Complete Mitogenome Data Research Articles

Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato

The larval stages of tapeworms in the species complex Echinococcus granulosus sensu lato cause a zoonotic disease known as cystic echinococcosis (CE). Within this species complex, genotypes G6 and G7 are among the most common genotypes associated with human CE cases worldwide. However, our understanding of ecology, biology and epidemiology of G6 and G7 is still limited. An essential first step towards this goal is correct genotype identification, but distinguishing genotypes G6 and G7 has been challenging. A recent analysis based on complete mitogenome data revealed that the conventional sequencing of the cox1 (366 bp) gene fragment mistakenly classified a subset of G7 samples as G6. On the other hand, sequencing complete mitogenomes is not practical if only genotype or haplogroup identification is needed. Therefore, a simpler and less costly method is required to distinguish genotypes G6 and G7. We compared 93 complete mitogenomes of G6 and G7 from a wide geographical range and demonstrate that a combination of nad2 (714 bp) and nad5 (680 bp) gene fragments would be the best option to distinguish G6 and G7. Moreover, this method allows assignment of G7 samples into haplogroups G7a and G7b. However, due to very high genetic variability of G6 and G7, we suggest to construct a phylogenetic network based on the nad2 and nad5 sequences in order to be absolutely sure in genotype assignment. For this we provide a reference dataset of 93 concatenated nad2 and nad5 sequences (1394 bp in total) containing representatives of G6 and G7 (and haplogroups G7a and G7b), which can be used for the reconstruction of phylogenetic networks.

Complete mitochondrial genome and phylogenetic analysis of Uca Borealis

In this study, the complete 15,662 bp mitochondrial genome was determined from Uca borealis using next-generation sequencing technology. It consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. Among the 37 genes, 23 genes (9 PCGs and 14 tRNA genes) are encoded on the heavy (+) strand while the remaining 14 genes (four PCGs, eight tRNA genes and two rRNA genes) are located on the light (−) strand. The AT-skew (0.01) for the whole mitogenome is slightly positive while GC-skew (−0.25) is negative, indicating a higher occurrence of As than Ts and Cs than Gs. The phylogenetic tree was constructed using MrBayes method based on the PCGs showed the present species clustered within the Brachyura. The complete mitogenome data would be useful for further study of U. borealis.

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 Pidorus atratus (Lepidoptera: Zygaenoidea: Zygaenidae)

The complete mitochondrial genome (mitogenome) of Pidorus atratus (Lepidoptera: Zygaenoidea: Zygaenidae) is described in this study. The circular molecule is 15,383 bp in length and contains 37 typical mitochondrial genes and one non-coding AT-rich region. All protein-coding genes (PCGs) start with ATN, except for cox1 gene with CGA; 10 of the 13 PCGs harbour the typical stop codon TAA, whereas cox1, cox2, and nad4 end with a single T. Two ribosomal RNA genes (rRNAs) are 1366 bp and 544 bp in length, respectively. The AT-rich region is 658 bp in size and harbours several features characteristic of the lepidopterans, including the motif ATAGA followed by a 20 bp poly-T stretch and a microsatellite-like (TA)9 element. The complete mitogenome data would be useful for further understanding the taxonomy and phylogeny of Zygaenoidea.

The complete mitochondrial genome of Cyclocheilichthys enoplos (Teleostei, Cyprinidae)

Here, we reported the complete mitochondrial genome of Cyclocheilichthys enoplos, which is widely distributed in Southeast Asia. The genome was 16,579 bp in length, containing 2 ribosomal RNA genes, 22 tRNA genes, a non-coding control region (D-loop), and 13 protein-coding genes. The overall base composition of C. enoplos was 33.1% for A, 24.5% for T, 14.9% for G, and 27.5% for C. Phylogenetic analysis showed that all Cyclocheilichthys species clustered together formed a monophyletic group. The complete mitogenome data of C. enoplos would provide a basis for further systematic studies of the genus Cyclocheilichthys.

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.

Complete mitochondrial genome and the phylogenetic position of the Lake Eyre hardyhead (Craterocephalus eyresii), a freshwater atherinid fish endemic to Lake Eyre Basin, South Australia

The Lake Eyre hardyhead (Craterocephalus eyresii) is an endemic freshwater fish living in the Lake Eyre basin in South Australia. Here, I report the full mitogenome description and the phylogenetic position of this species based on the mitogenome phylogenetics. The mitogenome is 16,602 bp-long with the standard 37 genes all included, with a genomic structure typical of a vertebrate mitogenome. A maximum likelihood phylogenetic analysis to confirm this species position was conducted, using a data set including publicly available 28 atherinomorphs, nine percomorphs, and two outgroups. The result confirms C. eyresii position's in Atherinoidei. The complete mitogenome data of C. eyresii reported here would be useful for further genetics, phylogeography, and phylogenetics studies involving this species.

