Total Nucleotide Composition Research Articles

The complete mitochondrial genome of the spotted knifejaw Oplegnathus punctatus

In this study, the mitochondrial genome was sequenced in a new commercial species, spotted knifejaw (O. punctatus), using next-generation sequencing and PCR-based methods. The overall length of the female O. punctatus mitochondrial genome was 16,508 bp. It contained 13 PCGs, 2 r-RNA genes, 22 t-RNA genes, and a displacement loop locus (a control region). The total nucleotide composition was 28.75% A, 25.69% T, 29.70% C, and 15.86% G, with a total A + T content of 54.44%. The results demonstrated that the mitochondrial genome of O. punctatus has a high sequence identity with that of another species of Perciformes. This finding provides a deeper understanding of mitogenomic diversity and evolution in marine fish.

Normalized Multipotential Redox Coding of DNA Bases for Determination of Total Nucleotide Composition.

The previously reported approach of orthogonal multipotential redox coding of all four DNA bases allowed only analysis of the relative nucleotide composition of short DNA stretches. Here, we present two methods for normalization of the electrochemical readout to facilitate the determination of the total nucleotide composition. The first method is based on the presence or absence of an internal standard of 7-deaza-2'-deoxyguanosine in a DNA primer. The exact composition of the DNA was elucidated upon two parallel analyses and the subtraction of the electrochemical signal intensities. The second approach took advantage of a 5'-viologen modified primer, with this fifth orthogonal redox label acting as a reference for signal normalization, thus allowing accurate electrochemical sequence analysis in a single read. Both approaches were tested using various sequences, and the voltammetric signals obtained were normalized using either the internal standard or the reference label and demonstrated to be in perfect agreement with the actual nucleotide composition, highlighting the potential for targeted DNA sequence analysis.

The first complete plastome of Chimonobambusa quadrangularis (Fenzl) Makino: assembly, annotation and phylogenetic analysis

Chimonobambusa quadrangularis (Fenzl) Makino is one of the ‘Square Bamboo’ due to its square-shaped culm. However, as an edible bamboo, there is no genomic information reported so far. In this study, we reported and characterized the first plastome of C. quadrangularis based on Illumina Hiseq sequencing. The plastome exhibited a typical angiosperm circular structure, containing four regions: large single-copy region (LSC: 83,125 bp), small single-copy region (SSC: 12,811 bp), and a pair of inverted repeat regions (IR: 21,802 bp). The plastome consisted of 139,540 bp in size, with 82 protein-coding genes, 39 tRNA genes, and eight rRNA genes. The total nucleotide composition consisted of 30.16% A, 30.97% T, 19.25% C, and 19.63% G. The G + C content of the whole plastome was 38.88%. Phylogenetic analysis based on the complete plastomes of six species indicated that C. quadrangularis was closed to C. hejiangensis. The plastome is helpful for studying the evolution of beneficial adaptations and developing bioremediation and biomedical science.

The complete mitochondrial genome of the chocolate chip sea cucumber Isostichopus badionotus (Echinodermata: Holothuroidea)

The chocolate chip sea cucumber, Isostichopus badionotus (Selenka 1867), is an ecologically and biomedically important species. In this study, we report the complete mitogenome sequence of the sea cucumber, I. badionotus (Echinodermata: Holothuroidea). The mitochondrial genome consisted of 16,319 bp, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The total nucleotide composition consisted of 31.61% A, 29.20% T, 23.48% C, 15.71% G, with a high A + T content of 60.81%. Phylogenetic analysis using the complete mitochondrial genome of I. badionotus is helpful in studying the evolution of beneficial adaptations to aid in bioremediation and biomedical research and development.

