Complete Mitochondrial DNA Sequence Research Articles

Taxonomic classification on phylogenic information appears a debatable approach: Lessons from the order Cypriniformes

Genes are often selected for molecular taxonomy citing their agreement to taxonomically derived species trees. These results are then used to define and edit existing taxonomic hierarchies of species. We counter the validity of this practice experimentally using mitochondrial genes routinely employed for the purpose. We constructed trees from complete mitochondrial DNA sequence (except D-loop) and its thirteen protein-coding genes namely ND1, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6, ATP8, COI, COII, COIII, and CYTB of 255 species of Cypriniformes fish using the maximum likelihood and Bayesian methods. While ND4, ND5, COI, COII, COIII, and CYTB formed trees at par with the species tree, no gene produced complete concurrence. Similarly, while few genes formed similar branching patterns at family (COI and COIII) or broad group (ND1, ND2, and ND3; ND5 and COII) levels, no two gene trees fully agreed with each other. Tajima's D estimates of all studied genes indicated non-random evolution, violating the basic assumption of molecular phylogenetics. Bootstrap or Posterior probability values were also poor for several taxa indicating low robustness. Our findings reiterate that tree concurrence noted in studies involving smaller sample sizes is not a reflection of the evolutionary signature of the species.

Range-wide phylogenomics of the Great Horned Owl (Bubo virginianus) reveals deep north-south divergence in northern Peru.

The Great Horned Owl (Bubo virginianus) inhabits myriad habitats throughout the Americas and shows complex patterns of individual and geographic morphological variation. The owl family Strigidae is known to follow ecogeographic rules, such as Gloger's rule. Although untested at the species level, these ecogeographic rules may affect B. virginianus plumage coloration and body size. Previous studies have indicated that, despite this species' morphological variability, little genetic differentiation exists across parts of their range. This study uses reduced representation genome-wide nuclear and complete mitochondrial DNA sequence data to assess range-wide relationships among B. virginianus populations and the disputed species status of B. v. magellanicus (Magellanic or Lesser Horned Owl) of the central and southern Andes. We found shallow phylogenetic relationships generally structured latitudinally to the north of the central Andes, and a deep divergence between a southern and northern clade close to the Marañón Valley in the central Andes, a common biogeographic barrier. We identify evidence of gene flow between B. v. magellanicus and other subspecies based on mitonuclear discordance and F-branch statistics. Overall differences in morphology, plumage coloration, voice, and genomic divergence support species status for B. v. magellanicus.

The complete mitochondrial genome and the transfer RNA gene rearrangement of Sillago sinica (Perciformes, Sillaginidae), with reference to the evolution of related species

In this study, the complete mitochondrial DNA sequence of Sillago sinica, a new member of Sillaginidae fishes in China, was obtained by conventional long-PCR amplification. The length of assembled mitogenome sequence was 16,572 bp, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNA genes, together with a control region and L-strand replication region just identical to typical bony fishes. An infrequent transfer RNA gene rearrangement event was observed between tRNA-Asn and tRNA-Ala genes that might result from gene sliding. The average genetic distance among 9 Sillago fishes was calculated to be 0.2631, with the least genetic variation between S. sinica and S. aeolus. ML phylogenetic tree constructed based on 13 protein-coding genes also implied the closest relationships between the two. The results provided insight into the mtDNA gene arrangement feature of S. sinica and lay the foundation for further genetic studies on Sillaginidae.

AN INDIVIDUAL OF THE VOLINTSEVO PERIOD FROM KURILOVKA: THE FIRST ARCHAEOGENETIC DATA

Despite the achievements of recent years of palaeogenomic research, the genetic features and diversity of the early Slavic population remain unexplored due to the cremation ritual common in the ancient Slavic tribes. Therefore, each find of an Early Slavic site is an important material. Such a unique Early Slavic object is an individual whose remains were found in a dwelling attributed to the Volintsevo culture from the Kurilovka 2 site in Kursk Region, which dates back to the end of the 7th – first half/middle of the 8th century AD. We extracted DNA from the tooth and used it for genetic analysis. We reconstructed the complete mitochondrial DNA sequence and determined that it belongs to the European haplogroup H1b. The results of the phylogenetic analysis testify the common maternal lineages of the individual from Kurilovka with Medieval and modern European samples and suggest a commonality of the early Slavic and northwestern European mitochondrial lineages.

