Major Non-coding Region Research Articles

Characterization of complete mitochondrial genome of fives tripe wrasse (Thalassoma quinquevittatum, Lay & Bennett, 1839) and phylogenetic analysis

To further supplement the genome-level features in related species, T. quinquevittatum complete mtDNA was firstly sequenced and de novo assembled by next-generation sequencing. The full-length mtDNA of T. quinquevittatum was a 16,896bp fragment, which was atypical of Labridae, with 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes (PCGs), 23 transfer RNA (tRNA) genes, and a major non-coding control region (D-loop region). Additionally, the mtDNA of T. quinquevittatum exhibited characteristics of A (27.1%), T (29.3%), G (17.8%), and C (25.8%) with a high A+T content (56.4%). Furthermore, the analysis of the average Ka/Ks in the 13 PCGs of three Labridae species indicated a strong purifying selection within this group. Additionally, the phylogenetic analysis based on 13 concatenated PCGs nucleotide and amino acid datasets, showed high value support for the following sister clade among the four genera (T. quinquevittatum, Halichoeres trimaculatus, Halichoeres melanurus, Parajulis poecilepterus). The complete mtDNA of the T. quinquevittatum provided important information for the study in population genetics and evolutionary theory.

Characterization of the complete mitochondrial genome of Phodopus roborovskii (Rodentia: Cricetidae) and systematic implications for Cricetinae phylogenetics

Phodopus roborovskii (subfamily Cricetinae) is widely distributed in the northern arid regions of China. This study reports its complete mitochondrial genome (mitogenome) for the first time. The complete sequence was 16,273 bp long, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 major noncoding region. The base composition and codon usage were described. The putative origin of replication for the light strand (OL) of P. roborovskii was approximately 45 bp long and was highly conserved in the stem-loop and adjacent sequences, but the starting sequence of replication varied between genera among Rodentia. We analyzed the three domains of the D-loop region, and the results indicated that the central domain had higher G + C content and lower A + T content than two peripheral domains. Phylogenetic analyses indicated high resolution in four main divergent clades using mitogenomes data within Cricetidae. Within Cricetinae clade, P. roborovskii was at basal position which was in line with previous researches, and it shared a common ancestor with other extant hamsters. This work validated previous molecular and karyotype researches using mitogenomes data, and provided a set of useful data on phylogeny and molecular evolution in Cricetidae species.

Updated mitochondrial phylogeny of Pteriomorph and Heterodont Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams and the thyasirid clam Conchocele cf. bisecta

The mitochondrial genomes of bivalves have often been used for comparative genomics and for resolving phylogenetic relationships. More than 100 bivalve complete mitochondrial genomes have been sequenced to date. However, few mitochondrial genomes have been reported for deep-sea chemosymbiotic bivalves, which belong to the subclasses Pteriomorphia and Heterodonta. In the present study, we sequenced the mitochondrial genomes of eight deep-sea chemosymbiotic bivalve species: three species of Bathymodiolus mussels (B. japonicus, B. platifrons, and B. septemdierum), four species of vesicomyid clams (Abyssogena mariana, A. phaseoliformis, Isorropodon fossajaponicum, and Phreagena okutanii, all of which were formerly classified in the genus Calyptogena), and one species of thyasirid clam (Conchocele cf. bisecta). With a few exceptions, these mitochondrial genomes contained genes that are typical of metazoans: 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The major non-coding region with a high A+T content of each genome, which contained tandem repeats and hairpins, was hypothesized to function as a control region. The phylogenetic trees of Pteriomorphia and Heterodonta were reconstructed based on the concatenated sequences of 14 shared genes. Bathymodiolus formed a monophyletic clade with asymbiotic Mytilidae mussels, the vesicomyid clams formed a monophyly that was sister to the Veneridae, and C. cf. bisecta branched basally in the Heterodonta. It is known that the gene orders of mitochondrial genomes vary among bivalves. To examine whether gene order variation exhibits phylogenetic signals, tree topologies based on the minimum number of gene rearrangements were reconstructed for two clades (superfamily Tellinoidea, which includes the Psammobiidae, Semelidae, Solecurtidae, and Tellinidae; and the clade comprising the Myidae, Mactridae, Arcticidae, Vesicomyidae, and Veneridae) with high statistical support in sequence-based phylogenies. The resulting tree topologies were almost identical to those of the sequence-based trees. Our present findings suggest that the evolution of bivalves could be precisely traced back through the analysis of mitochondrial genomes, and that such an analysis could contribute to understanding bivalve evolution and diversity.

