D-loop Region Research Articles

Characterization of the complete mitochondrial genome of the critically endangered Southern River Terrapin, Batagur affinis affinis (Reptilia: Geoemydidae)

In this study, we report the nearly complete mitochondrial sequence of Batagur affinis affinis. The assembled mitogenome consists of 13 PCGs, 22 tRNA genes, two rRNAs and one near-complete D-loop region. Of the annotated genes, the ND6 subunit gene and eight tRNA genes were encoded on the L-strand, while the remaining genes were dispersed on the H-strand. Except for CO1, which has a GTG start codon, all protein-coding genes begin with ATG. The mitogenome has been deposited in NCBI GenBank under the accession number OQ409915. Phylogenetic tree analysis based on publicly available mitogenomes indicate the sister grouping of B. affinis affinis with B. kachuga.

An Optimized Environmental DNA Method to Improve Detectability of the Endangered Sichuan Taimen (Hucho bleekeri)

Environmental DNA (eDNA) techniques have emerged as a cost-effective and non-invasive strategy for monitoring the distribution of endangered aquatic species. Despite their numerous advantages, operational uncertainty at each step of the process represents a significant challenge that can impact the reliability of results. Hence, the optimization of the eDNA analytic protocol is of utmost importance. In this study, the rare and endangered fish species Sichuan taimen was chosen as the target species to evaluate the concordance between different approaches (tissue, pond, and field water samples) for eDNA detection. The results showed that membrane filtration, collection of a 2-L water sample, and utilization of the DNeasy Tissue and Blood DNA extraction kit were suitable for the analysis of DNA in water samples. Furthermore, the mtDNA D-loop region demonstrated potential as a specific molecular marker for the precise identification of Sichuan taimen. Our results indicated that TaqMan fluorescence PCR can serve as the optimal detection method for reliable identification of target DNA even at extremely low concentrations in the field. This study established an optimized eDNA analysis protocol for Sichuan taimen detection, which will provide the basis for future resource investigations aimed at protection of this endangered aquatic species.

Polymorphisms of mtDNA in the D-loop region moderate the associations of BMI with HOMA-IR and HOMA-β among women with polycystic ovary syndrome: a cross-sectional study.

Polycystic ovary syndrome (PCOS) is one of the leading causes of infertility in women of childbearing age, and many patients with PCOS have obesity and insulin resistance (IR). Although obesity is related to an increased risk of IR, in clinical practice, PCOS patients exhibit different effects on improving insulin sensitivity after weight loss. Therefore, in the present study, we aimed to examine the moderating effect of polymorphisms of mtDNA in the D-loop region on the associations of body mass index (BMI) with the homeostasis model assessment of insulin resistance index (HOMA-IR) and pancreatic β cell function index (HOMA-β) among women with PCOS. Based on a cross-sectional study, women with PCOS were recruited from the Reproductive Center of the First Affiliated Hospital of Anhui Medical University from 2015 to 2018. A total of 520 women who were diagnosed with PCOS based on the revised 2003 Rotterdam criteria were included in the study. Peripheral blood was collected from these patients, followed by DNA extraction, PCR amplification, and sequencing at baseline. HOMA-IR and HOMA-β were calculated according to blood glucose-related indices. Moderating effect models were performed with BMI as an independent variable, polymorphisms of mtDNA in the D-loop region as moderators, and ln (HOMA-IR) and ln (HOMA-β) as dependent variables. To verify the stability of moderating effect, sensitivity analysis was performed withthe quantitative insulin sensitivity check index (QUICKI), fasting plasma glucose/fasting insulin (G/I), and fasting insulin as dependent variables. BMI was positively associated with ln (HOMA-IR) and ln (HOMA-β) (β = 0.090, p < 0.001; β = 0.059, p < 0.001, respectively), and the relationship between BMI and ln (HOMA-IR) or ln (HOMA-β) was moderated by the polymorphisms of mtDNA in the D-loop region. Compared with the respective wild-type, the variant -type of m.16217 T > C enhanced the association between BMI and HOMA-IR, while the variant-type of m.16316 A > G weakened the association. On the other hand, the variant-type of m.16316 A > G and m.16203 A > G weakened the association between BMI and HOMA-β, respectively. The results of QUICKI and fasting insulin as dependent variables were generally consistent with HOMA-IR, and the results of G/I as dependent variables were generally consistent with HOMA-β. Polymorphisms of mtDNA in the D-loop region moderate the associations of BMI with HOMA-IR and HOMA-β among women with PCOS.