The complete mitogenome of blue sheep (Pseudois nayaur) from the Indian Himalayan Region and its comparative phylogenetic relationship with other related species

The ‘Bharal’ or ‘Himalayan Blue Sheep’ (Pseudois nayaur) is endemic to the Himalayan and Tibetan Regions. There are gaps in the available database for the blue sheep mitogenome sequencing from the Indian region. We sequenced and characterized the whole mitogenome of one blue sheep individual using the Illumina Nova-seq 6000 platform, which was 16,718 bp in length. It included 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one non-coding control region (D loop). It was compared with other complete mitochondrial DNA sequences of blue sheep from the NCBI database. The whole mitogenome of blue sheep was found to be highly AT-biased (60%) and had a positive AT skew (0.121) and a negative GC skew (−0.341). In 13 PCGs of blue sheep, Leucine (15.58%) and tryptophan (2.72%) occurred most frequently. A typical secondary cloverleaf structure was observed for all tRNA genes except for tRNA-Ser, where a stable structure of dihydrouridine did not develop. The phylogenetic analysis showed Indian blue sheep population formed a separate clade with a genetic distance of 3.7 to 4.1% from the Chinese blue sheep population, suggesting it to be of a different lineage and genetically qualifies the status of distinct subspecies. The results of this study will help in further phylogenetic analysis of Indian blue sheep populations in the Western and Eastern Himalayan regions and in understanding lineage identification and evolution for further research.

Complete mitochondrial DNA sequence of Tupaia belangeri yaoshanensis (Wang, 1987) from Dayao Mountains in China

The tree shrew (Tupaia belangeri) is currently placed in the order Scandentia. Owing to their unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low maintenance costs in laboratory conditions, tree shrews have been proposed as alternative experimental animals to primates in biomedical research. In this study, we determined the complete mitochondrial genome of the subspecies Tupaia belangeri yaoshanensis (T.b. yaoshanensis). The mitochondrial DNA (mtDNA) is 16,777 bp long and contains 13 protein-coding genes (PCGs), two ribosomal RNA genes (12S and 16S), and 22 transfer RNA (tRNA) genes. The base composition of the mitogenome was A (32.28%), T (26.82%), G (14.79%), and C (26.11%). For the 13 PCGs, 1405 variable sites were found between T.b. yaoshanensis and T.b. chinensis (JN800724), of which 916 were synonymous and 489 were nonsynonymous. The frequency of mutations significantly varied among the different genes, with the highest value in the mt-NAD5 gene of tree shrews. Phylogenetic analysis based on the amino acid sequences of 13 PCGs revealed a closer relationship between the species of Scandentia and Lagomorpha. To the best of our knowledge, this is the first study to report the complete mitochondrial genome sequence of T.b. yaoshanensis.

The complete mitochondrial genome of sleek unicornfish, Naso hexacanthus (Acanthuridae, Perciformes)

The complete mitochondrial DNA sequence of sleek unicornfish, Naso hexacanthus was first determined in this study. The complete mitogenome is 16,611 bp in length composed of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The nucleotides consist of 33.8% A, 20.6% C, 25.0% G, 20.6% T. The gene order and direction are identical to those of N. lopezi and the species of Acanthuridae. The result would be useful to investigate genetic relationships among the species of Naso.

High Coverage Mitogenomes and Y-Chromosomal Typing Reveal Ancient Lineages in the Modern-Day Székely Population in Romania.

