Vertebrate Mitogenomes Research Articles

Insights into phylogenetic relationships and gene rearrangements: complete mitogenomes of two sympatric species in the genus Rana (Anura, Ranidae).

Mitochondrial genomes (also known as mitogenomes) serve as valuable molecular markers and have found widespread applications in molecular biology and ecology. There is abundant sequence variation in vertebrate mitogenomes, and occasionally, they exhibit gene rearrangements. In this study, two Chinese endemic Rana species, Ranajiemuxiensis and Ranahanluica, were sequenced and analyzed to obtain their complete mitogenomes. The two species were sympatrically distributed in the Zhangjiajie National Forest Park, in Wulingyuan District, Zhangjiajie City, Hunan Province, China. The mitogenome of R.jiemuxiensis was 17,506 bp, while that of R.hanluica was 17,505 bp, each comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding control region (D-loop). The gene content, nucleotide composition, and evolutionary rates of each mitogenome were analyzed and compared with those of congeners. A phylogenetic analysis based on 22 mitogenomes in Rana revealed that the two sympatric species were in two different lineages, indicating that they were genetically separated to a certain extent. Three types of gene rearrangement patterns were identified when examining the gene orders of the 22 Rana mitogenomes. Most of the species shared a second and dominant gene rearrangement pattern that originated from the first ancient pattern. A "tandem duplication - multiple deletion" hypothesis was proposed to explain the evolution of these different gene rearrangement patterns. This study provided valuable data references and enhanced our understanding of the phylogenetic implications and gene rearrangements of Rana species.

Comparative analyses of the complete mitochondrial genomes of two southern African endemic guitarfish, Acroteriobatus annulatus and A. blochii

Shark-like rays (order Rhinopristiformes) are among the most threatened cartilaginous fish globally. Despite this, unresolved taxonomic issues still exist within the group. To date, no studies have used complete mitochondrial genomes to assess the phylogenetic placement of Acroteriobatus within the non-monophyletic family Rhinobatidae. The current study reports the first complete mitochondrial genomes for Acroteriobatus annulatus and A. blochii. Similar to other rhinopristiforms, the complete sequences of A. annulatus (16,773 bp) and A. blochii (16,771 bp) were circular molecules with gene organisations identical to that of the typical vertebrate mitogenome. The A + T content was higher than the G + C content, with a bias towards A and C nucleotides observed in all complete mitogenomes. The stem-and-loop secondary structures of the putative origin of light-strand replication were found to have highly conserved synthesis and stem regions, with all substitutions and indels restricted to the loop structure. The ratios of non-synonymous to synonymous substitution rates indicated that purifying selection has been the dominant driver of evolution in rhinopristiform mitogenomes. Phylogenetic reconstructions placed Acroteriobatus as a sister-group to Rhinobatos, confirming its affiliation with the family Rhinobatidae. However, based on its apparent polyphyly with the aforementioned genera, the familial assignment of Pseudobatos is not fully resolved and requires further investigation.

Complete Mitochondrial Genome, Genetic Diversity and Phylogenetic Analysis of Pingpu Yellow Chicken (Gallus gallus).

In this study, the complete mitochondrial genome sequence of one female Pingpu Yellow chicken (PYC) and the D-loop sequences obtained from 60 chickens were analyzed to investigate their genetic diversity and phylogeny. The total length of the PYC mitogenome is 16,785 bp and that of the complete D-loop is 1231 to 1232 bp. The mitogenome comprises 22 transfer ribonucleic acids (tRNAs), 2 ribosomal ribonucleic acids (rRNAs), 13 protein-coding genes (PCGs), and 1 non-coding control region (D-loop). Additionally, the total length of the 13 PCGs is 11,394 bp, accounting for 67.88% of the complete mitogenome sequence, and the PCGs region has 3798 codons. A majority of the PCGs have ATG as the start codon. The haplotype and nucleotide diversity of PYC were 1.00000 ± 0.00029 and 0.32678 ± 0.29756, respectively. In the D-Loop data set, we found 25 polymorphic sites, which determined 18 haplotypes and 3 major haplogroups (A-C). Therefore, PYC has a classical vertebrate mitogenome, with comparatively high nucleotide diversity and potentially three maternal lineages. The neighbor-joining (NJ) tree analysis results showed PYC grouped with the Luhua (MT555049.1) and Nandan chickens (KP269069.1), which indicates that PYC is closely related to these two breeds.

