Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis最新文献

The genus Himantura, Müller and Henle 1837 (Myliobatiformes: Dasyatidae) comprises benthic stingrays inhabiting tropical and subtropical waters, including the biodiversity-rich Southwest Indian Ocean (SWIO). Despite their ecological significance and susceptibility to anthropogenic pressures, the genetic diversity and evolutionary relationships of Himantura species remain poorly understood. This study sequenced and characterised the complete mitochondrial genomes of the SWIO variants of Himantura leoparda (17,682 bp) and Himantura uarnak (17,670 bp), the latter representing the first mitogenome for this species. Each mitogenome exhibited the typical vertebrate structure: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Codon usage was strongly AT-biased, with leucine (CTA) and isoleucine (ATC) predominating. Elevated single nucleotide polymorphism diversity in ND4 suggests ongoing divergence with adaptive implications. Phylogenetic analysis of concatenated PCGs confirmed the monophyly of Himantura within Dasyatidae, with distinct separation between the two SWIO mitogenomes supporting recognition of two separate species. The SWIO H. leoparda variant was most closely related to the Indo-Pacific H. leoparda variant. These findings address taxonomic ambiguities within the genus and highlight the need for species-specific conservation strategies, providing essential mitogenomic data to support future Himantura research in the SWIO.

An analysis of partial sequences of the cytochrome c oxidase subunit I (COI) gene from 39 specimens of Emplectonema ex gr. gracile from the Sea of Okhotsk, Sea of Japan, and Yellow Sea has shown that almost all the studied specimens from the first two seas belong to Emplectonema viride, which is also distributed along the Pacific coast of North America. In the Sea of Okhotsk and Sea of Japan, only three haplotypes for this species have been identified, all differing from the haplotypes sampled from off the North American coast. One specimen from the Sea of Japan (Spokoinaya Bay, southern Primorsky Krai, Russia) and all the specimens from the Yellow Sea belong to E. gracile. Of the six haplotypes of Pacific E. gracile, four are also found in the Atlantic Ocean. It has been suggested that E. gracile is an invasive species to the Pacific Ocean.

This study presents a comprehensive analysis of the chloroplast genomes of two species belonging to the genus Cornus, Cornus sanguinea L. and Cornus sericea L. Both plastomes exhibit a typical circular quadripartite structure, with slight variations in the lengths of the large and small single-copy regions. The complete chloroplast genomes of C. sericea and C. sanguinea were assembled and characterized, with lengths of 158,244 bp and 158,663 bp, respectively. A total of 131 genes were identified in each cp genome, comprising 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Notably, tetra-, penta-, and hexa-nucleotide simple sequence repeats were absent in both genomes. We investigated the taxonomic relationships among the Cornaceae and the closely related families Hydrangeaceae, Nyssaceae, Garryaceae, Curtisiaceae, and Grubbiaceae. Phylogenetic analyses clustered C. sanguinea and C. sericea into a single well-supported clade Cornaceae, reflecting their close relationships with other species in the family, which is consistent with previous studies. Overall, this study provides new insights into the structure and features of the C. sericea and C. sanguinea cp genomes.

Mitochondrial DNA has unique biological characteristics, such as a high mutation rate and clonal inheritance, which make it an appropriate marker in molecular biology. However, exceptionally high mitochondrial divergences have been reported in terrestrial and marine invertebrates, plants, and certain vertebrate lineages, which complicates the interpretation of the results in DNA barcoding and evolutionary studies. The freshwater snails in the genus Semisulcospira have two mitochondrial DNA lineages: a normal mitochondrial lineage (mt-A type) and a highly divergent 'enigmatic' lineage (mt-B type). We assembled thirty-two mitogenomes of Semisulcospira to understand the molecular evolution of the mt-B type. We found that the mt-B type evolves faster than the mt-A type, has more non-synonymous mutations, and exhibits structural variations with truncated cob and cox3 genes. Our results showed that the observed molecular evolution of the mt-B type could result from a decreased efficiency of natural selection due to small population size and/or the accumulation of slightly deleterious mutations caused by mitochondrial sex ratio distortion.

Aluterus monoceros, commonly known as the Unicorn leatherjacket filefish, has a circumglobal distribution and was infrequently recorded in Indian trawl landings prior to 2008. In recent years, substantial catches have been reported from major fish landing centres along the Indian coast, establishing it as a targeted fishery. Despite its growing commercial importance, the population structure of this species remains largely unexplored. This study assesses the genetic diversity of A. monoceros along the Indian coastline using mitochondrial DNA markers. The analysis revealed high haplotype diversity, indicating considerable genetic variation within the species. Results from the Analysis of Molecular Variance (AMOVA) showed minimal genetic differentiation among populations. Low Φ_ST values suggested extensive gene flow among populations across the Indian coast. Neutrality tests further indicated signals of recent population expansions or selective sweeps. This study provides baseline information on the genetic diversity and population structure of A. monoceros, supporting the existence of a predominantly panmictic population with minor regional variation. The findings highlight the feasibility of managing populations along the Indian coast as a single genetic management unit.