Here we present 115 whole mitogenomes and 92 Y-chromosomal Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) profiles from a Hungarian ethnic group, the Székelys (in Romanian: Secuii, in German: Sekler), living in southeast Transylvania (Romania). The Székelys can be traced back to the 12th century in the region, and numerous scientific theories exist as to their origin. We carefully selected sample providers that had local ancestors inhabiting small villages in the area of Odorheiu Secuiesc/Székelyudvarhely in Romania. The results of our research and the reported data signify a qualitative leap compared to previous studies since it presents the first complete mitochondrial DNA sequences and Y-chromosomal profiles of 23 STRs from the region. We evaluated the results with population genetic and phylogenetic methods in the context of the modern and ancient populations that are either geographically or historically related to the Székelys. Our results demonstrate a predominantly local uniparental make-up of the population that also indicates limited admixture with neighboring populations. Phylogenetic analyses confirmed the presumed eastern origin of certain maternal (A, C, D) and paternal (Q, R1a) lineages, and, in some cases, they could also be linked to ancient DNA data from the Migration Period (5th-9th centuries AD) and Hungarian Conquest Period (10th century AD) populations.

Complete mitochondrial genome of a subspecies of the great cormorant, Phalacrocorax carbo hanedae (Kuroda, 1925) (Suliformes: Phalacrocoracidae)

We determined the complete mitochondrial DNA sequence of a subspecies of the great cormorant, Phalacrocorax carbo hanedae (Kuroda, 1925) using long PCR and primer walking methods. The mitochondrial genome was 19,020 bp in length and contained 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and two control regions. It is basically consistent with the characteristics of the mitochondrial genomes of other Suliformes species. Phylogenetic analysis using 12 species of Suliformes based on the sequences of 13 concatenated protein-coding genes confirmed the monophyly of P. carbo ssp.

Complete mitochondrial DNA sequence tries to settle hitherto putative history of Kayastha population of India.

Indian caste system is unique as it has an inimitable type of class system where the social ordering is done based on birth. Within the caste system, there is a distinct endogamous population known as the Kayastha, who have had inconclusive stratification records due to unidentified historical records. To gain a more inclusive view on the history and genetic affinities of Kayastha people, complete mitochondrial genomes from 15 individuals of a Kayastha population from North-western India have been sequenced. Interestingly, three novel sub-clades (U2b2a, M3d2, and M33a3b) have been identified that represent unique Kayastha motifs. The haplotype-based analysis suggests that the Kayastha population shares genetic affinities with the Indo-European and Sino-Tibetan populations found in the trans-Himalayan region. The FST based population comparison and the MDS plot indicates that Kayastha people have close maternal genetic affinity with the available genetic database of Brahmins, Kashmiris, and Tharus. The maternal genetic lineages among Kayastha population shows deep in situ origin that emerged much before settled life developed on this sub-continent. Both mtDNA and Y-chromosome markers, trace the genetic lineages of Kayastha population with Tharus, who regard themselves Kshatriya, corroborated by the oral history of the Kayasthas for their Kshatriya affiliation. It also validates genetic heritage of earliest settlers of India in both indigenous tribal and caste populations.

The complete mitochondrial genome of Sporophila nigricollis (Aves, Passeriformes).

Sporophila nigricollis, popularly known as Yellow-bellied Seedeater, is a commonly trafficked bird in Brazil. This study describes the complete mitogenome of the species and its phylogenetic position. DNA sample was sequenced on MiSeq (Illumina®) sequencer. Reads were assembled to reference using Geneious. A total of 11,740 paired sequence reads were used to produce the complete mitochondrial DNA sequence with average coverage of 176x. The mitogenome was found to be circular in shape and consisted of 16,777 base pairs. The mitochondrial genome was annotated with MITOS and verified with ExPASy. Its structure contains two ribosomal RNA (rRNA) genes, 22 transporter RNA (tRNA) genes, 13 protein-coding genes (PCGs) and one control region. Twelve of the 13 PCGs have ATG as start codon. Seven of the 13 PCGs contain a TAA stop codon. Most of the tRNA genes and PCGs are encoded on the heavy strand. Phylogenetic analyses were conducted with MEGA using the maximum likelihood method. Sporophila nigricollis grouped together with other Thraupidae species. This study presents the first complete mitogenome of Sporophila nigricollis and can be useful for research on evolution, ecology and conservation of this species.

