Complete Mitogenome Data Research Articles

Genomics of historical museum collections clarifies species diversity in Cuban hutias (Capromys)

Abstract Specimen-based taxonomic research is essential for understanding diversity and setting management frameworks for threatened mammal faunas, and ancient DNA techniques are increasingly used to extract information from taxonomically relevant historical specimens. The largest survivors of the depleted Caribbean mammal fauna are hutias in the genus Capromys, which is usually interpreted as containing a single species, C. pilorides. Previous studies have demonstrated genetic differentiation of Capromys populations across Cuba, but infrageneric species diversity and nomenclature remain unclear. We conducted ancient DNA analysis of historical Capromys samples using cytochrome b and complete mitogenome data sets, and including the 19th-century holotypes of 2 species now considered synonyms, C. fournieri and C. geayi. Our analyses identify distinct western and central/eastern Capromys clades that diverged 1.75 Mya based upon mitogenome data. These clades are separated by the Havana–Matanzas Channel, which represented a barrier to dispersal throughout the Neogene–Quaternary. Divergence date comparisons with other hutia species provide support for interpreting divergence between Capromys populations as species-level differentiation. Although we were unable to yield amplifiable DNA from the C. fournieri holotype, our analyses confidently assign the C. geayi holotype to the western Capromys clade. We therefore recognize 2 extant Capromys species: C. geayi (western Cuba) and C. pilorides (central/eastern Cuba and Cayman Islands).

Revisiting the genus Pseudocuneopsis (Bivalvia, Unionidae): Morphology, mitochondrial phylogenomics, and the description of a new species

AbstractSpecies diversity can be underestimated due to a lack of regional studies and limitations in research methods. China is widely recognized as one of the primary hotspots for the biodiversity of freshwater mussels as it harbours a wealth of endemic species. Pseudocuneopsis was recently established to belong to the Unioninae subfamily within Unionidae and is endemic to China. Recent research has expanded the diversity and range of distribution of this genus. However, sufficient data is required to precisely determine the phylogenetic relationships within Pseudocuneopsis. This study conducted an integrative taxonomy using morphological, COI barcode, and complete maternal mitogenome data to clarify the taxonomy of Pseudocuneopsis. Both morphological and COI barcode data supported the validity of all Pseudocuneopsis species. Furthermore, a new species, Pseudocuneopsis yemaoi sp. n. was described from a tributary of the Man River in Hubei, China. Mitochondrial phylogenomic analyses showed that P. yemaoi was closely related to P. sichuanensis and resolved phylogenetic relationship as (P. capitata + (P. yangshuoensis + (P. sichuanensis + P. yemaoi))). Our results highlight the significance of utilizing integrative classification methods. Moreover, we propose enhancing the research and preservation measures of minor streams in China, as these streams may house distinctive species.

The complete mitochondrial genome of Erinaceus concolor (Mammalia: Eulipotyphla) from Türkiye with phylogenetic implications

As a reference mitogenome, the complete mitochondrial genome of the white-breasted hedgehog, Erinaceus concolor, was firstly presented in this study by employing Long-Range PCR and Next-Generation Sequencing. The total lengths of the mitogenomes were 17.451 bp and 17.455 bp. A total of 37 genes, namely two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a non-coding D-loop were encoded in the mitogenome, compatible with the previously reported mitogenomes belonging to representatives of the family Erinaceidae (Mammalia: Eulipotyphla). Maximum Likelihood and Bayesian Inference phylogenetic analyses of Eulipotyphla and Erinaceidae based on the complete mitogenomes revealed a conventional relationship for the relevant organism's groups. Divergence time analyses based on complete mitogenome data revealed that evolutionary divergence events within Erinaceidae began about 58.87 Myr ago corresponding to the early Eocene, and the basal split of Erinaceus dates back to approximately 11.01 Myr ago in the late Miocene. Single cytochrome b-based analyses can be considered weaker, as they produce phylogenies that are relatively inconsistent with the natural classification of Eulipotyphla and put the onset of evolutionary divergence events earlier. The genetic information obtained as a result of this study can be used as a genetic resource for conservation biology studies; it will also undoubtedly contribute to the understanding of molecular evolution of E. concolor and closely related taxa.

