. We conducted a genome survey of male and female Tor tambra collected in Thailand. The genome sizes of the male and female fish were approximately 1,671 and 1,645 Mb, respectively, with repeat contents of approximately 33%. The heterozygosity ratios of the male and female fish, which were 0.34% and 0.39%, respectively, suggested that the sex of T. tambra is determined by the ZW system. A sex marker was identified in silico and confirmed by PCR amplification. The result indicated that T. tambra has a ZZ/ZW sex determination system. Subsequently, comparative genomic and phylogenetic analyses of T. tambra and other fish in the Cyprinidae family were performed to explore the genetic diversity and evolution of the species. We also assembled the complete mitochondrial genome sequences of the T. tambra collected in Thailand. A phylogenetic tree of different Tor species, constructed based on mitochondrial genome sequences, indicated that T. tambra was closely related to T. tambroides. We believe this is the first genome survey of a species from the Tor genus or Mahseer group. Our results may help identify Tor species, providing a reference for genetic studies of the Tor genus and other mahseer fish.

ФИЛОГЕНЕТИЧЕСКИЙ АНАЛИЗ ПОЛНЫХ ПОСЛЕДОВАТЕЛЬНОСТЕЙ МИТОХОНДРИАЛЬНОГО ГЕНОМА ОВЕЦ КУЙБЫШЕВСКОЙ ПОРОДЫ

Here, we present the results of a phylogenetic analysis of sheep of the Kuibyshev breed. Complete mitochondrial genome sequences of Russian sheep breed were obtained and then analyzed considering separate mitochondrial markers. The level of polymorphism in separate mitochondrial markers was established. Genetic diversity indicators were calculated for separate mitochondrial genes and for the complete mitochondrial genome. Based on the analysis, a phylogenetic tree was constructed, and the haplogroup assignment of the studied sheep was determined. Regular genetic monitoring will contribute to the accumulation of knowledge on the polymorphisms of all mitochondrial markers. Our study resulted in gaining new knowledge, which deepen the understanding of the role of mitochondrial DNA in the life functions support of sheep.

Complete mitochondrial genome sequencing reveals double-buried Jomon individuals excavated from the Ikawazu shell-mound site were not in a mother–child relationship

Complete mitochondrial genome sequencing reveals double-buried Jomon individuals excavated from the Ikawazu shell-mound site were not in a mother–child relationship