Conserved Sequence Blocks Research Articles

Complete mitochondrial genome and phylogenic analysis of the mudskipper Scartelaos gigas (Perciformes, Gobiidae)

In this paper, the complete mitochondrial genome sequence of Scartelaos gigas was firstly determined. The circular genome (16 717 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The overall base composition of S. gigas is 28.9% for C, 28.3% for A, 26.4% for T, 16.4% for G, with a slight A + T bias of 54.7%. In the control region, the termination-associated sequence and conserved sequence block domains were found, but the tandem repeat structure was not found. It has the typical vertebrate mitochondrial gene arrangement. The phylogenic analysis using the Neighbor-Joining method showed that the fishes belonging to Gobiidae, Odontoburidae, and Eleotridae formed three branches grouped with other fishes into one clade which separated from the mammals. We hope that the results from the present study will provide useful molecular information for the further studies on genetic structure and demographic history of S. gigas.

The mitochondrial genome of Schizothorax esocinus (Cypriniformes: Cyprinidae) from Northern Pakistan

The mitochondrial DNA sequence represents a mainstay of phylogenetics. It allows biologists to elucidate the evolutionary relationships among species. It also permits an examination of the relatedness of populations, hence got importance in the field of biology. The current study was designed to know the mitochondrial sequence of Schizothorax esocinus, a delicious fish belonging to family Cyprinidae. In this study, the complete mitochondrial genome of S. esocinus from Northern Pakistan was determined. The mitogenome of S. esocinus was found to be 16 591 bp in length and consisted of 13 protein coding genes, 22 tRNA genes, two rRNA genes, and one control region. All genes were encoded on heavy strain except ND6 and few tRNA genes. The overall base composition was T 25.5%, C 27.0%, A 29.8% and G 17.7%, A + T content 55.3% and G + C content 47.7%. The length of control region (CR) was 938 bp and contained putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB) and control region also contained a microsatellite region (TA). This is the very first study reported from a reservoir of large cold water bodies in Pakistan which have a great potential for conservation of cold water fish species. This mitogenome sequence would be useful to know the phylogenetic status of the fish.

Live sharksucker Echeneis naucrates (Linnaeus 1758) mitochondrial genome: the first report of Echeneidae complete mitochondrial genome

The complete mitochondrial genome of Echeneis naucrates is 16,611 bp in length. It comprises a control region, 13 protein-coding genes, 2 ribosomal RNAs (rRNAs) and 22 transfer RNAs (tRNAs), with an arrangement typical of vertebrate mitochondrial genomes. Base composition on the heavy strand is 30.24% A, 25.45% C, 15.02% G and 29.29% T. The control region is 940 bp in length, containing putative termination associated sequences (TASs) and conserved sequence blocks (CSBs). Two copies of a tandem repeat (AATATTAT) were found in all six individuals investigated. The hypothesis of selection for an optimal number of repeats as well as the evolutionary dynamics of tandem repeats in E. naucrates control regions await further investigations.

Complete mitogenome sequences of a Korean spine loach, Iksookimia koreensis (Kim, 1975)

Here, we present the complete mitogenome sequences from a Korean spine loach (Iksookimia koreensis Kim 1975), an endemic species of Korea. The total length of mitogenome was 16 563 bp, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region (D-loop). Except for ND6 and eight tRNA genes, all of the other mitochondrial genes were encoded on the heavy strand. The control region harbored conserved sequence blocks (CSB-D, E, F, CSB-1, CBS-2 and CBS-3) and TA-nucleotide microsatellite repeats in its 3′ end. Our complete mitogenomes will be valuable resources for phylogeny, genetics and conservation of the genus Iksookimia.