Complete mitochondrial genome and phylogenetic analysis of Ixodes persulcatus (taiga tick)

Ixodes persulcatus is a species of hard tick which is a predominant tick species that spreads a wide array of serious human and animal pathogens. Here, we first assemble the complete mitogenome of I. persulcatus of China. The total length of the mitogenome was 14,539 bp included 36 genes and with a mitogenome structure similar to other ticks. Phylogenetic tree was constructed based on the complete mitogenome of I. persulcatus and closely related 19 species ticks to assess their phylogenic relationship and evolution. We also analyze the differences between the mitogenomes of I. persulcatus of Japan and China. The complete mitogenome data would be useful for further study of I. persulcatus.

Complete mitochondrial genome of stripped eel catfish (Plotosus lineatus)

The complete mitochondrial genome of stripped eel catfish, Plotosus lineatus, is sequenced in this study. The mitochondrial genome sequence is 16 480 bp in length, with the base composition of 24.7% A, 31.8% T, 27.8% G and 15.7% C. The G + C content is 43.5%. The mitochondria includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one D-loop region. Except for NAD6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. Plotosus lineatus was confirmed to be closely related to P. japonicus (GenBank: KR270437.1), based on our phylogenetic analysis on complete mitochondrial genome sequences of 13 species. Our complete mitogenome data are going to provide the basis for taxonomic and phylogenetic research of catfishes.

The complete mitochondrial genome sequence of the giant mudskipper, Periophthalmodon schlosseri (Perciformes: gobiidae)

The complete mitochondrial genome sequence of the giant mudskipper, Periophthalmodon schlosseri, was first reported in this study. The circle genome is 16 470 bp in length, with the base composition of 28.4% T, 15.4% G, 29.2% A and 27.0% C. The mitogenome includes 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one D-loop region. Only the NADH dehydrogenase subunit 6 (NAD6) and eight tRNA genes are encoded on the light strand. The mitochondrial gene arrangement of P. schlosseri is similar to those of most other gobies. The phylogenetic analysis using the neighbor-joining method showed that the kinship between Periophthalmodon and Periophthalmus is closer than those between Periophthalmodon and other selected genera. Our complete mitogenome data are going to provide the basis for taxonomic and phylogenetic research of amphibious mudskippers.

The complete mitochondrial genome sequence of Triplophysa stenura (Teleostei, Cypriniformes): genome characterization and phylogenetic analysis

The nemacheilid genus Triplophysa is widely distributed in the Qinghai-Tibet Plateau and its adjacent areas. The complete mitochondrial genome of the loach Triplophysa stenura collected from the Peigucuo Lake was sequenced. The genome was 16,569 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding control region (D-loop). Most of the genes were encoded on the heavy strand, except for ND6 and eight tRNA genes. The overall base composition of T. stenura was 27.8% for A, 28.4% for T, 25.4% for C, 18.4% for G, with a slight A + T rich feature (56.2%). Phylogenetic analyses showed that all Triplophysa species clustered together and T. stenura formed a sister relationship with T. tibetana. The complete mitogenome data of T. stenura would provide essential information in understanding phylogenetic relationships among Triplophysa species.

Complete mitochondrial genome of Rhynchocinetes durbanensis (Rhynchocinetidae: Rhynchocinetes)

The complete mitochondrial genome of Rhynchocinetes durbanensis (Rhynchocinetidae: Rhynchocinetes) was sequenced in this study. The genome sequence was 17,695 bp in size, with the base composition of 35.14% A, 32.98% T, 20.34% G and 11.55% C of the light strand. The gene order and genes were the same as that found in other previously reported shrimps, including 13 protein-coding genes, 24 transfer RNA genes and two ribosomal RNA genes. Except for ND5, ND4, ND4L, ND1 genes and eight tRNA genes and two ribosomal RNA genes, all other mitochondrial genes were encoded on the heavy strand. The start codon of COX1 gene was not determined. These complete mitogenome data provide the basis for taxonomic and conservation research of Rhynchocinetes durbanensis, and closely related species.

The complete mitochondrial genome of a cyprinid fish; Metzia longinasus (Teleostei, Cypriniformes)

The long polymerase chain reaction and primer walking method were applied for the sequencing of the complete mitochondrial genome sequence of a cyprinid species (Metzia longinasus) collected from the Hongshuihe River of the Pearl River drainage, Guangxi Province in China. It is 16,614 bp in length, containing 2 rRNA, 22 tRNA, 13 protein-coding genes and 1 control region generally found in most vertebrates. Most of the mitochondrial genes are encoded on the heavy strand except for eight tRNA and ND6 genes. The base composition of this genome was 31.9% A, 26.2%C, 26.2%T and 15.7%G, showing a lower level of G (15.7%) and a slighter AT bias (58.1%). This is the 2nd completely sequenced mitogenome from genus Metzia. The mtDNA sequence of M. longinasus shared 93% sequence similarity with that of M. formosae and it could contribute to a better solution of its phylogenetic position within cyprinid fishes based on the complete mitogenomic data.

Complete mitochondrial genome of Parachromis managuensis (Perciformes: Cichlidae)

The complete mitochondrial genome of Parachromis managuensis (Perciformes: Cichlidae) is sequenced in this study. The genome sequence was 16 526 bp in length, with the base composition of 28.1% A, 25.5% T, 15.4% G, 31.0% C. The gene order and genes are the same as found in other previously reported cichlid fish, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 D-loop region. Except for ND6 gene and eight tRNA genes, all other mitochondrial genes were encoded on the heavy strand. Parachromis managuensis was closely related to Amphilophus citrinellus and Petenia splendid, based on its complete mitochondrial genome sequences. This complete mitogenome data provide the basis for taxonomic and conservation research of Parachromis managuensis.