Ancient and modern mitogenomes of red deer reveal its evolutionary history in northern China

Red deer (Cervus elaphus/hanglu/canadensis) are a group of closely-related species that survived through the Last Glacial period in Eurasia and expanded into North America. The evolutionary modes of red deer in Europe through glacial and interglacial cycles have been established relatively well based on both modern and ancient genomes, while the evolutionary and migratory history of red deer in Asia are not so clear. Northern China, as the southern border of their current distribution, is a significant area for exploring the evolution of wapitoids (Cervus canadensis). Here, we constructed six mitochondrial genomes (lengths of 13,282–16,306 bp) from Late Pleistocene fossil cervid materials in Northeastern China, and four modern complete mitochondrial DNA sequences (16,798–16943 bp) from Northern China. Phylogenetic analyses suggest four clades in wapitoids, with our new individuals clustered into three out of the four clades. BEAST analysis indicates that the divergence between elaphoids (including Cervus elaphus and Cervus hanglu) and the complex of ‘wapitoids + sika deer (Cervus nippon)’ occurred at approximately 1.37 million years ago (Ma, 95%Cl: 1.64–1.15 Ma). Bayesian skyline plots (BSPs) show that the effective maternal population size of wapitoids had a slight and stable expansion between Marine isotope stages (MIS) 7–3, and then shrank from the beginning of the Last Glacial Maximum (LGM). Combined with the divergence dates, population dynamics, and fossil findings in Northern China, we infer that after wapitoids migrated eastward from Central Asia to Northeastern Asia, they had multiple migrations southward into Northern China. The current distribution of wapitoids in Northern China was likely shaped by these migrations as well as habitat fragmentation. Meanwhile, the radiocarbon dates of ancient individuals indicate that the Northeast China Plain, located at the same latitude as European refugia, may have provided a refugium for megafaunal species such as red deer to survive the LGM.

The Nursehound Scyliorhinus stellaris Mitochondrial Genome-Phylogeny, Relationships among Scyliorhinidae and Variability in Waters of the Balearic Islands.

The complete mitochondrial DNA sequence of the Nursehound Scyliorhinus stellaris has been determined for the first time and compared with congeneric species. The mitogenome sequence was 16,684 bp in length. The mitogenome is composed of 13 PCGs, 2 rRNAs, 22 transfer RNA genes and non-coding regions. The gene order of the newly sequenced mitogenome is analogous to the organization described in other vertebrate genomes. The typical conservative blocks in the control region were indicated. The phylogenetic analysis revealed a monophyletic origin of the Scyliorhininae subfamily, and within it, two subclades were identified. A significant divergence of Scyliorhinus spp. together with Poroderna patherinum in relation to the group of Cephaloscyllium spp. was observed, except for Scyliorhinus torazame, more related to this last cited clade. A hypothesis of a divergent evolution consequent to a selective pressure in different geographic areas, which lead to a global latitudinal diversity gradient, has been suggested to explain this phylogenetic reconstruction. However, convergent evolution on mitochondrial genes could also involve different species in some areas of the world.

The complete mitochondrial genome and phylogenetic analysis of Euurobracon yokahamae (Hymenoptera: Braconidae)

Euurobracon yokahamae is a parasitoid wasp found solely in Asia, and is endangered in some countries. The complete mitochondrial DNA sequence of E. yokahamae was sequenced using next-generation sequencing (NGS). The mitogenome of this species is 14,974bp long and encodes for 13 protein-coding genes (PCGs), 22 transfer RNAs, and 2 ribosomal RNAs. Maximum likelihood phylogenetic analysis of the mitochondrial genome of braconid species was performed. Tree topology showed that E. yokahamae was closely related to another species of the same genus.