Sequence and organization of the complete mitogenome of a Siberian stone loach, Barbatula toni (Dybowsky, 1869) (Cypriniformes: Balitoridae)

In this study, we determined the complete mitogenome sequence of Siberian stone loach, Barbatula toni (Dybowsky, 1869). The total length of mitogenome is 16 623 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop). The genome organization and gene order were identical to that of the typical vertebrates. The control region harbors conserved sequence blocks (CSB-D, E, F, CSB-1, CBS-2 and CBS-3) and TA-nucleotide microsatellite repeats in its 3′ end. The complete mitogenome may provide important molecular data for further phylogenetic analyses for higher taxa of teleost fishes, especially for the fishes in order Cypriniformes.

Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element.

The majority of mitochondrial DNA replication events are terminated prematurely. The nascent DNA remains stably associated with the template, forming a triple-stranded displacement loop (D-loop) structure. However, the function of the D-loop region of the mitochondrial genome remains poorly understood. Using a comparative genomics approach we here identify two closely related 15 nt sequence motifs of the D-loop, strongly conserved among vertebrates. One motif is at the D-loop 5′-end and is part of the conserved sequence block 1 (CSB1). The other motif, here denoted coreTAS, is at the D-loop 3′-end. Both these sequences may prevent transcription across the D-loop region, since light and heavy strand transcription is terminated at CSB1 and coreTAS, respectively. Interestingly, the replication of the nascent D-loop strand, occurring in a direction opposite to that of heavy strand transcription, is also terminated at coreTAS, suggesting that coreTAS is involved in termination of both transcription and replication. Finally, we demonstrate that the loading of the helicase TWINKLE at coreTAS is reversible, implying that this site is a crucial component of a switch between D-loop formation and full-length mitochondrial DNA replication.

Complete mitochondrial genome of Vaginulus alte and Homoiodoris japonica

The complete mitochondrial genome sequence of Vaginulus alte and Homoiodoris japonica are described first in the article. The mitogenomes (14 772 bp and 14 601 bp) contain 22 tRNA genes, two ribosomal RNA genes, and 13 protein-coding genes, and one putative control region (CR). CR is not well characterized due to the lack of discrete conserved sequence blocks. This characteristic is similar with CRs of other invertebrate mitochondrial genomes, which is the typical bivalvia mitochondrial gene composition.

Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes).

Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.

The complete mitochondrial genome of Sillago sihama (Perciformes: Sillaginidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Sillago sihama has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is a circular molecule of 17 003 bp in length and contains 37 mitochondrial genes and a control region. Within the control region, we identified the variable number tandem repeats, as well as the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F∼CSB-A) and the conserved sequence block domains (CSB-1, CSB-2, and CSB-3).

Mitochondrial DNA control region of three mackerels, genus Rastrelliger: structure, molecular diversity and phylogenetic relationship

The complete mitochondrial control regions (CR) of three mackerels (Rastrelliger spp.) were examined and analyzed. The CR contained three domains, in which three termination-associated sequences (TAS-I, TAS-II and TAS-III), two central conserved sequence blocks (CSB-E, CSB-D), three conserved sequence blocks (CSB-I, CSB-II, and CSB-III) and a putative promoter were detected. Molecular indices analyses of the aligned complete CR sequences showed high level of haplotype diversities and genetic divergences among the three species. The intraspecific divergence among species of this genus ranked from 0.25% to 1.62% and interspecific divergence from 1.90% to 4.30%. The phylogenetic tree shows monophyly with R. brachysoma as a basal species of Rastrelliger. Applying the average divergence rate for fish control regions, the results suggest that the time of separation among Rastrelligers could have occurred in the middle Pleistocene era.

Complete mitochondrial genome of the Loligo duvaucelii

In this study, we determined the complete mitochondrial genome of the little squid (Loligo duvaucelii). The genome is 17,413 bp in length, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. duvaucelii is 40.01% A, 32.33% T, 19.14% C and 8.52% G, with a high A + T bias of 72.34%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a phylogenetic analysis of 10 species of Cephalopoda based on the complete mitochondrial genome, the result showed that the Loliolus uyii is most closely related to L. duvaucelii. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Cephalopoda.