New insights about the introduction of the Portuguese oyster,Crassostrea angulata, into the North East Atlantic from Asia based on a highly polymorphic mitochondrial region

It is commonly presumed that the Portuguese oyster Crassostrea angulata was introduced into the North East (NE) Atlantic from Asia. The analysis of the nucleotide sequence of a highly polymorphic non-coding mitochondrial region (major noncoding region - MNR) of C. angulata samples collected in Europe (Portugal), Africa (Morocco) and Asia (Shantou and Taiwan) provided new insight into the introduction of this species into the NE Atlantic. Sixty haplotypes and a nucleotide diversity of 0.0077 were observed in 130 analyzed sequences. Higher nucleotide diversity levels were observed in NE Atlantic sites than in Asian sites and significant genetic differentiation was found between the two. Our results suggest that C. angulata might have been introduced to the NE Atlantic by multiple introductory events, though the exact origins remain unknown since none of the analyzed Asian sites seemed to have been a source of introduction. The nucleotide diversity of C. angulata was higher than that previously reported for Pacific oyster C. gigas in Europe and Asia for the same mitochondrial region. The results obtained in the present study suggest that NE Atlantic C. angulata stocks are a unique genetic resource, which highlights the importance of their conservation.

Complete mitochondrial genome of javeline goby (Synechogobius hasta)

In this study, we cloned and sequenced the complete mitochondrial DNA (mtDNA) of Synechogobius hasta to characterize and compare their mitochondrial genomes. The total length of the mitochondrial genome is 16,655 bp with an accession number KM891736. The organization of the mitochondrial genomes was similar to those reported from other fish mitochondrial genomes containing 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region. Except for ND6 and 8 tRNAs, all other genes are encoded on the heavy strand. The base composition of the 13 mitochondrial protein-coding genes in the third position was relatively low (9.7%). The complete mitogenome may provide important date set for the study of genetic mechanism of S. hasta.

Analysis of heteroplasmy in the major noncoding region of mitochondrial DNA in the blood and atherosclerotic plaques of carotid arteries

For identification of somatic mitochondrial DNA (mtDNA) mutations, the mtDNA major noncoding region (D-loop) sequence in blood samples and carotid atherosclerosis plaques from patients with atherosclerosis was analyzed. Five point heteroplasmic positions were observed in 4 of 23 individuals (17%). Only in two cases could heteroplasmy have resulted from somatic mutation, whereas three heteroplasmic positions were found in both vascular tissue and blood. In addition, length heteroplasmy in a polycytosine stretches was registered at nucleotide positions 303-315 in 16 individuals, and also in the 16184-16193 region--in four patients. The results suggest that somatic mtDNA mutations can occur during atherosclerosis, but some heteroplasmic mutations may appear in all tissues, possibly being inherited.

The complete mitochondrial genome of Crassostrea gasar (Bivalvia: Ostreidae)

The complete mitochondrial genome of Crassostrea gasar was sequenced using the Ion Proton technology in combination with 454 Roche GS-FLX plataform data. We assembled a 17,686 bp complete circular mitochondrial genome, containing 13 protein-coding genes, a major non-coding region (MNR), two ribosomal RNA genes and 24 transfer RNA genes. Phylogenetic analysis of concatenated amino acid sequences from mitochondria showed monophyletic clades formed with high bootstrap values. This is the first complete mitochondrial sequence of an oyster from South America. Mitogenome sequence was deposited in GenBank under the accession number KR856227.