Genetic Characterization and Phylogenetic Analysis of Fasciola Species Isolated From Yaks on Qinghai-Tibet Plateau, China.

The present study determined the complete mitochondrial DNA (mt DNA) sequence of Fasciola intermediate (isolated from yaks) based on gene content and genome organization. According to our findings, the genome of Fasciola intermediate was 13,960 bp in length, containing 2 ribosomal RNA (rRNA) genes, 12 protein-coding genes (PCGs), and 22 transfer RNA (tRNA) genes. The A+T content of genomes was 63.19%, with A (15.17%), C (9.31%), G (27.51%), and T as the nucleotide composition (48.02%). Meanwhile, the results showed negative AT-skew (-0.52) and positive GC-skew (0.494). The AT bias significantly affected both the codon usage pattern and amino acid composition of proteins. There were 2715 codons in all 12 protein-coding genes, excluding termination codons. Leu (16.72%) was the most often used amino acid, followed by Val (12.74%), Phe (10.90%), Ser (10.09%), and Gly (8.39%). A phylogenetic tree was built using Maximum-Likelihood (ML) through MEGA 11.0 software. The entire mt DNA sequence of Fasciola intermediate gave more genetic markers for investigating Trematoda population genetics, systematics, and phylogeography. Hence, for the first time, our study confirmed that yaks on the Qinghai-Tibet plateau have the infestation of Fasciola intermediate parasite.

The complete mitochondrial genome of the true limpet Scurria scurra (Lottiidae)

The complete mitochondrial DNA sequence of the scurrinid limpet Scurria scurra (Lesson 1830) is reported here. This mitogenome is 18,482 bp long and includes two rRNA genes, 13 protein-coding genes, and 24 tRNAs. The genus Scurria is a nascent model group for marine ecological studies. This mitogenome will help to gain a better understanding of the phylogenetic relationships within Patellogastropoda, the most primitive group of extant gastropods.

A new genus name for pygmy lorises, Xanthonycticebus gen. nov. (Mammalia, primates)

Lorisiformes are nocturnal primates from Africa and Asia with four genera, with two (Arctocebus and Loris), three (Perodicticus) and nine (Nycticebus) recognised species. Their cryptic lifestyle and lack of study have resulted in an underappreciation of the variation at the species and genus level. There are marked differences between the pygmy slow loris Nycticebus pygmaeus and the other Nycticebus species and, in the past, several authors have suggested that these may warrant recognition at the generic level. We here combine morphological, behavioural, karyotypical and genetic data to show that these contrasts are, indeed, significantly large and consistent. We propose Xanthonycticebus gen. nov. as a new genus name for the pygmy slow lorises and suggest a common name of pygmy lorises. Based on analysis of complete mitochondrial DNA sequences, we calculate the divergence of pygmy from slow lorises at 9.9–10.0%. The median date, calculated for the divergence between Xanthonycticebus and Nycticebus, is 10.5 Mya (range 4.9–21.0 Mya). Xanthonycticebus differs from Nycticebus by showing sympatry with other slow loris species, by habitually giving birth to twins, by showing seasonal body mass and whole body coat colour changes (absent in other species living at similar latitudes) and a multi-male, multi-female social system. Pygmy lorises are easily recognisable by the absence of hair on their ears and more protruding premaxilla. Xanthonycticebus is threatened by habitat loss and illegal trade despite legal protection across their range and all slow lorises are listed on appendix 1 of CITES. The suggested nomenclatural changes should not affect their legal status.