Characterisation of the Complete Mitochondrial Genome of Critically Endangered Mustela lutreola (Carnivora: Mustelidae) and Its Phylogenetic and Conservation Implications

In this paper, a complete mitochondrial genome of the critically endangered European mink Mustela lutreola L., 1761 is reported. The mitogenome was 16,504 bp in length and encoded the typical 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes, and harboured a putative control region. The A+T content of the entire genome was 60.06% (A > T > C > G), and the AT-skew and GC-skew were 0.093 and −0.308, respectively. The encoding-strand identity of genes and their order were consistent with a collinear gene order characteristic for vertebrate mitogenomes. The start codons of all protein-coding genes were the typical ATN. In eight cases, they were ended by complete stop codons, while five had incomplete termination codons (TA or T). All tRNAs had a typical cloverleaf secondary structure, except tRNASer(AGC) and tRNALys, which lacked the DHU stem and had reduced DHU loop, respectively. Both rRNAs were capable of folding into complex secondary structures, containing unmatched base pairs. Eighty-one single nucleotide variants (substitutions and indels) were identified. Comparative interspecies analyses confirmed the close phylogenetic relationship of the European mink to the so-called ferret group, clustering the European polecat, the steppe polecat and the black-footed ferret. The obtained results are expected to provide useful molecular data, informing and supporting effective conservation measures to save M. lutreola.

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

BackgroundModern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.ResultsAs part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.ConclusionsOur results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

The complete mitochondrial genome of the vulnerable Australian crest-tailed mulgara (Dasycercus cristicauda)

In this announcement, we report the complete mitogenome of the vulnerable Crest-tailed Mulgara (Dasycercus cristicauda) (Krefft, 1867). The mitogenome was 17,085 bp in length and contained 13 protein-coding genes, two rRNA genes, 22 tRNAs and a 1583 bp variable control region (D-loop). The features of the D. cristicauda mitogenome are consistent with other vertebrate mitogenomes but, in contrast to other marsupials, appears to contain a functional tRNA-Lysine with a UUU anticodon. Phylogenetic analysis of available entire mitogenomes reveals it forms a cluster with other marsupials in the Dasyuromorphia order within the Australidelphian clade, being most closely related to the Northern Quoll and the Tasmanian Devil.

Mitochondrial genome of Diploderma micangshanense and its implications for phylogeny of the genus Diploderma

The lizard Diploderma micangshanense, which belongs to the family Agamidae is endemic to China. Here, we determined the complete mitogenome of D. micangshanense using an Illumina Hiseq X Ten sequencer. This mitogenome’s structure is a typical circular molecule of 16,467 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The overall base composition of D. micangshanensis is 34.1% A, 23.64% T, 13.62% C, and 28.64% G with a slight AT bias of 57.74%. Most mitochondrial genes except ND6 and seven tRNAs were encoded on the heavy strand. Notably, the trnP gene was encoded on the heavy strand instead of its typical light strand position, providing an example of gene inversion in vertebrate mitogenomes. Phylogenetic analysis indicated that D. micangshanensis had a close relationship with D. zhaoermii.

Channa argus BMH from Baima Hu Lake: sequencing and phylogenetic analysis of the mitochondrial genome

Northern snakehead, Channa argus, is a commercially important food fish species in China. In the present study, the complete mitochondrial genome of C.argus from the Baima Hu Lake was characterized. It is 16,558 bp in length, consist of 22 tRNA genes, 13 PCD genes, 2 rRNA genes, and 1 D-loop region. The overall base composition of the C. argus mitogenome is 27.26% A, 24.21% T, 31.58% C and 16.95% G, exhibits a similar AT bias (51.47%) feature to other vertebrate mitogenomes. The phylogenetic analysis showed that C. argus clustered in genus Channa. The present resultes provide useful information to population genetics and conservation biology studies of Channa fishes.

Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics.

Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.

Mitogenome analysis of dwarf pufferfish (Carinotetraodon travancoricus) endemic to southwest India and its implications in the phylogeny of Tetraodontidae

The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish, Carinotetraodon travancoricus (dwarf pufferfish or Malabar pufferfish) endemic to southwest India. The genome is 16487 bp in length and consist of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region like all the other vertebrate mitogenomes. The protein-coding genes ranged from 165 bp (ATP synthase subunit 8) to 1812 bp (NADH dehydrogenase subunit 5) and comprised of 11310 bp in total, constituting 68.5% of the complete mitogenome. Some overlaps have been observed in protein-coding genes by a total of 7 bp. The AT skew (0.032166) and GC skew (-0.29746) of the mitogenome indicated that heavy strand consists equal amount of A and T, but the overall base composition was mainly C skewed. The noncoding D-loop region comprised 869 bp. The conserved motifs ATGTA and its complement TACAT associated with thermostable hairpin structure formation were identified in the control region. The phylogenetic analysis depicted a sister group relationship of C. travancoricus with euryhaline species Dichotomyctere nigroviridis and D. ocellatus with 100% bootstrap value rather than with the other freshwater members of Carinotetraodon species from Southeast Asia. The data from this study will be useful for proper identification, genetic differentiation, management and conservation of the dwarf Indian pufferfish.