Sequencing and analysis of the complete mitochondrial genome of Amur minnow from China

The complete mitogenome sequence of Amur minnow (Rhynchocypris lagowskii) was determined using long PCR. The genome was 16,594 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The overall base composition of the heavy strand is A (28.60%), C (26.32%), T (27.40%), and G (17.68%). The control region was 927 bp in length and the A + T content of the region was 63.32%. The extended termination-associated sequence domain, the central conserved domain, and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur minnow. Mitochondrial genomes analyses based on maximum parsimony (MP), neighbor-joining (NJ), and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 15 Cyprinidae species. It appeared that no less than two major phyletic lineages were present in Leuciscinae. The main clades within the Leuciscinae supported are: A clade is the Tribolodon. A clade (Rhynchocypris) with the Oreoleuciscus as the sister taxon to Tribolodon was supported by bootstrap values of 49%. The five different geographical populations of the R. lagowskii formed a paraphyletic group with the high bootstrap value (45%) in all examinations.

The complete mitochondrial genome of Cherskii’s sculpin (Cottus czerskii) (Scorpaeniformes: Cottidae)

The complete mitogenome sequence of Cherskii’s sculpin (Cottus czerskii) is determined using long PCR. The genome is 16,534 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. The overall base composition of the heavy strand is A (26.4%), C (30.1%), T (26.1%) and G (17.5%). The control region is 857 bp in length and the A + T content of the region is 61.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Cherskii’s sculpin. Mitochondrial genome analyses based on MP, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 21 Actinopterygii species. It appears that no less than two major phyletic lineages were present in Actinopterygii. The main clades within the Perciformes and Scorpaeniformes supported are: a clade including the Scombridae, Kyphosidae and Percichthyidae; a clade (Cottidae) with the Trichodontidae as the sister taxon to Pholidae, Anarhichadidae and Zoarcidae, which was supported by bootstrap values of 92%. The five Cottus species formed a paraphyletic group with the high bootstrap value (100%) in all examinations.

The complete mitochondrial genome of Eurasian water shrew (Neomys fodiens)

The complete mitogenome sequence of Eurasian water shrew (Neomys fodiens) was determined using long PCR. The genome was 17,260 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 control region. The overall base composition of the heavy strand is A (33.0%), C (23.2%), T (30.9%) and G (12.9%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Eurasian water shrew. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. Neomys elegans, Soriculus fumidus, and N. fodiens formed a monophyletic group with the high bootstrap value (100%) in all examinations. This clade with the Anourosorex squamipes as the sister taxon to Sorex.

The complete mitochondrial genome of Gloydius intermedius (Squamata: Viperidae: Crotalinae) from China

The mitochondrial genome sequence of Gloydius intermedius is analyzed and presented for the first time. The genome was 17, 226 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control region. The overall base composition was A (32.4%), C (28.8%), T (25.9%), and G (12.9%). The base compositions clearly presented the A–C skew, which was most obvious in the protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of G. intermedius. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the 13 Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae supported are: A clade including the Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, G. saxatilis) with the Ovophis appeared as the sister taxon to Protobothrops and was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100 %) in all examinations.

The complete mitochondrial genome of Amur bitterling (Rhodeus sericeus) from China

The complete mitogenome sequence of Amur bitterling (Rhodeus sericeus) was determined using long PCR. The genome was 16,581 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand was A (28.9%), C (27.2%), T (26.6%), and G (17.3%). The control region was 925 bp in length and the A + T content of the region was 63.5%. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of Amur bitterling. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity to the 13 Cyprinidae species. It appeared that no less than three major phyletic lineages were present in Cyprinidae. A clade (Rhodeus and Tanakia) with the R. lighti and R. Sinensis as the sister taxon to Acheilognathus was supported by bootstrap values of 100%. The close relationship of Amur bitterling to other Rhodeus species, especially R. pseudosericeus, is consistent with the results confirmed using morphology analysis.

Mitochondrial DNA genomes organization and phylogenetic relationships analysis of eight anemonefishes (pomacentridae: amphiprioninae).