Complete mitochondrial genome of the Galápagos sea lion, Zalophuswollebaeki (Carnivora, Otariidae): paratype specimen confirms separate species status.

The endangered Galápagos sea lion (Zalophuswollebaeki) inhabits the Galápagos Islands off the coast of Ecuador. We present a complete mitochondrial genome (16 465 bp) of a female paratype from the collections of the Natural History Museum Oslo, Norway, assembled from next-generation sequencing reads. It contains all canonical protein-coding, rRNA, tRNA genes, and the D-loop region. Sequence similarity is 99.93% to a previously published conspecific mitogenome sequence and 99.37% to the mitogenome sequence of the sister species Z.californianus. Sequence similarity of the D-loop region of the Z.wollebaeki paratype mitogenome is >99%, while the sequence difference to the Z.californianus sequences exceeds 2.5%. The paratype mitogenome sequence supports the taxonomic status of Z.wollebaeki as a separate species.

Comparative Mitochondrial Genomes between the Genera Amiota and Phortica (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability.

To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143-16,803 bp and 15,933-16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica.

Genetic monitoring of sterlet juveniles (Acipenser ruthenus) in the Volga river

The aim of the work was to carry out genetic monitoring of the natural reproduction of juveniles (larvae and underyearlings) of sterlet (Acipenser ruthenus Linnaeus, 1958), caught in the middle and lower spawning zones of the Volga River for the period 2021–2022, which is necessary and relevant in the context of a decrease in the number of sturgeon species of fish. The study of fish was carried out according to five nuclear markers and a fragment of the control region of mitochondrial DNA.According to the results of microsatellite analysis, sterlet individuals were characterized by species-specific dominant alleles and high values of the main indicators of genetic diversity: the number of alleles, allelic diversity and heterozygosity, and a slight deficit of heterozygotes was noted. By analyzing of the nucleotide sequences of the mtDNA D-loop region a high level of diversity of maternally inherited haplotypes was revealed, reflecting the number of females involved in natural reproduction. According to the monitoring data, no differences in the distribution and number of identified variants of the D-loop region were registered in the interannual aspect. During the study period, 48 sterlet mitochondrial haplotypes were recorded, of which 18 mtDNA variations were unique, occurring in the Volga-Caspian fishery basin. In the study of sterlet larvae by molecular genetic methods in the Volga River was revealed the process of hybridization between stellate sturgeon and sterlet (Acipenser stellatus × Acipenser ruthenus).

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.

Genetic Diversity and Population Structure Analysis of Chinese Mitten Crab (Eriocheir sinensis) in the Yangtze and Liaohe Rivers

Recently, the economic traits of Chinese mitten crab (Eriocheir sinensis) varieties have had a negative tendency. Meanwhile, the status of wild germplasm resources of E. sinensis is unknown, hindering the utilization of wild germplasm resources and the green development of the E. sinensis industry. Thus, the conservation of the wild E. sinensis germplasm resource is of great significance. To this end, we collected wild E. sinensis from two different river basins, the Yangtze River basin, and the Liaohe River basin, and analyzed the genetic diversity as well as the genetic differentiation in E. sinensis populations. Based on eight microsatellite markers, we found moderate genetic diversity in E. sinensis populations regardless of river basin. Based on the mitochondrial D-loop region, we found that all populations are at mutation drift equilibrium, while the Nm between any two populations is greater than 1. We hypothesized the existence of island model gene flow patterns among E. sinensis. Interestingly, genetic differentiation among E. sinensis populations was low, except that between Liaohe and Anqing or Shanghai populations. Additionally, geometric morphological analysis could distinguish E. sinensis from different basins, with an accuracy of 94.2–100%. Given the similar genetic diversity in the two basins, the genetic convergence of E. sinensis from different basins deserves further attention.