Two novel cricetine mitogenomes: Insight into the mitogenomic characteristics and phylogeny in Cricetinae (Rodentia: Cricetidae)

Both Cricetus cricetus and Phodopus sungorus mitochondrial genomes (mitogenomes) were sequenced and elaborated for the first time in the present study. Their mitogenomes contained 37 genes and showed typical characteristics of the vertebrate mitogenome. Comparative analysis of 10 cricetine mitogenomes indicated that they shared similar characteristics with those of other cricetines in terms of genes arrangement, nucleotide composition, codon usage, tRNA structure, nucleotide skew and the origin of replication of light strand. Phylogenetic relationship of the subfamily Cricetinae was reconstructed using mitogenomes data with the methods of Bayesian Inference and Maximum Likelihood. Phylogenetic analysis indicated that Cricetulus kamensis was at basal position and phylogenetically distant from all other Cricetulus species but had a close relationship with the group of Phodopus, and supported that the genus Urocricetus deserved as a separate genus rank. The phylogenetic status of Tscherskia triton represented a separate clade corresponding to a diversified cricetine lineage (Cricetulus, Allocricetulus, and Cricetus).

Complete mitochondrial genome and the phylogenetic position of the stellate puffer (Arothron stellatus)

The complete mitochondrial genome of the stellate puffer (Arothron stellatus) was first determined in this study. It was a 16,475 bp circular molecule and consisted of 37 genes with typical gene order in vertebrate mitogenome. Its nucleotide content was 29.0% A, 32.0% C, 15.9% G and 23.1% T. This mitogenome had 30 bp short intergenic spaces located in 12 gene junctions and 28 bp overlaps located in 7 gene junctions. In the protein-coding genes, two start codons (GTG and ATG) and two stop codons (TAG and TAA/TA/T) were found. The 22 tRNA genes ranged from 64 bp (tRNA-Cys) to 74 bp (tRNA-Leu1 and tRNA-Lys). The phylogenetic result showed that Takifugu xanthopterus was most closely related to the reef-related A. stellatus among all Tetraodontiformes species.

Complete mitochondrial genome of the East Asian fish-eating bat: Myotis ricketti (Chiroptera, Vespertilionidae)

I report the complete mitochondrial genome (mitogenome) of the East Asian fish-eating bat (Myotis ricketti or M. pilosus), also known as the Rickett’s big footed bat. The total length of the circular M. ricketti mitogenome is 17,098 base pairs, containing 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region (D-loop region). The gene order and organisation of this mitogenome are similar to most of other determined vertebrate mitogenomes, with the nucleotide base composition of A 34.22%, T 30.32%, C 22.80%, and G 12.66%. Besides, the mitogenomic D-loop region contains 29 copies of a tandem repeat sequence of six nucleotides (CATACG). The phylogenetic analysis indicates that M. ricketti is closely related to M. macrodactylus and M. petax. This study will contribute to the investigations of phylogeny and evolution for Myotis and its relevant taxa.

Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes

Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.

Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species

Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae lizards into six subfamilies and showed (((((Agaminae, Draconinae), Amphibolurinae), Hydrosaurinae), Uromastycinae), Leiolepinae), which was different from the previous studies. J. flaviceps had a closer relationship to Pseudocalotes species than Acanthosaura species, and they formed a well-supported lineage of Draconinae subfamily. There were nine mitochondrial gene rearrangement types among the 27 Agamidae species, and six of them were found in the Agaminae group. The trnP gene of J. flaviceps mitogenome was encoded on the heavy strand instead of its typical light strand position, providing an example of gene inversion in vertebrate mitogenomes. J. flaviceps shared the same gene arrangement type (inverted trnP gene) with other Draconinae species, strongly implying a single occurrence of the trnP inversion in the ancestral draconine lineage. Our study helps to understand mitogenome evolution and phylogenetic relationship of Agamidae species.