The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae).

Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1-trnI-trnL2-trnW-trnM-trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.

Characterization of the complete mitochondrial genome of the longhorn beetle, Batocerahorsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles.

Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocerahorsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B.horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B.horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and compared with the existing mitochondrial genomes of Batoceralineolata and B.rubus in GenBank (MF521888, MW629558, OM161963, respectively). The secondary structure of transfer RNA (tRNA) was predicted using tRNAScan-SE server v.1.21 and MITOS WebSever. Thirteen protein-coding genes (PCGs) and two ribosomal RNA gene sequences of 21 longhorn beetles, including B.horsfieldi, plus two outgroups, Dryopsernesti (Dryopidae) and Heterocerusparallelus (Heteroceridae), were analyzed. The phylogenetic tree was constructed using maximum likelihood and Bayesian inference methods. In this study, we successfully obtained the complete mitochondrial genome of B.horsfieldi for the first time, which is 15 425 bp in length. It contains 37 genes and an A + T-rich region, arranged in the same order as the recognized ancestor of longhorn beetles. The genome of B.horsfieldi is composed of 33.12% A bases, 41.64% T bases, 12.08% C bases, and 13.16% G bases. The structure, nucleotide composition, and codon usage of the new mitochondrial genome are not significantly different from other longhorn mitochondrial genomes. Phylogenetic analyses revealed that Cerambycidae formed a highly supported single clade, and Vesperidae was either clustered with Cerambycidae or formed a separate clade. Interestingly, B.horsfieldi, B.rubus and B.lineolata were clustered with Monochamus and Anoplophora species in both analyses, with high node support. Additionally, the VesperidaeSpiniphilusspinicornis and Vesperussanzi and the 19 Cerambycidae species formed a sister clade in the Bayesian analysis. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research, and provide a foundation for future relevant research.

Addressing the complex phylogenetic relationship of the Gempylidae fishes using mitogenome data.

The Gempylidae (snake mackerels) family, belonging to the order Perciformes, consists of about 24 species described in 16 genera primarily distributed in tropical, subtropical, and temperate seas worldwide. Despite substantial research on this family utilizing morphological and molecular approaches, taxonomy categorization in this group has remained puzzling for decades prompting the need for further investigation into the underlying evolutionary history among the gempylids using molecular tools. In this study, we assembled eight complete novel mitochondrial genomes for five Gempylidae species (Neoepinnula minetomai, Neoepinnula orientalis, Rexea antefurcata, Rexea prometheoides, and Thyrsites atun) using Ion Torrent sequencing to supplement publicly available mitogenome data for gempylids. Using Bayesian inference and maximum-likelihood tree search methods, we investigated the evolutionary relationships of 17 Gempylidae species using mitogenome data. In addition, we estimated divergence times for extant gempylids. We identified two major clades that formed approximately 48.05 (35.89-52.04) million years ago: Gempylidae 1 (Thyrsites atun, Promethichthys prometheus, Nealotus tripes, Diplospinus multistriatus, Paradiplospinus antarcticus, Rexea antefurcata, Rexea nakamurai, Rexea prometheoides, Rexea solandri, Thyrsitoides marleyi, Gempylus serpens, and Nesiarchus nasutus) and Gempylidae 2 (Lepidocybium flavobrunneum, Ruvettus pretiosus, Neoepinnula minetomai, Neoepinnula orientalis, and Epinnula magistralis). The present study demonstrated the superior performance of complete mitogenome data compared with individual genes in phylogenetic reconstruction. By including T. atun individuals from different regions, we demonstrated the potential for the application of mitogenomes in species phylogeography.

First Report of Complete Mitochondrial Genome in the Tribes Coomaniellini and Dicercini (Coleoptera: Buprestidae) and Phylogenetic Implications.