African wild dogs (Lycaon pictus) are the sole representative of their genus, and form an ancestral lineage most closely related to Asian dholes (Cuon alpinus) and Ethiopian wolves (Canis simensis). They suffered tremendous demographic losses over the past decades and have low levels of mitochondrial (mtDNA) variation, previously measured with a 381 bp segment of the Control region (CR). In this study, we did a whole mitochondrial genome (mitogenomes) comparison of 20 wild dogs from South Africa and Zimbabwe. We questioned (i) whether low levels of mtDNA diversity (typically seen in the CR) are also observed in other regions of the mitogenome, (ii) how mitogenomic diversity in wild dogs compares to other species, and (iii) how mitogenomic lineages have diverged across time. We found that mtDNA diversity was low across the genome, with 5 unique haplotypes across 16,829-17,531 bp (and only 11 CR haplotypes across their entire range), and a nucleotide diversity (π) of 0.0009, which is much lower than most other animal species. We also found an imperfect tandem repeat ('ACACATACGT') at the flanks of the CR, with a total length that extends much further than typically observed in animals, varying between 43-989 bp among individuals. Because the CR is noncoding, this may have occurred due to DNA slippage in a lack of selective constraints. The low number of haplotypes may be the effect of historic population contractions and recent demographic losses, which wild dogs are known to have experienced.

Assessing genetic diversity among potential populations provides crucial insights for genetic improvement programs targeting long-domesticated fish species. In this study, we evaluated genetic diversity levels using mitochondrial control region sequences of snakeskin gourami from one cultured and two wild populations (Ca Mau, CM and Kien Giang, KG) in the Mekong Delta, Viet Nam, alongside two other wild populations from Cambodia and Thailand. A total of 128 samples yielded 46 haplotypes, with five populations collectively contributing 42 unique haplotypes. All populations exhibited relatively high levels of genetic diversity, with haplotype diversity ranging from 0.719 to 0.877 and nucleotide diversity from 0.0075 to 0.0107. Statistically significant genetic differences were detected between the cultured and wild populations (F_ST range: 0.205-0.313), whereas weak genetic structure was observed among wild populations along the Mekong basin. These findings suggest that the cultured population holds potential as a base for genetic improvements, but crossbreeding between genetically distinct cultured and wild stocks should be carefully evaluated before large-scale seed production.

Hibernation is an elaborate response strategy employed by numerous mammals to survive in cold conditions that involves active suppression of metabolism. Despite the role of mitochondria as energy metabolism centers during hibernation, the adaptive and evolutionary mechanisms of mitochondrial genes in hibernating animals, like hedgehogs in eulipotyphlan species, are not yet fully understood. In this study, we sequenced and assembled mitochondrial genomes of the hibernating four-toed hedgehog (Atelerix albiventris) and the non-hibernating Asian house shrew (Suncus murinus). While no significant positive selection was detected, we identified unique amino acid substitutions and accelerated evolutionary rates of mitochondrial proteins and the encoding genes in hibernating hedgehogs. Moreover, the distinctive evolutionary patterns indicated a potential link among the adaptive evolution of mitochondrial genes (such as ATP6, CYTB, and ND6), the phenotypes of hibernation and longevity in eulipotyphlan species. These three genes evolved rapidly in hibernating Erinaceidae species and exhibited significant correlations with the two distinct phenotypes, indicating their pivotal roles in the evolution of hibernation and longevity. These findings provide insights into the genetic mechanisms responsible for metabolic plasticity and longevity in eulipotyphlan hibernators, with implications for other mammalian taxa.

The shallow water reef-building 'maze' or 'brain' stony coral Meandrina meandrites (fam. Meandrinidae) is currently experiencing major environmental problems in the Caribbean Sea. In this study, we assembled the mitochondrial genome of M. meandrites to support future conservation of this imperiled coral. We also explored the phylogenetic position of this coral in the Class Scleractinia utilizing the phylogenetic signal provided by translated mitochondrial protein-coding genes (PCGs). A complete mitochondrial genome of M. meandrites, 17,196 bp in length, was assembled using short-reads next-generation sequencing (NGS) sequencing with the target-restricted-assembly pipeline GetOrganelle. The newly assembled mitochondrial genome of M. meandrites encoded 13 PCGs, two ribosomal genes (ribosomal RNA), and two transfer genes (tRNAs). It also contains two relatively long non-coding regions 400 and 1,877 bp long. A group I intron bisected the nad5 PCG. Each of the two tRNAs exhibited a canonical 'cloverleaf' secondary structure. The mitochondrial genome of M. meandrites is identical to that of a conspecific assembled using HiFi PacBio long reads (available in GenBank with accession number OY855917 but without a companion paper) with the exception of four single nucleotide variants. The aforementioned comparison indicates that the mitochondrial genome assembled from a short-read NGS dataset is reliable (complete and accurate). A maximum-likelihood phylomitogenomic analysis based on PCGs (translated) supported the monophyly of the order Scleractinia and placed M. meandrites in a moderately to well-supported clade with Astrangia sp. (family Astrangidae). This newly assembled mitochondrial genome can be used as a reference to support conservation planning, including biomonitoring of this stony coral using environmental DNA.