Genetic diversity and population structure of wild Macrobrachium nipponense populations across China: Implication for population management

Macrobrachium nipponense, is an important economic indigenous prawn and is widely distributed in China. However, most these genetic structure analysis researches were focused on a certain water area, systematic comparative studies on genetic structure of M. nipponense across China are not yet available. In this study, D-loop region sequences was used to investigate the genetic diversity and population structure of 22 wild populations of M. nipponense through China, containing the major rivers and lakes of China. Totally 473 valid D-loop sequences with a length of 1110bp were obtained, and 348 variation sites and 221 haplotypes were detected. The haplotype diversity (h) was ranged from 0.1630 (Bayannur) ~ 1.0000 (Amur River) and the nucleotide diversity π value ranged from 0.001164 (Min River) ~ 0.037168 (Nen River). The pairwise genetic differentiation index (FST) ranged from 0.00344 to 0.91243 and most pair-wised FST was significant (P < 0.05). The lowest FST was displayed in Min River and Jialing River populations and the highest was between Nandu River and Nen River populations. The phylogenetic tree of genetic distance showed that all populations were divided into two branches. The Dianchi Lake, Nandu River, Jialing River and Min River populations were clustered into one branch. The neutral test and mismatch distribution results showed that M. nipponense populations were not experienced expanding and kept a steady increase. Taken together, a joint resources protection and management strategy for M. nipponense have been suggested based on the results of this study for its sustainable use.

Complete mitochondrial genomes reveal the phylogenetic relationships of Duoma with eight representative sheep breeds and two ovis species

The Ovis aries Duoma breed is one of the most important alpine grassland-type sheep breeds in China. In this current study, we first reported the complete mitochondrial genome of Duoma sheep. Mitochondrial genome is 16,618 bp in length and exhibits the same typical structure as the other published sheep breeds. The genome contains 37 genes (22 tRNA, two rRNA, and 13 protein-coding genes (PCGs)) and a control region (D-loop region). Phylogenetic analysis shows that the Duoma sheep breed is closer to Ganjia sheep. Our findings will help the further evolution and conservation studies of Duoma sheep.

Phylogeographic Patterns of the Greater Cane Rat (Thryonomys Swinderianus) Populations from Eastern, Western and Southern Africa and Implications for Wildlife Conservation

Background and aim: African Greater Cane (ACG) rat populations are widely distributed across Africa but the ancestral origin of populations inhabiting different geographical regions is unknown. There is currently no information available on the genetic differentiation of these populations resulting from long-time geographical isolation, environmental and anthropogenic pressures they face in each region. This limits our ability to understand potential speciation processes in AGC and their implications for their conservation and of other small wild mammals exposed to similar ecological conditions in the savannah biomes in Africa. Methods: We analyzed mitochondrial genes targeting the D-loop region of AGC samples from two blocks of the Eastern Arc Mountains in Tanzania (eastern), three agro-ecological zones in Ghana (western) and four sites in South Africa (southern) to characterize the phylogeographical patterns of the species. Results: AGC populations from Tanzania revealed higher haplotype diversity than those from the two other régions. Analysis of variance (AMOVA) revealed higher genetic variations within than between populations in all geographic regions. Demographic history analysis revealed a negative and significant Tajima’s D for a single southern African population as well as close relatedness with the Eastern Africa populations, suggesting a common ancestral origin. Conclusion: This is the first study to compare maternal lineages of AGC populations from eastern, western and southern Africa and provides a basis for future genetic studies of the species, its evolutionary ecology and the conservation of these populations across their range. Conservation implications: Evidence of recent population size expansion underpinned by high genetic diversity observed in the Uluguru urban (Tanzania) Guinea savannah (Ghana) and Kwazulu Natal (South Africa) populations suggest that the AGC populations are not currently threatened, consistent with the current IUCN status. Also, the distinct haplotypes observed in each region suggest that the populations can be managed as meta-populations, thus providing opportunities for potential local game-farming programs.

Differentiation of cattle and buffalo meat using multiplex polymerase chain reaction

Authentication of origin of animal species is of paramount importance owing to economic, social, religious, forensic and public health considerations. In the present study, a multiplex polymerase chain reaction (mPCR) was developed by designing unique species-specific forward and a common reverse primers flanking mitochondrial D-loop region for the authentication of cattle (Bos indicus / B. taurus) and buffalo (Bubalus bubalis) species. Novel mPCR amplified 382 bp product specific to cattle and 336 bp specific to buffalo. Possibility of cross amplification in other species was rules out by testing as many as 25 other animal species. The novel mPCR assay developed in this study for the authentic identification and differentiation of meats of cattle and buffalo could be applied for the differentiation of samples derived from cattle and buffalo in diagnostic laboratories thereby ensuring prompt labelling of products, protecting consumer sentiments and enforcement of laws.