The mitochondrial genome of Grapsus albolineatus (Decapoda: Brachyura: Grapsidae) and phylogenetic associations in Brachyura

Complete mitochondrial genomes (mitogenomes) can provide useful information for phylogenetic relationships, gene rearrangement, and evolutionary traits. In this study, we determined the complete mitochondrial DNA sequence of the herbivorous crab Grapsus albolineatus. It is a typical metazoan mitochondrial genome. The total size is 15,583 bp, contains the entire set of 37 genes, and has an AT-rich region. Then, 23 of the 37 genes were encoded by the heavy (+) strand while 14 are encoded by the light (−) strand. Compared with the pan-crustacean ground pattern, two tRNA genes (tRNA-His and tRNA-Gln) were rearranged and the tandem duplication/random loss model was used to explain the observed gene rearrangements. The phylogenetic results showed that all Grapsidae crabs clustered together as a group. Furthermore, the monophyly of each family was well supported, with the exception of Menippidae. In general, the results obtained in this study will contribute to the better understanding of gene rearrangements in Grapsidae crab mitogenomes and provide new insights into the phylogeny of Brachyura.

Mitogenome sequence comparison in the endangered congeneric Pinna nobilis and Pinna rudis bivalves.

The pen shells Pinna nobilis and Pinna rudis are large wedge-shaped bivalve molluscs. Both species are threatened by different anthropogenic pressures. In the last few years, P. nobilis populations have significantly reduced due to massive mortality events. The complete mitochondrial DNA sequences of these congeneric species have been determined and compared for the first time. The mitogenome sequences of P. nobilis and P. rudis were 18,919bp and 18,264bp in length, respectively. Each mitogenome is composed of 12 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA (tRNAs) genes and non-coding regions. A putative Adenosine Triphosphate synthase subunit 8 gene could only be proposed for P. nobilis. Both newly sequenced mitogenomes present a conserved gene order between them, comparable to the closely related Atrina pectinata, but global arrangement greatly differs from other available bivalve mitochondrial sequences. Multiple copies of tRNA-Cys were identified, located in different positions probably due to mechanisms of mitochondrial genome rearrangements, and detected 2 and 3 times in P. rudis and in P. nobilis, respectively. A close relationship was shown between Pinna species and Atrina pectinata and a consistent clustering showing a monophyletic origin of Pinnidae family sequences was evidenced. The mitochondrial genomes will provide a valuable genetic resource for further studies on population genetics and species identification.

Evaluation of Maternal Genetic Background of Two Hungarian Autochthonous Sheep Breeds Coming from Different Geographical Directions.

Simple SummaryBy the 19th century, adequately producing, independent domestic animal breeds had developed in many regions around the globe. However, from the middle of the 20th century they have largely been replaced by high-performing, specialized, single-purpose cosmopolitan breeds. Breed maintenance is an activity aimed at rescuing old breeds from the threat of extinction. This process includes recording the valuable traits of a rare breed, specific diversity conservation selection, and utilization in the original production environment. Additionally, it deals with the history of breeds and the study of their genetic makeup. The aim of this paper is to evaluate the maternal genetic background of two autochthonous sheep breeds in Hungary.The aim of our research was the evaluation of the maternal genetic background of two Hungarian autochthonous sheep breeds of different geographical origin. A major argument for the preservation of endangered animal breeds is their documented past and historical importance. These also include the registration of pedigree data. This is the first study to evaluate and compare Tsigai and Cikta sheep in Hungary. Our investigation is based on two complete sequences of mitochondrial DNA (cytochrome b gene and control region). Our research was performed on these two sheep breeds with markedly different breed histories and breed characteristics to determine a possible common maternal genetic background, as ultimately the origin of both breeds can be traced back to Asia Minor. Between 2015 and 2017, a total of 203 biological samples were taken using a newly introduced founder sampling method. We found that the prevailing haplogroup B accounted for over 80% of both breeds, strengthening the common ancestral root. However, the pairwise genetic differentiation estimates (KST) calculated using the sequence-based statistics for cytochrome b gene and control region were 0.034 and 0.021, respectively (both at level p < 0.05); thus, revealing genetic differentiation in both sequences between the Tsigai and Cikta. We note that the known different history of the breeds is clearly justified by the currently studied deviations in their maternal genetic background.