The phylogenetic placement of Odontobutis obscura base on complete mitochondrial DNA sequence

In our research, 16 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of Odontobutis obscura. The aim of our research was to provide some important genetic background information for conservational practice of these valuable fish species. The total length of the mitochondrial genome is 16 864 bp and deposited in the GenBank with accession numbers KT438552. The gene arrangement and transcriptional direction were similar to other bony fishes which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNAs) and a major non-coding control region. The nucleotide skewness for the coding strands of O. obscura (GC-skew = −0.26) is biased toward G and the negative GC-skew ranges from −0.51(ND2) to −0.24(CO1). The phylogenetic analysis showed that the Gobiiformes could be divided into three groups, Eleotridae, Odontobutidae and Rhyacichthyidae. The O. Obscura and O. Potamophila are sister species and clustered together.

The complete mitochondrial genome of Gyrodactylus gurleyi (Platyhelminthes: Monogenea)

Gyrodactylus gurleyi, was inhabited on the fins and gills of goldfish (Carassius auratus), which belonged to the family Gyrodactylidae. In this study, we sequenced the complete mitochondrial genome of G. gurleyi with the total length of 14 771 bp. The mitogenome contained 12 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and two major non-coding regions (NC1 and NC2). The overall AT content was 72.1%. In phylogenetic analysis, G. gurleyi and G. kobayashii clustered together and then united with the clade of other three Gyrodactylus species (G. salaris, G. thymalli and G. derjavinoides) with high nodal support.

The complete mitochondrial genome of the yellow-spotted triggerfish (Pseudobalistes fuscus)

The yellow-spotted triggerfish (Pseudobalistes fuscus), a member of the genus Pseudobalistes, belongs to the family Balistidae. Here, we describe the complete mitochondrial genome sequence of P. fuscus. The genome, 16,480 bp in length, is comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and a major non-coding region. The gene content and order are in accord with the common vertebrate form. A phylogenic tree was constructed based on the complete mitogenomes of P. fuscus and six closely related species to estimate their phylogenic relationship. Our data present an important genetic resource for the biological studies of the family Balistidae.

The complete mitochondrial genome of Gyrodactylus kobayashii (Platyhelminthes: Monogenea)

The complete mitochondrial genome of Gyrodactylus kobayashii was 14 786 bp in length, containing 12 protein-coding genes (lacking Atp8), 22 tRNA genes, two rRNA genes and two major non-coding regions (NC1 and NC2). The overall A + T content of mitochondrial genome was 71.6%. A close relationship between G. kobayashii and the three Gyrodactylus species (G. salaris, G. thymalli and G. derjavinoides) was uncovered in the phylogenetic tree based on amino acid sequences.

Phylogenetic analysis of the Mongolian gerbil (Meriones unguiculatus) from China based on mitochondrial genome.

Meriones unguiculatus (Gerbillinae, Rodentia) is widely used as an animal model of human disease. Here, we provide the first report of the complete mitochondrial genome sequence of M. unguiculatus (GenBank accession Nos. KF425526 and NC_023263). The sequence contained the conserved vertebrate pattern of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 major noncoding region. We identified one extended termination-associated sequence and one conserved sequence block in the non-coding region. The putative origin of replication for the light strand (OL) was 35 bp long. The OL stem and adjacent sequences were highly conserved, but the loop region differed from those of other rodent species. Base composition and codon usage of the 13 protein-coding genes in M. unguiculatus were compared with those of 23 rodent species with previously sequenced mitochondrial genomes. An A+T content of 63.0% was present in M. unguiculatus; this is similar to the Murinae average (62.4 ± 0.8%) and falls between the average for Mus musculus (63.1 ± 0.1%) and Rattus sp (61.7 ± 0.4%). The AT and GC skew values of M. unguiculatus were 0.035 and -0.28, respectively, similar to those of Cricetinae species (0.057 ± 0.05 and -0.31 ± 0.05). The codon families exhibited similar abundance in all 24 species. Analysis of phylogenetic relationships with 23 other rodent species using neighbor-joining and maximum likelihood protocols and the 12 protein-coding regions on the H strand showed that M. unguiculatus should be classified as genus Meriones, sub-family Gerbillinae, family Muridae.