Sequencing and analysis of the complete mitochondrial genome in Anopheles culicifacies species B (Diptera: Culicidae)

The complete mitochondrial genome sequence of Anopheles culicifacial species B was sequenced in this study. The length of the mitochondrial genome is 15 330 bp, which contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a non-coding control region. The gene order and the gene composition are consistent with those previously reported for other mosquito species. The initiation codon of the PCGs complies with the ATN rule except for COI using TCG and ND5 using GTG as a start codon, and the termination codon is TAA or imcomplete, an only T. The total base composition is 40.4% A, 38.1% T, 12.4% C, and 9.1% G. The phylogenetic tree based on the sequences of 13 protein-coding genes showed that these species were classified into two clades, corresponding to the subgenus Cellia and subgenus Nyssorhynchus. An. culicifacies species B of Myzomyia Series was clustered with An. gambiae of Pyretophorus Series with a high bootstrap value of 100%. The complete mitogenome data can provide a basis for molecular identification and phylogenetic studies of mosquito species.

The complete mitochondrial genome sequence of the little egret (Egretta garzetta)

Many phylogenetic questions in the Ciconiiformes remain unresolved and complete mitogenome data are urgently needed for further molecular investigation. In this work, we determined the complete mitogenome sequence of the little egret (Egretta garzetta). The genome was 17,361 bp in length and the gene organization was typical of other avian mtDNA. In protein-coding genes (PCGs), a C insertion was found in ND3, and COIII and ND4 terminated with incomplete stop codons (T). tRNA-Val and tRNA-Ser (AGY) were unable to fold into canonical cloverleaf secondary structures because they had lost the DHU arms. Long repetitive sequences consisting of five types of tandem repeats were found at the 3′ end of Domain III in the control region. A phylogenetic analysis of 11 species of Ciconiiformes was done using complete mitogenome data and 12 PCGs. The tree topologies obtained with these two strategies were identical, which strongly confirmed the monophyly of Ardeidae, Threskiorothidae and Ciconiidae. The phylogenetic analysis also revealed that Egretta was more closely related to Ardea than to Nycticorax in the Ardeidae, and Platalea was more closely related to Threskiornis than to Nipponia in the Threskiornithidae. These findings contribute to our understanding of the phylogenetic relationships of Ciconiiformes based on complete mitogenome data.

The complete mitochondrial genome of leopard cat, Prionailurus bengalensis chinensis (Carnivora:Felidae)

The full-length of the mitochondrial (mt) genome of Prionailurus bengalensis chinensis was first determined in this study and consisted of a 16,990 bp fragment, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a control region (CR), and an origin of L-strand replication (OLR). The total base composition of the heavy strand was A, 33.0%; G, 13.6%; C, 26.0%; and T, 27.4%, with a slight AT bias of 60.4%. The complete mitogenomic data of P. b. chinensis may provide an important data set for further phylogenetic and taxonomic analyses of Genus Prionailurus species.

Complete mitochondrial genome of Himalayan buzzard (Buteo buteo burmanicus)

In this study, the complete sequence of the mitochondrial (mt) genome of Buteo buteo burmanicus was determined. This mitogenome was 18,231 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a control region (CR) and a pseudo-control region (ψCR). The overall base composition of the heavy strand was A, 30.8%; G, 13.2%; C, 31.8%; and T, 24.2%, with a slight AT bias of 65.1%. The complete mitogenomic data may provide more informative for phylogenetic approach for soft corals phylogeny especially for Buteo species.

Complete mitochondrial DNA genome of tetraploid Carassius auratus gibelio

The complete mitochondrial genome was sequenced from the tetraploid Carassius auratus gibelio in this study. The genome sequence was 16,576 bp in length. The mitochondrial genome contains 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 2 non-coding regions (control region and origin of light-strand replication). All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition is 31.61% A, 25.81% T, 26.62% G, 15.96% C, with an A+T bias of 57.42%. The complete mitogenome data provides useful genetic markers for the studies on the molecular identification, population genetics, phylogenetic analysis and conservation genetics.

Complete mitochondrial genome of Junceella fragilis (Gorgonacea, Ellisellidae)

In this article, the complete mitogenome of the Octocorallia, zooxanthellate, Junceella fragilis has been amplified and sequenced. This mitochondrial genome consists of 18,724 bp, with 14 protein-coding genes, 2 ribosomal RNA genes, 1 transfer RNA genes, no intron was observed. It has been observed that a mitochondrial mismatch repair (mtMutS) gene was present in all octocorals. The overall base composition of the heavy strand was A, 29.1%; G, 20.4%; C, 33.0%; and T, 17.5%, with a slight AT bias of 62.1%. The complete mitogenomic data may provide more informative for phylogenetic approach for soft corals phylogeny especially for octocorallian species.