Complete mitochondrial genome of the nesting Colombian Caribbean loggerhead turtle: first approach of tRNAs and phylogenetic analysis

The loggerhead marine turtle, Caretta caretta, is a widely distributed and endangered species that is facing critical population decline, especially in Colombian Caribbean rookeries. Mitochondrial DNA sequence data are of great importance for the description, monitoring, and phylogenetic analyses of migratory turtle populations. In this study, the first full mitochondrial genome of a loggerhead turtle nesting in the Colombian Caribbean was sequenced and analyzed. This mitochondrial genome consists of 16 362 bp with a nucleotide composition of T: 25.7 %, C: 27 %, A: 35 % and G: 12 %. Sequence annotation of the assembled molecule revealed an organization and number of coding and functional units as reported for other vertebrate mitogenomes. This Colombian loggerhead turtle (Cc-AO-C) showed a novel D-Loop haplotype consisting of thirteen new variable sites, sharing 99.2 % sequence identity with the previously reported Caribbean loggerhead CC-A1 D-Loophaplotype. All 13 protein-coding genes in the Cc-AO-C mitogenome were compared and aligned with those from four other loggerhead turtles from different locations (Florida, Greece, Peru, and Hawaii). Eleven of these genes presented moderate genetic diversity levels, and genes COII and ND5 showed the highest diversity, with average numbers of pair-wise differences of 16.6 and 25, respectively. In addition, the first approach related to t-RNAs 2D and 3D structure analysis in this mitogenome was conducted, leading to observed unique features in two tRNAs (tRNATrp and tRNALeu). The marine turtle phylogeny was revisited with the newly generated data. The entire mitogenome provided phylogenetically informative data, as well as individual genes ND5, ND4, and 16S. In conclusion, this study highlights the importance of complete mitogenome data in revealing gene flow processes in natural loggerhead turtle populations, as well as in understanding the evolutionary history of marine turtles.

The complete mitochondrial genome of the toad species Oreolalax xiangchengensis (Anura: Megophryidae) and phylogenetic analyses

Oreolalax xiangchengensis is an alpine toad species of Megophryidae. We determined its complete mitogenome. The mitogenome has a length of 17,110 bp, containing 13 protein-coding genes, 2 rRNA genes, 23 tRNA genes, and a control region. It has a tandem duplication of tRNA-Met gene and a translocation of tRNA-Trp gene compared with typical vertebrate mitogenomes. Phylogenetic analyses based on the mitogenome sequences of 18 Megophryidae species were conducted to access phylogenetic assignments of O. xiangchengensis.

The complete mitochondrial genome of red-fronted parrot (Poicephalus gulielmi) revealed a new gene rearrangement within the order Psittaciformes

Vertebrate mitogenomes are thought to be selected for compactness. Therefore, the increasing number of avian mitogenomes comprising duplicated regions is surprising. Such regions were proposed for at least 26 parrot genera based on the length of PCR products. However, complete mitogenomes with the duplications were shown only for six genera. These duplications evolved probably from the ancestral tRNATHR/tRNAPRO/ND6/tRNAGLU/CR and were subjected to subsequent degeneration. Here, we report the mitogenome of Poicephalus gulielmi (the subfamily Psittacinae) with a unique duplication tRNATHR/pseudoND6/CR1/tRNAPRO/ND6/tRNAGLU/CR2. This region is different from all other identified regions and resembles mostly the arrangements in Amazona and Pionus from the subfamily Arinae.

Revealing the complete mitogenome sequence of Hypsugo alaschanicus based on next generation sequencing

Hypsugo alaschanicus belong to Chiroptera, which is the only type of mammals with the real ability to fly. The complete mitochondrial genome of H. alaschanicus based on next generation sequencing data thus determined had 37 genes for 13 proteins, 22 tRNAs, and 2 rRNAs together with a major non-coding region in a typical gene arrangement of vertebrate mitogenomes. Phylogenetic analysis shows that Pipistrellini is multiline origin, Pipistrellus-like bats can be divided into three groups: Pipistrellini-Nyctalini, Vespertilionini-Eptesicini, and Asian Pipistrelles. Hypsugo alone become a clade, Vespertilio and Eptesicus phylogenetic relationship are closer, Pipistrellus and Nyctalus have a close phylogenetic relationship.

Complete mitochondrial genome of the smallmouth hardyhead (Atherinosoma microstoma) and its phylogenetic position among the Atheriniform fishes

In this paper, I report the full mitochondrial genome sequence of the smallmouth hardyhead (Atherinosoma microstoma), an endemic marine fish from the shallow coastal waters of southeastern Australia. The mitogenome is 16,573 bp-long with the standard 37 genes all included, with a genomic structure typical of a vertebrate mitogenome. In order to confirm the phylogenetic position of this species, phylogenetic trees were inferred using a data set including publicly available 28 atherinomorph, nine percomorph, and two outgroup mitogenome sequences. The complete mitogenome data of A. microstoma reported here will be useful for further genetics, phylogeography, and phylogenetics studies involving this species.