The phylogenetic analysis of Acrossocheilus paradoxus among the acrossocheilus base on complete mitochondrial DNA sequence

In our research, we used 17 sets of primers to amplify the complete mitochondrial DNA (mtDNA) of Acrossocheilus paradoxus. The total length of the mitochondrial genome is 16 597 bp and deposited in the GenBank with accession numbers KT751364. The gene arrangement and transcriptional direction were similar to other bony fishes which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region. Most genes were encoded on the H-strand, except for the ND6 and 8 tRNA genes, encoding on the L-strand. The nucleotide skewness for the coding strands of A. Paradoxus (GC-skew= −0.24, AT-skew = 0.07) is biased toward A and C. The negative GC-skew ranges from −0.35(ND6) to −0.21(CO1) and the AT-skew showed more positive varying from −0.23(ND4L) to 0.42(ND6). The phylogenetic analysis demonstrated that Acrossocheilus clustal together as one group.

Complete mitochondrial genome sequence of Chenghua pig (Sus Scrofa) and its phylogenetic analysis

Chenghua pig is one of the famous indigenous breeds of Sichuan province in China. In the study, the complete mitochondrial genome of Chenghua pig was first determined. The total mitochondrial genome is 16,760 bp in length and its overall base composition of the circle genome is A (34.71%), T (25.79%), C (26.20%) and G (13.30%), respectively, indicating an A–T (60.50%)-rich feature. It contains the typical structure, including 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and a major non-coding control region (D-Loop region). The D-loop region contains two different repeat motifs. According to the phylogenetic tree, we can infer that it is reasonable to divide Chenghua pig into the genus Sus Scrofa in southwest China. The mitochondrial genome would play an important role in population genetics and phylogenetic analysis of Sus Scrofa.

Complete mitochondrial genome sequence of Hemiculter bleekeri

In our research, the complete mitochondrial DNA (mtDNA) of Hemiculter bleekeri was obtained from the dorsal myotome of the fish. The total length of the mitochondrial genome is 16,617 bp and deposited in GenBank with accession number KU198332. The gene arrangement was similar to other bony fishes, which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region. The mtDNA may provide some important genetic background information of this valuable fish. The G contents was relatively low in the total mtDNA with the GCskewthinsp;= −0.22. The negative GC-skew ranging from −0.51(ATP8) to −0.19(CO1), and the more positive AT-skew varying from −0.26(ATP8) to −0.03(CO1). The phylogenetic analysis demonstrated that H. Bleekeri was clustered together with Hemiculter leucisculus, which could be a sister species.

Inheritance and phylogenetic analysis of Tylosurus acus melanotus based on the complete mitochondrial genomes

In our research, 17 sets of primers were used to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) of the Tylosurus acus melanotus in order to analyse the inheritance and evolutionary relationship of this species. The total length of the mitochondrial genome is 16,723 bp and deposited in the GenBank with accession numbers KU605633. The gene arrangement was similar to other bony fishes which contained 37 genes (13 protein-coding genes, 2 ribosomal RNA and 22 transfer RNAs) and a major non-coding control region. Most genes were encoded on the H-strand, except for the ND6 and 8 tRNA genes, encoding on the L-strand. The mtDNA may provide some important genetic background information for this valuable fish. The nucleotide skewness for the coding strands of T. acus melanotus (GC-skew = −0.21) is biased towards G and the negative GC-skew ranges from -0.53(ATP8) to -0.12(CO2) and the AT-Skew showed more positive varying from −0.17(ND3) to 0.26(ATP6). The phylogenetic analysis demonstrated that T. acus melanotus was clustered together with Ablennes hians, but far away from Cololabis saira which belongs to Beloniformes, Belonidae.

Complete mitochondrial genome of the Liuyang black goat and its phylogenetic relationship with other Caprinae

In this study, the complete mitochondrial genome sequence of the Liuyang black goat was investigated, and phylogenetic relationships between the Liuyang black goat and other species of Caprinae were analyzed. The total length of the mitochondrial genome was 16,715 bp, which consisted of 33.50% A, 27.27% T, 25.98% C, and 13.25% G. The mitochondrial genome contained a major non-coding control region (D-loop region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. Neighbor-joining and maximum-parsimony trees of Caprinae constructed using 13 mitochondrial protein-coding genes showed that the Liuyang black goat is phylogenetically closest to Hemitragus jemlahicus (the Himalayan tahr) and Blue sheep to form clade A. Tibetan antelopes clustered separately in clade B and so did sheep in clade C.