Characterization of the complete mitochondrial genome of the Macaroni penguin Eudyptes chrysolophus from the Barton Peninsula, King George Island, Antarctica

The Macaroni penguin Eudyptes chrysolophus is a small crested penguin. In this study, the complete mitochondrial genome of E. chrysolophus is revealed for the first time. The mitogenome sequence is circular and 17,059 bp in length. It contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes similar to other Spheniscidae species. The total nucleotide composition is 30.53% (A), 32.86% (C), 13.96% (G), and 22.66% (T), and 46.81% for overall GC contents. The phylogenetic analysis shows a close relationship between E. chrysolophus and E. schlegeli. Our findings would be useful for further studies on phylogenetics and evolutionary history of the genus Eudyptes.

Characterization of the complete mitochondrial genome of Chrysochir aureus and phylogenetic studies of Sciaenidae

The complete mitochondrial genome of Chrysochir aureus was sequenced. The full length of the mitochondrial genome was 16,501 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.95% A, 29.99% C, 26.29% T, and 16.77% G. Twelve PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of C. aureus described in this study could be a useful basis for management of this species and laid a foundation for further research involved with phylogenetic relationship within Sciaenidae.

Characterization of the complete mitochondrial genome of Ilisha striatula (Clupeiformes, Pristigasteridae) and phylogenetic studies of Clupeiformes

In this study, the complete mitochondrial genome of Ilisha striatula is presented, and we also discussed its mitochondrial characteristics. The full length of the mitochondrial genome was 16,847 bp, including 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNA genes, one non-coding control region (CR), and one origin of replication on the light-strand. The total nucleotide composition of the mitochondrial genome was 31.11% A, 24.62% T, 29.10% C, 15.16% G, and AT was 55.73%. The phylogenetic tree based on the ML method supported the placement of I. striatula in a close relationship with I. elongata. These data contribute to a better understanding of the systematics of the Pristigasteridae.

Characterization of the complete mitochondrial genome of Ostorhinchus novemfasciatus and phylogenetic studies of Apogoninae

The complete mitochondrial genome of Ostorhinchus novemfasciatus was first presented in this study. The full length of the mitochondrial genome was 16,779 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.0% A, 30.2% C, 26.2% T and 17.5% G. 12 PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of O. novemfasciatus described in this study could be a useful basis for the management of this species and laid a foundation for further research involved with phylogenetic relationship within Apogoninae.

The complete mitochondrial genome of Acanthogobius stigmothonus (Perciformes, Gobiidae)

The complete mitochondrial genome of Acanthogobius stigmothonus is first sequenced in this study. This genome was 16,666 bp in size and contained 37 classic genes, including 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. The gene organization and nucleotide composition were the same with those found in most other Gobiidae fishes. Among 37 genes, 28 were encoded by the heavy strand, while nine were encoded by the light strand. The total nucleotide composition of this genome was 27.4% for adenine (A), 17.6% for guanine (G), 28.2% for cytosine (C), and 26.8% for thymine (T), with a high A + T content of 54.2%. This study will provide a better understanding of population genetic diversity of A. stigmothonus and offer useful information for future studies concerning Gobiidae mitogenome evolution.

Characterization of the complete mitochondrial genome of Hyphessobrycon herbertaxelrodi (Characiformes, Characidae) and phylogenetic studies of Characiformes

In this study, the complete mitochondrial genome of Hyphessobrycon herbertaxelrodi is presented, and we also discussed its mitochondrial characteristics. The full length of the mitochondrial genome was 17,417 bp, including 13 protein coding genes (PCGs), 2 ribosomal RNAs (12S and 16S), 22 transfer RNA genes, 1 non-coding control region (D-loop), and 1 origin of replication on the light-strand. The total nucleotide composition of mitochondrial DNA was 29.76%A, 29.88%T, 25.35%C, 15.01%G, and AT was 59.64%. The phylogenetic tree suggested that H. herbertaxelrodi shared the most recent common ancestor with Astyanax giton, Grundulus bogotensis, Astyanax paranae, and Oligosarcus argenteus.