Assembly, Characterization, and Phylogenetic Relationships of Mitogenomes of Two Species of Mexican Trout (Oncorhynchus chrysogaster and O. mykiss nelsoni)

In this study, the complete mitochondrial genomes of the Mexican golden trout, Oncorhynchus chrysogaster, and Nelson’s trout, O. mykiss nelsoni, were assembled and characterized. The mitogenomes were 16,655 bp and 16,661 bp long, respectively, and were composed of 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes (all with typical ‘cloverleaf’ secondary structures). The length of the D-loop regions was among the longest found in Salmonids, and mitochondrial synteny in both species was identical to that reported in other Salmonids. Selective pressure analysis in the PCGs indicated that purifying selection, mainly among cox and nd genes families, likely generated the main differences between the two studied species. Nine tRNA genes showed slight differences relative to other O. mykiss subspecies, which were identical between the two study taxa. The origin of the light-strand replication has a loop that was especially large in O. mykiss nelsoni. Phylogenetic analysis indicated that O. chrysogaster and O. mykiss nelsoni are sister species, contrary to the expectation that O. chrysogaster would cluster with O. gilae. As previous studies have suggested, O. chrysogaster and O. mykiss nelsoni share common ancestry with North American trout species.

Comparison between D-loop methylation and mtDNA copy number in patients with Aicardi-Goutières Syndrome.

Aicardi-Goutières Syndrome (AGS) is a rare encephalopathy with early onset that can be transmitted in both dominant and recessive forms. Its phenotypic covers a wide range of neurological and extraneurological symptoms. Nine genes that are all involved in nucleic acids (NAs) metabolism or signaling have so far been linked to the AGS phenotype. Recently, a link between autoimmune or neurodegenerative conditions and mitochondrial dysfunctions has been found. As part of the intricate system of epigenetic control, the mtDNA goes through various alterations. The displacement (D-loop) region represents one of the most methylated sites in the mtDNA. The term "mitoepigenetics" has been introduced as a result of increasing data suggesting that epigenetic processes may play a critical role in the control of mtDNA transcription and replication. Since we showed that RNASEH2B and RNASEH2A-mutated Lymphoblastoid Cell Lines (LCLs) derived from AGS patients had mitochondrial alterations, highlighting changes in the mtDNA content, the main objective of this study was to examine any potential methylation changes in the D-loop regulatory region of mitochondria and their relationship to the mtDNA copy number in peripheral blood cells of AGS patients with mutations in various AGS genes and healthy controls. We collected blood samples from 25 AGS patients and we performed RT-qPCR to assess the mtDNA copy number and pyrosequencing to measure DNA methylation levels in the D-loop region. Comparing AGS patients to healthy controls, D-loop methylation levels and mtDNA copy number increased significantly. We also observed that in AGS patients, the mtDNA copy number increased with age at sampling, but not the D-loop methylation levels, and there was no relationship between sex and mtDNA copy number. In addition, the D-loop methylation levels and mtDNA copy number in the AGS group showed a non-statistically significant positive relation. These findings, which contradict the evidence for an inverse relationship between D-loop methylation levels and mtDNA copy number, show that AGS patients have higher D-loop methylation levels than healthy control subjects. Additional research is needed to identify the function of these features in the etiology and course of AGS.

Historical Landscape Evolution Shaped the Phylogeography and Population History of the Cyprinid Fishes of Acrossocheilus (Cypriniformes: Cyprinidae) According to Mitochondrial DNA in Zhejiang Province, China

Geological events and landscape features, as well as changes in the climate during the Pliocene period, have shaped the distribution of genetic diversity and demographic history of freshwater fish in mainland China. In this study, we investigated the phylogeny and population genetic structure of Acrossocheilus species (A. fasciatus, A. kreyenbergii and A. wenchowensis) in the Zhejiang region by the mitochondrial cytochrome b (cyt-b) and control (D-loop) region s. Mitochondrial phylogenetic analysis revealed three major lineages (lineages A, B and C), which may represent A. fasciatus, A. wenchowensis and A. kreyenbergii, respectively. Our results revealed that A. fasciatus and A. wenchowensis diverged from A. kreyenbergii in the Zhejiang region. The uplift of the Wuyi Mountains and the Xianxia Mountains served as an important geographic barrier in the diversification of the three Acrossocheilus species. The most recent common ancestors (TMRCAs) of the three lineages and lineages A + B were dated to 1.859 and 1.614 myr, respectively. Our results indicate that the effective population sizes of A. fasciatus and A. wenchowensis remained constant from the past to the present, as supported by ABC analysis. For conservation and protection, a strategy is required because of their genetic uniqueness, and we suggest that the two regions divided by the Xianxia Mountains be regarded as different management units (Mus), conforming to the major zoological regions of the Zhejiang region.