The complete mitochondrial genomes (mitogenomes) of the tribes Coomaniellini and Dicercini were sequenced and described in this study, including Coomaniella copipes (16,196 bp), Coomaniella dentata (16,179 bp), and Dicerca corrugata (16,276 bp). These complete mitogenomes are very similar in length and encoded 37 typical mitochondrial genes, including 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and 13 protein-coding genes (PCGs). Most of PCGs had typical ATN start codons and terminated with TAR. Among these mitogenomes, Leu2 (L2), Ile (I), Ser2 (S2), and Phe (F) were the four most frequently encoded amino acids. Moreover, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) among the available sequenced species of the family Buprestidae using Bayesian inference and Maximum-likelihood methods. The results showed that a Chrysochroninae species interspersed in Buprestinae, and Coomaniellini is more closely related to Dicercini than Melanophilini. Moreover, the clade of Buprestidae was well separated from outgroups and the monophyly of Agrilinae is confirmed again. Our whole mitogenome phylogenetic results support that the genus Dicerca can be transferred from Chrysochroinae to Buprestinae; whether Dicercini can be completely transferred remains to be further verified after enriching samples. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research.

Characterization of the complete mitochondrial genome of Haemaphysalis (Alloceraea) kolonini (Ixodidae) and its phylogenetic implications.

Ticks transmit diverse pathogens that cause human and animal diseases, leading to an increasing number of new challenges around the world. Genomic data research could help advance our learning of phylogenetic analysis and molecular evolution. Mitochondrial genome DNA has been helpful in illustrating the phylogenetic analysis of eukaryotes containing ticks. In this research, we sequenced and assembled the circular complete mitogenome information of Haemaphysalis kolonini. The 14,948-bp mitogenome consists of 37 genes which included 13 genes for protein-coding, two genes for ribosomal RNA, 22 genes for transfer RNA, and two control regions (D-loops). Overall, the composition and arrangement of genes were compared with Haemaphysalis ticks previously recorded in Genbank. The phylogenetic tree based on Maximum likelihood (ML) and Bayesian inference (BI) computational algorithms showed that H. kolonini has a close relationship with Haemaphysalis inermis. The complete mitogenome data provide a preferable perception to the phylogenetic relationship than the single-gene data analysis. To our knowledge, this is the first research exploring the complete mitogenome for the species H. kolonini. Our results provide new insights for further research on the evolution, population genetics, systematics, and molecular ecology of ticks.

Diversification of tiny toads (Bufonidae:Amazophrynella) sheds light on ancient landscape dynamism in Amazonia

AbstractMajor historical landscape changes have left significant signatures on species diversification. However, how these changes have affected the build-up and maintenance of Amazonia’s megadiversity continues to be debated. Here, we addressed this issue by focusing on the evolutionary history of a pan-Amazonian toad genus that has diversified throughout the Neogene (Amazophrynella). Based on a comprehensive spatial and taxonomic sampling (286 samples, all nominal species), we delimited operational taxonomic units (OTUs) from mitochondrial DNA sequences. We delimited 35 OTUs, among which 13 correspond to nominal species, suggesting a vast underestimation of species richness. Next, we inferred time-calibrated phylogenetic relationships among OTUs based on complete mitogenomic data, which confirmed an ancient divergence between two major clades distributed in eastern and western Amazonia, respectively. Ancestral area reconstruction analyses suggest that the Andean foothills and the Brazilian Shield region represent the ancient core areas for their diversification. These two clades, probably isolated from one other by lacustrine ecosystems in western Amazonia during the Miocene, display a pattern of northward and eastward dispersals throughout the Miocene‒Pliocene. Given the ecological association of Amazophrynella with non-flooded forests, our results reinforce the perception that ancient Amazonian landscape changes had a major impact on the diversification of terrestrial vertebrates.