The whole mitochondrial genome of Sarcophaga kanoi (Diptera: Sarcophagidae)

Sarcophaga kanoi Park, 1962, a widely distributed flesh fly in Southeast Asia, is important in forensic entomology. Notably, its mitochondrial genome could provide the unique and accurate molecular information in species identification which facilitate forensic practices in estimation of postmortem interval especially in putrefied cadaver cases. Thus, we sequenced and characterized the whole mitochondrial genome (mitogenome) of S. kanoi for the first time, which was collected from Southern China in this study. The 15,319 bp mitogenome contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and a putative control region. The total nucleotide composition of this circular genome was 39.7% for A, 9.3% for G, 14.2% for C, and 36.8% for T. To better understand the genetic relationship, the phylogenetic analysis was constructed according to the 13 PCGs sequence of S. kanoi and other 11 species. The phylogenetic tree showed that the S. kanoi was placed in a sub-clade with S. similis. Our study updated the new genetic information for dipteran mitogenomes, which could broaden the background knowledge for forensic entomology, molecular genetics and developmental biology. It has the potential application on the species identification using genetic markers.

Characterization of the complete mitochondrial genome of Chinese Konosirus punctatus (Clupeiformes, Clupeidae) and phylogenetic studies of Clupeiformes

The Dotted Gizzard Shad (Konosirus punctatus) was one of the most important commercial fish species in China, Japan and Korea. In this study, the complete mitochondrial genome of K. punctatus was presented. The full length of the mitochondrial genome was 16,705 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, one non-coding control region (CR) and one origin of replication on the light-strand. The total nucleotide composition of mitochondrial DNA was 25.79%A, 25.09%T, 29.05%C, 20.08%G, and AT was 50.88%. The mitochondrial genome provides an important resource for solving taxonomic problems and studying molecular evolution.

The complete mitochondrial genome of Lasiopodomys brandtii

In this study, the complete mitochondrial (mt) genome sequence of Lasiopodomys brandtii was determined using Illumina NovaSeq platform. The assembled genome was 16,557 bp in length and included 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. The total nucleotide composition frequencies present clearly the A-T skew (59.5%), which mostly in D-loop and PCGs regions. Whole mt genome phylogenetic analysis revealed a closely related among Lasiopodomys, Proedromys, and Microtus with high support. It would provide further evolutionary research for the subfamily Arvicolinae.

Identification of the complete mitochondrial genome of the king penguin Aptenodytes patagonicus (Sphenisciformes: Spheniscidae: Aptenodytes)

The complete mitochondrial genome of the king penguin Aptenodytes patagonicus was firstly determined. The mitogenome is 17,477 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The total nucleotide composition is 31.0% A, 22.2% T, 33.1% C, and 13.8% G, with a total A + T content of 53.2%. The phylogenetic analysis demonstrates a close relationship between A. patagonicus and A. forsteri. These results provide fundamental information for further phylogeny and genetic studies on Aptenodytes genus.

The complete mitochondrial genome of Opisthotropis latouchii (Squamata: Colubridae)

Opisthotropis latouchii is an endemic species which inhabits flowing streams in China. In this study, the complete mitochondrial genome of O. latouchii was determined using high-throughput sequencing data. The mitogenome was 17,051 bp in length and contained 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 2 control regions. The total nucleotide composition was 34.09% A, 25.35% T, 27.39% C, and 13.16% T, respectively. The phylogenetic analysis showed that O. latouchii was closely related with Nerodia sipedon in Colubridae.

Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas.

The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.

Identification of the complete mitochondrial genome of Garra pingi pingi (Cypriniformes, Cyprinidae)

Garra pingi pingi, an endemic species to China, is mainly distributed in the upper Yangtze River and its tributaries. In present study, the complete mitochondrial genome of G. pingi pingi was first determined using the next-generation sequencing technology and annotated using bioinformatic tools. The circular mitochondrial genome was 16,599 bp long, contained 13 protein-coding genes, 2 ribosomal RNA genes (rRNA), 22 transfer RNA (tRNA) genes, an origin of light-strand replication (OL) and one displacement loop locus (D-loop). Most mitochondrial genes were encoded on the heavy strand, except for ND6 and eight tRNA genes. The total nucleotide composition was 31.48% A, 25.79% T, 26.66% C, 16.07% G, with 57.27% AT, respectively. Phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences indicated that G. pingi pingi showed a close relationship with G. imberba. These data provide fundamental information not only for unravelling the population structure and differentiation, but also for further conservation genetics studies on Labeonini species.