Mitochondrial DNA Polymorphism in HV1 and HV2 Regions and 12S rDNA in Perimenopausal Hypertensive Women.

Estrogens enhance cellular mitochondrial activity. The diminution of female hormones during menopause may have an effect on the mitochondrial genome and the expression of mitochondrial proteins. Hence, oxidative stress and the pro-inflammatory state contribute to the formation of systemic illnesses including arterial hypertension (AH). This study aimed to determine the types and frequency of mutations in the mitochondrial DNA (mtDNA) nucleotide sequence in the hypervariable regions 1 and 2 (HV1 and HV2) and the 12S RNA coding sequence of the D-loop in postmenopausal women with hypertension. In our study, 100 women were investigated, 53 of whom were postmenopausal and 47 of whom were premenopausal (53.9 ± 3.7 years vs. 47.7 ± 4.2 years, respectively). Of those studied, 35 premenopausal and 40 postmenopausal women were diagnosed with AH. A medical checkup with 24 h monitoring of blood pressure (RR) and heart rate was undertaken (HR). The polymorphism of the D-loop and 12S rDNA region of mtDNA was examined. Changes in the nucleotide sequence of mtDNA were observed in 23% of the group of 100 women. The changes were identified in 91.3% of HV1 and HV2 regions, 60.9% of HV1 segments, 47.5% of HV2 regions, and 43.5% of 12S rDNA regions. The frequency of nucleotide sequence alterations in mtDNA was substantially higher in postmenopausal women (34%) than in premenopausal women (10.6%), p = 0.016. A higher frequency of changes in HV1 + HV2 sections in postmenopausal women (30.2%) compared to the premenopausal group (10.6%) was detected, p = 0.011. Only postmenopausal women were found to have modifications to the HV2 segment and the 12S rDNA region. After menopause, polymorphism in the mtDNA region was substantially more frequent in women with arterial hypertension than before menopause (p = 0.030; 37.5% vs. 11.5%). Comparable findings were observed in the HV2 and HV1 regions of the AH group (35% vs. 11.5%), p = 0.015, in the HV1 segment (25% vs. 11.5%), p = 0.529, and in the HV2 segment, 12S rDNA (25% vs. 0%). More than 80% of all changes in nucleotide sequence were homoplasmic. The mtDNA polymorphisms of the nucleotide sequence in the HV1 and HV2 regions, the HV2 region alone, and the 12S RNA coding sequence were associated with estrogen deficiency and a more severe course of arterial hypertension, accompanied by symptoms of adrenergic stimulation.

Lahaul-Zanskar-Sham Valley Corridor in Indian Trans Himalayan Region Facilitates Dispersal and Gene Flow in Himalayan Ibex.

Wildlife corridors that connect mosaic habitats in heterogeneous mountainous landscapes can be of high significance as they facilitate the genetic and demographic stability of free-ranging populations. Peripheral populations of widespread species are usually ignored in conservation planning. However, these populations retain locally common alleles and are genetic reservoir under the changing climatic conditions. Capra sibirica has widespread distribution, and its southern peripheral population is distributed in the Indian trans-Himalayan region (ITR). In the present study, we studied the spatial distribution and genetic make-up of Himalayan ibex from the ITR following the landscape genetics approach. We obtained 16 haplotypes at the mitochondrial d-loop region and found a stable demography in the past with a recent decline. With 10 nuclear microsatellites, we ascertained 111 unique individuals assigned into two clusters following Bayesian and non-Bayesian clustering analysis with several admixed individuals. We also recorded 25 first-generation migrants that reflected relatively high dispersal and gene-flow across the range. We identified a 19,835 sq.km suitable area with 13,311 sq.km in Ladakh and 6524 sq.km in Lahaul-Spiti. We identified a novel movement corridor for Himalayan ibex across the Lahaul-Zanskar-Sham valley (L-Z-SV) that displayed a fairly good conductance with low genetic divergence among the samples collected on the L-Z-SV corridor. We propose declaring a protected area in the Lahaul and Kargil districts to prioritize dedicated conservation efforts for the Himalayan ibex and other sympatric ungulates that impart a major role in the diet of large carnivore and balancing ecosystem services in the trans-Himalayan region.