The complete mitochondrial genome of Hemitripterus villosus (Pallas, 1814) from Zhoushan archipelago

In this study, we used whole genome sequencing to obtain the complete mitochondrial genome of Hemitripterus villosus. This mitochondrial genome, consisting of 17,449 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 1799 bp in length, is located between tRNAPro and tRNAPhe. We identified short tandem repeat sequences in the control region, which contributed largely to the relatively long mitogenome. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, phylogenetic analysis and conservation genetics.

The complete mitochondrial genome of Platycephalus sp.1 (Teleostei, Platycephalidae) obtained by whole genome sequencing

In this study, we used next-generation sequencing to obtain the complete mitochondrial genome of Platycephalus sp.1. This mitochondrial genome, consisting of 16,552 base pairs (bp), contains 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and two non-coding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 877 bp in length, is located between tRNAPro and tRNAPhe. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. The overall base composition shows 25.83% of T, 29.98% of C, 27.01% of A, and 17.18% of G, with a slight A + T rich feature (52.84%). The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

Complete Mitochondrial Genomes Reveal Population-Level Patterns in the Widespread Red Alga Gelidiella fanii (Gelidiales, Rhodophyta)

Although complete mitogenomic data have been widely applied in human and other animal population studies, they are extremely limited for florideophycean red algal populations. Gelidiella fanii is a recently described rhodophyte, previously misidentified as G. acerosa, a cosmopolitan agar-yielding species from tropical to subtropical waters. To decipher patterns in genetic diversity and geographic distribution for G. fanii, we obtained 10 complete mitogenomes including two outgroups, G. acerosa and G. flabella. The mitogenomes ranged in size from 25,223 bp to 25,281 bp and had 48 genes, which are similar in general structure, gene order and content, and presence of a group II intron. Phylogenomic analysis revealed that G. fanii was monophyletic and clearly separate from G. acerosa. The range of G. fanii was extended from Southeast Asia and northern Australia to Eritrea, Juan de Nova Island, and Kenya in the west, and to Hawai‘i and Tetiaroa Atoll to the east. Haplotype network analysis of cox1 revealed seven geographically structured groups: Southeast Asia, Kenya/Juan de Nova Island, Indonesia, northern Australia, the Philippines, Tetiaroa Atoll, and Hawai‘i. This regional structure has likely resulted from the separation and isolation of an ancient widespread population during the Pleistocene. This study demonstrates that mitogenome sequencing is a powerful genotyping tool for studies of genetic diversity, biogeography, and conservation of economically valuable marine algal species.

Complete mitochondrial DNA genome of banded cichlid Heros severus Heckel, 1840 (Perciformes: Cichlidae)

In this study, we sequenced the complete mitochondrial genome of Heros severus Heckel, 1840 (Perciformes, Cichlidae). This mitochondrial genome, consisting of 16,577 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 917 bp in length, is located between tRNAPro and tRNAPhe. Within the control region, typical conserved domains, such as the termination-associated sequence (TAS), central, and conserved sequence blocks domains were identified. The overall base composition of the heavy strand shows 27.6% of T, 26.3% of C, 29.3% of A, and 16.8% of G, with a slight A + T rich feature (56.9%). The complete mitogenome data provide useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis, and conservation genetics.

The complete mitochondrial genome of Jaydia lineata (Perciformes, Apogonidae) obtained by next-generation sequencing

In this study, we used next-generation sequencing to obtain the complete mitochondrial genome of Jaydia lineata. This mitochondrial genome, consisting of 16,510 base pairs (bp), contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and 2 noncoding control regions (control region and origin of light-strand replication) as those found in other vertebrates. Control region, of 848 bp in length, is located between tRNAPro and tRNAPhe. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified. The overall base composition shows 26.71% of T, 28.46% of C, 27.24% of A and 17.58% of G, with a slight A + T rich feature (53.95%). The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases.

Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.