Isolation and characterization of the complete mitochondrial genome of Taenioides anguillaris (Gobiidae: Amblyopinae) with phylogenetic consideration

Here we first isolated and characterized the complete mitochondrial genome DNA of Taenioides anguillaris. It was 16 974 bp in length, and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a putative control region. The structure and the gene arrangement of this genome were identical to those isolated from other Gobiidae fishes. Twenty-eight genes were encoded by heavy strand, while nine genes were encoded by light strand. The total nucleotide composition of this genome was 28.7% for A, 15.6% for G, 28.6% for C, and 27.1% for T, with a high A + T content of 55.8%. From the neighbor-joining (NJ) phylogenetic tree, we can find that T. anguillaris was genetically closest to species Odontamblyopus rubicundus among 20 species within suborder Gobioidei. This work should be helpful for the studies on population genetic diversity and molecular evolution in T. anguillaris and related fish species.

The complete mitochondrial genome sequence and gene organization of Amblychaeturichthys hexanema (Gobiidae: Amblychaeturichthys) with phylogenetic consideration

We sequenced and characterized the complete mitochondrial genome of Amblychaeturichthys hexanema and uncovered its molecular phylogenetic relationship. This genome was 18 642 bp in size, and contained 37 classic genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The gene organization and nucleotide composition were the same with those found in most other Gobiidae fishes. In contrast, gene NADH 6 was obviously larger than the same gene identified from other Gobiidae species. Two big repeat regions were detected on both sides of D-loop region. The A + T content (71.2%) of D-loop region was higher than any other region in this genome. Among 37 genes, 28 were encoded by the heavy strand, while nine were encoded by the light strand. The total nucleotide composition of this genome was 28.6% for A, 15.8% for G, 27.2% for C, and 28.3% for T, with a high A + T content of 56.9%. Phylogeny analysis of 22 fish species within Gobioidei showed that A. hexanema and Chaeturichthys stigmatias first formed a single cluster, then they together with other 17 species grouped a big branch. This work should be helpful for the studies on population genetic diversity and molecular evolution of Gobiidae fish species.

Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.)

Micro-RNAs (miRNA) are regulatory non-coding class of small RNAs functioning in many organisms. Using computational approaches we have identified 20 conserved opium poppy (Papaver somniferum L.) miRNAs belonging to 16 miRNA families in Expressed Sequence Tags (EST) database. The existence of ESTs suggested that the miRNAs were expressed in P. somniferum. Lengths of mature miRNAs varied from 20 to 23 nucleotides located at the different positions of precursor RNAs. Uracil was found to be a dominant nucleotide in both poppy pre-miRNA sequences (31.28 +/- 7.06% of total nucleotide composition) and in the first position at the 5' end of the mature poppy miRNAs. We have applied quantitative real-time PCR (qRT-PCR) assays to compare and validate expression levels of selected P. somniferum miRNAs and their target transcripts. As a result, some of the predicted miRNAs and their target genes were found to be differentially expressed in P. somniferum leaf and root tissues. A meaningful correlation between three of the four analyzed pairs of miRNAs and their target transcript expression levels was detected. Additionally, using these predicted miRNAs as queries, 41 potential target mRNAs were found in National Center for Biotechnology Information (NCBI) protein-coding nucleotide (mRNA) database of all plant species. Some of the target mRNAs were found to be transcription factors regulating plant development, morphology, and flowering time. Other target mRNAs of identified conserved miRNAs involve in metabolic processes, signal transduction, and stress responses. This study reports the first identification of opium poppy miRNAs.