The first representative of Coelomactra antiquata mitochondrial genome from Liaoning (China) and phylogenetic consideration

Coelomactra antiquata is a famous delicacy and a promising new candidate for aquaculture, which belongs to the family Mactridae (Mollusca: Veneroida). The complete mitochondrial genome of C. antiquata (Liao Ning province, in China, LN) was finished, which is the first representative from this province. The results showed that the total length of LN-mtDNA sequence is 16,797 bp and the content of A + T is 65.01%. It encodes 35 genes, including 12 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. All coding genes are encoded on the heavy strand. Compared with the typical gene content of animal mitochondrial genomes, atp8 and trnSer(UCN) genes are missing in the mitochondrial genome. The complete mitochondrial genome contains 26 non-coding regions (1598 bp), one major non-coding region consists of 1046 bp in which 4.9 tandem repeat sequences (99bp per sequence) was observed. The phylogenetic tree showed that Liaoning population was clustered into one clade with Shandong (Rizhao, Jiaonan and Jimo) and Guangxi (Beihai) populations, meanwhile all of them are far from the Fujian populations (Pingtan, Zhangzhou and Changle). So, Liaoning, Shandong and Guangxi populations have a close relationship. Actually, Fujian is located between Liaoning, Shandong and Guangxi. So, the result challenges the previously assumed relevance between geographic distance and genetic distance. The genetic distance of Liaoning C. antiquata and Fujian (Changle, Zhangzhou and Pingtan) C. antiquata (0.176–0.177) is greater than the genetic distance between Mytilus galloprovincialis and Mytilus trossulus (0.160). The genetic difference of Liaoning population and Fujian populations has reached species level.

Complete mitochondrial genome of the endangered Lycaenid butterfly Shijimiaeoides divina (Lepidoptera: Lycaenidae)

The lycaenid butterfly, Shijimiaeoides divina (Lepidoptera: Lycaenidae), has been listed in Korea as a class II endangered wild species since 2012. Therefore, the mitogenome sequence is necessary to better understand genomic characteristics of the species. The 15 259-bp complete mitochondrial genome of the species consists of a typical set of genes, including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes, and 1 major non-coding AT-rich region, with an arrangement typical of Ditrysia (trnM-trnI-trnQ between the AT-rich region and ND2). The 379-bp A + T-rich region has a trnK-like sequence. Phylogenetic analysis using 13 protein-coding genes of the families Lycaenidae and Riodinidae with outgroups from species in Nymphalidae indicates that each family is a strong monophyletic group and that S. divina, belonging to Polyommatinae, is correctly placed as a sister to the within-subfamilial species Cupido argiades with the highest support.

Complete mitochondrial genome of the earthworm, Amynthas jiriensis (Clitellata: Megascolecidae)

To date, a very limited number of complete clitellate mitochondrial genome (mitogenome) sequences are available. Therefore, in the present study, we elucidated the complete mitogenome sequence of Amynthas jiriensis (Clitellata: Megascolecidae), a species endemic to South Korea. Its 15 151-bp-long genome contains the 37 genes typical of metazoan mitogenomes [13 protein-coding genes (PCG), 2 rRNA genes, and 22 tRNA genes], and one major non-coding control region. All 37 genes were transcribed from the same DNA strand. The arrangement of the A. jiriensis mitogenome is identical to those of all available clitellate mitogenomes. All the 13 PCGs start with the ATG codon. Five PCGs (COI, ND6, CytB, ATP6, and ND4L) end with TAA, and COII ends with TAG, whereas the remaining PCGs end with the incomplete stop codon. The phylogenetic analysis using 13 PCGs has shown the species of Pheretimoid genera, including A. jiriensis, formed a complexity.