Conserved Sequence Block Domain Research Articles

Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae

Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as ‘vulnerable’, ‘endangered’, and ‘near threatened’, respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a ‘cloverleaf’ secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.

The second complete mitogenome of Scolopsis ciliata (Perciformes, Nemipteridae) to analyze control region structure and intraspecific variation

In this study, we reported the complete mitogenome of Scolopsis ciliata sampled from the Beibu Gulf, South China Sea. It was 16,734 bp in length and contained 37 canonical mitochondrial genes and 2 non-coding regions. Fifty-one single nucleotide polymorphisms and five insertion and deletions were detected between two S. ciliata mitogenomes, suggesting a high level of intraspecific genetic variation in the species. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), and conserved sequence block domain (CSB-1, CSB-2, and CSB-3). The phylogenetic analysis of 21 complete mitogenome sequences well supports the phylogenetic position of S. ciliata and reveals the phylogenetic relationship of the genus Scolopsis.

The second complete mitogenome of Nemipterus virgatus to dissect control region structure and phylogenetic problem of the superfamily Sparoidea (Teleostei, Perciformes)

In this study, we determined the complete mitogenome of Nemipterus virgatus of which the length was 17,073 bp, including 37 canonical mitochondrial genes and 2 non-coding regions. The control region contained termination associated sequence domain (TAS), central conserved domain (CSB-F, CSB-E, CSB-D, CSB-C, and CSB-A), conserved sequence block domain (CSB-1, CSB-2, and CSB-3), and tandem repeat sequence domain (TTD). Nine single nucleotide polymorphisms and three insertion of tandem repeat sequence (each length in 28 bp) were detected between two N. virgatus mitogenomes. The phylogenetic analysis showed that the families Nemipteridae, Sparidae, Centracanthidae, and Lethrinidae did not gather into a monophyly of superfamily Sparoidea in the neighbor-joining tree.

Sequencing and analysis of the complete mitochondrial genome of the Eurasian least shrew (Sorex minutissimus) from China

The complete mitogenome sequence of the Eurasian least shrew (Sorex minutissimus) was determined using long PCR. The genome was 17,061 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 is A (32.6%), C (24.7%), T (29.1%) and G (13.6%). 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 the Eurasian least shrew. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. The ten Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

The complete mitochondrial genome of Atrobucca nibe (Perciformes: Sciaenidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Atrobucca nibe has been determined by polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,504 bp in length, including the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding regions (control region and L-strand replication origin), the gene contents of which are identical to those observed in most bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS) and the conserved sequence block domain (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B, CSB-A, CSB-1, CSB-2, CSB-3).

Sequencing and analysis of the complete mitochondrial genome of the Siberian large-toothed shrew (Sorex daphaenodon) from China

The complete mitogenome sequence of the Siberian large-toothed shrew (Sorex daphaenodon) was determined using long PCR. The genome was 17,407 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 (33.1%), C (24.7%), T (29.0%), and G (13.2%). The base compositions present clearly the A–T skew, which is most obvious 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 the Siberian large-toothed shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The 11 Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

The complete mitochondrial genome of Pampus minor (Liu & Li, 1998) (Perciformes: Stromateidae)

In this study, the complete mitochondrial genome sequence of Pampus minor has been determined by long polymerase chain reaction and primer walking methods. The mitochondrial genome is a circular molecule of 16,690 bp in length, including the typical structure of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding regions (L-strand replication origin and control region), the gene contents of which are identical to those observed in most bony fishes. The overall base composition of the heavy strand shows 29.9% of T, 24.7% of C, 30.6% of A and 14.7% of G, with a slight A + T rich feature (60.5%). Within the control region, we identified the termination-associated sequence domain (TAS), and the conserved sequence block domains.

Structural characteristics of the control region of the Beaufortia kweichowensis mitochondrial genome

In present study, we identified the structural characteristics of the Beaufortia kweichowensis mtDNA control region using the next-generation sequencing method. Result showed that the control region could be further divided into three parts, including the extended termination associated sequence domain (ETAS), the central conserved domains (CSB-F, CSB-E, CSB-D) and the conserved sequence block domains (CSB-1, CSB-2, CSB-3), and their conserved sequences were identified.