Anemonefishes (Pomacentridae Amphiprioninae) are a group of 30 valid coral reef fish species with their phylogenetic relationships still under debate. The eight available mitogenomes of anemonefishes were used to reconstruct the molecular phylogenetic tree; six were obtained from this study (Amphiprion clarkii, A. frenatus, A. percula, A. perideraion, A. polymnus and Premnas biaculeatus) and two from GenBank (A. bicinctus and A. ocellaris). The seven Amphiprion species represent all four subgenera and P. biaculeatus is the only species from Premnas. The eight mitogenomes of anemonefishes encoded 13 protein-coding genes, two rRNA genes, 22 tRNA genes and two main non-coding regions, with the gene arrangement and translation direction basically identical to other typical vertebrate mitogenomes. Among the 13 protein-coding genes, A. ocellaris (AP006017) and A. percula (KJ174497) had the same length in ND5 with 1,866 bp, which were three nucleotides less than the other six anemonefishes. Both structures of ND5, however, could translate to amino acid successfully. Only four mitogenomes had the tandem repeats in D-loop; the tandem repeats were located in downstream after Conserved Sequence Block rather than the upstream and repeated in a simply way. The phylogenetic utility was tested with Bayesian and Maximum Likelihood methods using all 13 protein-coding genes. The results strongly supported that the subfamily Amphiprioninae was monophyletic and P. biaculeatus should be assigned to the genus Amphiprion. Premnas biaculeatus with the percula complex were revealed to be the ancient anemonefish species. The tree forms of ND1, COIII, ND4, Cytb, Cytb+12S rRNA, Cytb+COI and Cytb+COI+12S rRNA were similar to that 13 protein-coding genes, therefore, we suggested that the suitable single mitochondrial gene for phylogenetic analysis of anemonefishes maybe Cytb. Additional mitogenomes of anemonefishes with a combination of nuclear markers will be useful to substantiate these conclusions in future studies.

Sequencing and analysis of the complete mitochondrial genome of tundra shrew (Sorex tundrensis) from China

The complete mitogenome sequence of tundra shrew (Sorex tundrensis) was determined using long PCR. The genome was 17,444 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes, 1 origin of L strand replication and 1 control region. The overall base composition of the heavy strand is A (32.9%), C (24.8%), T (29.0%), and G (13.3%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of tundra shrew. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. The three Sorex species formed a monophyletic group with the high bootstrap value (100 %) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of Gloydius saxatilis (Squamata: Viperidae: Crotalinae)

The mitochondrial genome sequence of Gloydius saxatilis is analyzed and presented for the public for the first time. The genome was 17,218 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 control regions. The overall base composition was A (32.3%), C (28.9%), T (25.8%), and G (13.0%). The base compositions presented clearly the A-C skew, which was most obviously in the protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of G. saxatilis. Mitochondrial genomes analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the thirteen Crotalinae species. It appeared that no less than two major phyletic lineages were present in Crotalinae. The main clades within the Crotalinae supported are: A clade including the Protobothrops. A clade (G. brevicaudus, G. ussuriensis, G. intermedius, G. saxatilis) with the Ovophis as the sister taxon to Protobothrops and was supported by bootstrap values of 88%. The four Gloydius species formed a paraphyletic group with the high bootstrap value (100%) in all examinations.

Complete mitochondrial genome of Acrossocheilus parallens (Cypriniformes, Barbinae)

The omnivorous fish Acrossocheilus parallens (Cypriniformes, Barbinae) is endemic to China. In this paper, the complete mitochondrial genome sequence of A. parallens was firstly determined. The circle genome (16,592 bp) comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The overall base composition of A. parallens is 31.0% for A, 24.7% for T, 28.0% for C, and 16.3% for G, with a slight A + T bias of 55.7%. The termination-associated sequence and conserved sequence block domains were found in the control region. It has the typical vertebrate mitochondrial gene arrangement.