The complete mitochondrial genome of Punchinello butterfly, Zemeros flegyas (Lepidoptera: Riodinidae) and its phylogenetic implications

The complete mitochondrial genome (mitogenome) of Zemeros flegyas (Lepidoptera: Riodinidae) is 15,219 bp in length, harboring typical 37 mitochondrial genes (13 PCGs, 22 tRNAs, and 2 rRNAs) and an AT-rich region. The Z. flegyas mitogenome includes a cox1 gene with an atypical CGA(R) start codon and three genes (cox1, nad5, nad4) exhibiting incomplete stop codons. The putative AT-rich region is 385 bp long with several structures characteristic of lepidopteran. Phylogenetic analysis showed that Z. flegyas is closely related to other riodinids. The complete mitogenome data provided here would be useful for further understanding the higher systematics of Riodinidae.

Characterization of the complete mitochondrial genome sequence of Nibea diacanthus and its phylogenetic implication

The blackspotted croaker (Nibea diacanthus) is an important food fish of Indo-West Pacific and China. To study the phylogenetic status, we sequenced the complete mitochondrial genome of N. diacanthus. The mitogenome is 16,532 bp in length and composed of 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. The gene composition and the structural arrangement of N. diacanthus complete mtDNA were identical to most of other vertebrates. The phylogenetic analysis using the complete mitochondrial genome revealed that the N. diacanthus might be separated from Nibea genera of Argyrosominae, which was inconsistent with that based on morphology. The complete mitogenome data would be useful for the evolution and conservation genetic studies of Sciaenidae.

Insights into matrilineal genetic structure, differentiation and ancestry of Armenians based on complete mitogenome data.

Distinctive peculiarities of Armenians such as their millennia-long genetic isolation and strong national identity attract a keen interest while studying the demographic history of the West Asia. Here, to examine their fine-scale matrilineal genetic structure, ancestry and relationships with neighboring populations, we analyzed 536 complete mitogenomes (141 of which are novel) from 8 geographically different Armenian populations, covering the whole stretch of historical Armenia. The observed patterns highlight a remarkable degree of matrilineal genetic heterogeneity and weak population structuring of Armenians. Moreover, our phylogeographic analysis reveals common ancestries for some mtDNA lineages shared by West Asians, Transcaucasians, Europeans, Central Asians and Armenians. About third of the mtDNA subhaplogroups found in Armenian gene pool might be considered as Armenian-specific, as these are virtually absent elsewhere in Europe, West Asia and Transcaucasia. Coalescence ages of most of these lineages do not exceed 3.1kya and coincide well with the population size growth started around 1.8-2.8kya detectable only in the Bayesian Skyline Plots based on the Armenian-specific mtDNA haplotypes.

The complete mitochondrial genome of yellow-bibbed lory, Lorius chlorocercus (Psittaciformes Psittacidae), with its phylogenetic relationship

In this study, the complete 17,855 bp mitochondrial genome of Lorius chlorocercus was obtained using sanger sequencing. It consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The overall base composition is 22.5% T, 33.18% C, 30.42% A, and13.9% G. The phylogenetic tree was constructed using neighbour-joining (NJ) method based on 19 parrot species. Phylogenetic analysis showed that L. chlorocercus was closest to Melopsittacus undulates. The complete mitogenome data would be useful for further study on the molecular evolution of L. chlorocercus.

Characterization of the complete mitochondrial genome of Eysarcoris aeneus (Heteroptera: Pentatomidae), with its phylogenetic analysis

In this study, the complete 16,065 bp mitochondrial genome of Eysarcoris aeneus was determined from China using next-generation sequencing technology. It consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. Among them, 23 genes were located on J-strand, and the other genes (nad5, nad4, nad4L, nad1, trnQ, trnC, trnY, trnF, trnH, trnP, trnL1, trnV, 12S rRNA, and 16S rRNA) were located on the N-strand. The phylogenetic tree was constructed using MrBayes method based on the 13 protein-coding genes (PCGs) showed the present species clustered within the Pentatomidae. The complete mitogenome data would be useful for further study of Pentatomoidea and Pentatomomorpha.