Sequencing and analysis of the complete mitochondrial genome of the taiga shrew (Sorex isodon) from China

The complete mitogenome sequence of the taiga shrew (Sorex isodon) was determined using long PCR. The genome was 17,008 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication and one control region. The overall base composition of the heavy strand is A (32.5%), C (24.5%), T (28.5%), and G (13.5%). 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 the taiga shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The eight Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Complete mitochondrial genome of the Pleuronichthys lighti (Pleuronectiformes, Pleuronectidae) with phylogenetic consideration

Mitochondrial genome has been used to shed light on many fields of both basic and applied research, including the study of molecular evolution. The complete mitochondrial genome sequence of 17368 bp nucleotides from the Pleuronichthys lighti was determined. It was a circular double-stranded DNA molecule with identical set of 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes as well as a non-coding control region. Stand asymmetry in the nucleotide composition was reflected in the codon usage of genes oriented in opposite directions. In the control region, we identified the extended termination associated sequence domain, the central conserved sequence block domain and the conserved sequence block domain, and two complete repeat region. They were “TTACAATA” and “TGTTGTAA”, respectively. All known 12 mitochondrial genomes of Pleuronectinae fishes were downloaded and analyzed; there were 5570 variable sites in the consensus sequences of 15241 base pairs, calculation of total sites were 35.5%. The highest sequence divergence was 50% (ATP8) and the Kimura-2-parameter genetic distance was 0.235 (ND6), whereas the COIII had the lowest sequence divergence (28.8%) and genetic distance (0.128); the protein coding genes were mainly acted by purifying selection which was detected by selection tests. Analysis of confidence and the information content for per nucleotide revealed ND5, ATP6, COI and ND4 genes were suitable molecular markers for phylogenetic study of Pleuronectinae fishes. Phylogenetic analysis using Bayesian computational algorithms based on COI genes provided support for the taxonomic status of P. lighti, which was consistent with the traditional taxonomy.

Sequencing and analysis of the complete mitochondrial genome of the Ussuri shrew (Sorex mirabilis) from China

The complete mitogenome sequence of the Ussuri shrew (Sorex mirabilis) was determined using long PCR. The genome was 17,315 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.6%), C (25.2%), T (28.8%), and G (13.4%). 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 the Ussuri shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of the slender shrew (Sorex gracillimus) from China

The complete mitogenome sequence of the slender shrew (Sorex gracillimus) was determined using long PCR. The genome was 17,002 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.5%), C (25.5%), T (28.5%), and G (13.5%). 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 the slender shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of the masked shrew (Sorex caecutiens) from China

The complete mitogenome sequence of the masked shrew (Sorex caecutiens) was determined using long PCR. The genome was 17,096 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.9%), C (24.5%), T (29.3%), 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 the masked shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of flat-skulled shrew (Sorex roboratus) from China

The complete mitogenome sequence of flat-skulled shrew (Sorex roboratus) was determined using long PCR. The genome was 17,153 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 is A (33.1%), C (24.4%), T (29.4%), and G (13.1%). 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 flat-skulled shrew. Mitochondrial genome analyses based on MP, ML, NJ and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

The complete mitochondrial genome of Pholis nebulosus (Perciformes: Pholidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Pholis nebulosus has been determined by long polymerase chain reaction and primer-walking methods. The mitogenome is a circular molecule of 16 524 bp in length, including the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions (L-strand replication origin and control region), the gene contents of which are identical to those observed in most bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), and the conserved sequence block domain (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B, CSB-A, CSB-1, CSB-2, CSB-3).

The complete mitochondrial genome of Thryssa kammalensis (Clupeiformes: Engraulidae)

In this study, the complete mitochondrial genome (mitogenome) sequence of Thryssa kammalensis has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16 968 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, two ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence (TAS) domain, the central conserved sequence block domains (CSB-F, CSB-E and CSB-D) and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3). There are eight copies of tandem repeats of 38 bp in the control region, which contain TAS.

Complete mitochondrial DNA sequence of the endangered fish (Bahaba taipingensis): Mitogenome characterization and phylogenetic implications.

To understand the systematic status of Bahaba taipingensis within Sciaenidae, the complete mitochondrial genome (mitogenome) sequence of Chinese bahaba has recently been determined by long PCR and primer walking methods. The complete mitochondrial genome is 16500 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes) as well as a control region (CR) as other bony fishes. Within the control region, we identified the extended termination associated sequence domain (ETAS), the central conserved sequence block domain (CSB-D, SCB-E and CSB-F) and the conserved sequence block domain (CSB-1, CSB-2 and CSB-3). Phylogenetic analyses revealed that Bahaba taipingensis is more closely related to Pseudosciaeniae than Argyrosominae and Sciaeninae. Additionally, Bahaba taipingensis is the sister taxon of Miichthys miiuy, and those two are sister to Collichthys plus Larimichthys.

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 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).

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.