Comparative Analysis of Complete Mitochondrial Genome of Ariosoma meeki (Jordan and Snider, 1900), Revealing Gene Rearrangement and the Phylogenetic Relationships of Anguilliformes

The mitochondrial genome structure of a teleostean group is generally considered to be conservative. However, two types of gene arrangements have been identified in the mitogenomes of Anguilliformes. In this study, we report the complete mitochondrial genome of Ariosoma meeki (Anguilliformes (Congridae)). For this research, first, the mitochondrial genome structure and composition were analyzed. As opposed to the typical gene arrangement pattern in other Anguilliformes species, the mitogenome of A. meeki has undergone gene rearrangement. The ND6 and the conjoint tRNA-Glu genes were translocated to the location between the tRNA-Thr and tRNA-Pro genes, and a duplicated D-loop region was translocated to move upstream of the ND6 gene. Second, comparative genomic analysis was carried out between the mitogenomes of A. meeki and Ariosoma shiroanago. The gene arrangement between them was found to be highly consistent, against the published A. meeki mitogenomes. Third, we reproduced the possible evolutionary process of gene rearrangement in Ariosoma mitogenomes and attributed such an occurrence to tandem repeat and random loss events. Fourth, a phylogenetic analysis of Anguilliformes was conducted, and the clustering results supported the non-monophyly hypothesis regarding the Congridae. This study is expected to provide a new perspective on the A. meeki mitogenome and lay the foundation for the further exploration of gene rearrangement mechanisms.

Mitochondrial DNA diversity and genetic structure of striped dolphin Stenella coeruleoalba in the Northern Ionian Sea

In the framework of global and EU policies focused on stopping the loss of biodiversity process, deepening the genetic variability, especially of populations species identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. This is more urgent for cetacean species in the Mediterranean because they assume a key ecological role in the marine food web and are severely affected by numerous and different anthropogenic pressures. This study aims to increase information on the genetic variability of striped dolphin in the Northern Ionian Sea by investigating the population structure, phylogenetic relationships and phylogeographic patterns using two mtDNA markers. From October 2020 to August 2021, a total of 88 skin tissue samples were collected from free-ranging dolphins in the Gulf of Taranto by applying the non-invasive technique of skin swabbing. An acceptable amount of DNA was extracted from 86 samples and used for subsequent genetic analysis conducted on the partial sequences of 421 and 704 bp in length of the cytb gene and D-loop control region, respectively. In addition, the sequences of the two mtDNA markers were joined together to compose a mtDNA concatenated sequence of 1125 bp for each sampled dolphin in order to investigate the genetic variability of the species population in the study area. Genetic analysis highlighted a low nucleotide diversity and high haplotypic diversity of the striped dolphin of the Gulf of Taranto, suggesting a population in rapid expansion after a period of reduction in size and diversity of the initial population. The phylogenetic analyses revealed the presence of at least two different lineages of Stenella coeruleoalba in the Mediterranean Sea, one specific to the Northern Ionian Sea and one shared with the Mediterranean population, confirming results already obtained for the local unit in the Gulf of Taranto. The results point out a potential problem of hybridization between striped and common dolphins which needs to be further investigated. Therefore, increasing the analysis of several markers may increase understanding of the genetic diversity of the population in the Ionian Sea and represent a useful tool to support the implementation of future effective conservation measures.

Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family.

The Huaibei grey donkey (HGD) is an endangered species and a vital native breed in Anhui Province, China. However, its complete mitogenome, phylogeny, and maternal origin remain unclear. The objectives of this study were to detect the genetic diversity of the HGD and investigate its phylogenetic relationship with other breeds to inform conservation management. The complete mitogenome of the HGD was sequenced through next-generation sequencing, and the most variable region in the mitochondrial DNA displacement-loop (D-loop) was amplified via a polymerase chain reaction (PCR). Next, we used the median-joining network (MJN) to calculate the genetic relationships among populations and the neighbor-jointing method to build a phylogenetic tree and speculate as to its origin. The results showed that the mitogenome contains 22 tRNAs, 2 rRNAs, 13 PCGs, and 1 D-loop region. Analyzing the D-loop region of the HGDs, we identified 23 polymorphic sites and 11 haplotypes. The haplotype and nucleotide diversity were 0.87000 (Hd) and 0.02115 (Pi), respectively. The MJN analysis indicated that the HGD potentially has two maternal lineages, and phylogenetic analysis indicated that the Somali lineage could be the most probable domestication center for this breed. Therefore, our mitogenome analysis highlights the high genetic diversity of the HGD, which may have originated from the Somali wild ass, as opposed to the Asian wild ass. This study will provide a useful resource for HGD conservation and breeding.