Putative Control Region Research Articles

The mitochondrial genome of the assassin bug Sclomina erinacea (Hemiptera: Reduviidae)

The complete mitochondrial genome (mitogenome) of the assassin bug, Sclomina erinacea Stål, was determined in the present study. The sequenced mitogenome is a typical circular DNA molecule which is 15,828 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a putative control region. All protein-coding genes are initiated by ATN codons and terminated by TAA or TAG codons except COII, COIII and ND4 which use a single T residue as the stop codon. All tRNAs have the cloverleaf structure with the exception of tRNASer(AGN) and the length of them range from 62 to 70 bp. The control region is 818 bp long with an A + T content of 67.1%. The phylogenetic analysis supports the monophyly of Harpactorinae and Sclomina erinacea is the closest relative to Macracanthopsis nodipes.

The complete mitochondrial genome of Helan Mountain chukar Alectoris chukar potanini (Galliformes: Phasianidae)

The complete mitochondrial genome of Helan Mountain chukar (Alectoris chukar potanini) was first determined. The genome was 16,685 bp in length, comprising 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a putative control region. The phylogenetic analysis based on the complete mitochondrial genome sequences revealed a close relationship between A. chukar potanini and Tetraogallus tibetanus. This work is expected to provide a set of fundamental data on further genetic studies of this protected species.

Complete mitochondrial genome of the marine mysid Siriella sp. (Crustacea, Mysida, Mysidae)

The complete mitochondrial genome of the marine mysid, Siriella sp. was obtained by conventional polymerase chain reaction (PCR) method. Total length of Siriella sp. mitochondrial genome was 14,706 bp, with the base composition of 27% A, 21% C, 22% G, and 30% T with a high AT bias of 57%. The mitogenome of Siriella sp. contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative control region. Maximum likelihood method-based phylogenetic reconstruction suggested the evolutionary relationship to other mysids within the order Mysida. Since Mysida contains numerous species across a wide range of water habitats, this information will provide an essential molecular reference to elucidate biogeography, phylogenetic distance, and evolutionary diversity in mysids. This is the first mitogenome information in the genus Siriella.

The complete mitochondrial genome of Thalassoma lunare (Labriformes, Labridae)

Thalassoma lunare is one of most important genera of Labridae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of T. lunare. The mitogenome has 17,073 base pairs (57.7% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study will provide useful genetic information for future phylogenetic and taxonomic classification of Labridae.

Complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Crustacea: Decapoda: Pandalidae) in Korean water

The complete mitochondrial genome of green shrimp, Chlorotocus crassicornis (Costa, 1871) was generated by the combination of next-generation sequencing platform and long PCR technique. The mitochondrial genome of C. crassicornis was 16,500 bp, in which 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a putative control region was encoded. Based on the 13 protein-coding genes region, the phylogenetic tree was clearly demonstrated that C. crassicornis is closest to Pandalopsis japonica and Pandalus borealis with 77% identity. This mitogenome information will be helpful for the further studies of deep-sea fisheries resources management strategies in Korea including C. crassicornis species.

Phylogenetic analysis of the complete mitochondrial genome of Orestias ascotanensis (Cyprinodontiformes, Cyprinodontidae)

The complete mitochondrial genome of this species was first determined in this study, which is 16,617 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, a putative control region, and 1 origin of replication on the light-strand. The overall base composition includes C(27.11%), A(26.68%), T(29.15%), G(17.04%) and three degenerate bases are R, R and S. Moreover, the 13 PCGs encode 3800 amino acids in total, 12 of which use the initiation codon ATG except COI that uses GTG. Most of them have TAA as the stop codon, whereas ND5 ends with AGA, four protein-coding genes (ND1, ND2, ND3 and Cytb) ended with TAG, and two protein-coding genes (COII and ND4) ended with the incomplete stop codon represented as a single T. The phylogenetic tree based on the Neighbor Joining method was constructed to provide relationship within Cyprinodontidae, which could be a useful basis for management of this species.

Characterization of the complete mitochondrial genome of Purpuricenus temminckii (Coleoptera: Cerambycidae)

The complete mitochondrial genome of Purpuricenus temminckii (GenBank accession number MN527358) is 15,689 bp in length, and contains 13 protein-coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes, and a putative control region. The overall base composition is A (39.56%), C (17.52%), G (10.90%), and T (32.02%), with a high AT bias of 71.58%. All tRNAs have the typical cloverleaf structure except for trnS1 and the length of them range from 62 to 71 bp. Phylogenetic tree showed that P. temminckii was clustered with three Cerambycidae species, which agree with the traditional classification.

The complete mitochondrial genome of sea cucumber Stichopus monotuberculatus (aspidochirotida: Stichopodidae)

The sea cucumber, Stichopus monotuberculatus, is an economically important holothuroid in China due to its larger body size and valuable nutrition. However, the taxonomic revision studies of Stichopodidae have been one of the most controversial issues in recent years. Moreover, there remain considerable doubts about a complex of cryptic species within S. monotuberculatus. In this study, we report the complete mitochondrial genome of S. monotuberculatus. The mitogenome has 16,274 base pairs (60.4% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study adds one more available complete mitogenomes of Stichopus and will provide useful genetic information for future evolutionary and taxonomic classification of Stichopodidae.

The complete mitochondrial genome of the jewel beetle Coraebus cavifrons (Coleoptera: Buprestidae)

The complete mitochondrial genome (mitogenome) of the jewel beetle, Coraebus cavifrons, was sequenced and described in the present study. The mitogenome of Coraebus cavifrons is a typical circular DNA molecule of 15,686 bp. All of the 37 mitochondrial genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) were annotated and a putative control region with 1135 bp in length was found between tRNAIle and srRNA. Protein-coding genes all initiate with ATN codons except for COII uses GTG. Most of the protein-coding genes use TAA or TAG as the stop codon, but COII, COIII, and ND5 terminate with a single T. All tRNAs have the clover-leaf structure except for tRNASer(AGN) and the length of them range from 60 to 71 bp. Genome organization and nucleotide composition of the mitogenome were also noted. Our phylogenetic analysis of Elateriformia supported the monophyly of Buprestoidea and the sister relationship between Buprestoidea and (Byrrhoidea + Elateroidea).

The complete mitochondrial genome of bobo croaker Pseudotolithus elongatus (Perciformes: Sciaenidae)

The complete mitochondrial genome of Pseudotolithus elongatus (Perciformes: Sciaenidae) is determined based on NGS technology. The assembled mitogenome is a 16,497 bp in length containing a typical set of the 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and the 1 putative control region. The overall base composition is A (27.8%), T (25.3%), G (16.1%), and C (30.8%) with an A-T content of 53.1%. The phylogenetic analysis of 36 mitogenomes from the GenBank indicated that P. elongatus is closely related to the Aplodinotus grunniens. This mitogenome information of the P. elongatus would be useful to understand evolutionary and phylogenetic analysis of the family Sciaenidae fishes.

The complete mitochondrial genome of a grasshopper endemic to the Qinghai-Tibet plateau, Uvaroviola multispinosa (Acrididae: Oedipodinae)

The grasshopper Uvaroviola multispinosa (Acrididae: Oedipodinae), is an agricultural pest to pasture and limitedly distributed in Qinghai-Tibet plateau of China. The complete mitochondrial genome of U. multispinosa is 15,620 bp long, which comprises of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA (tRNA) genes and a putative non-coding control region (GenBank accession ID: MK829651). These genes are unequally distributed on different DNA chains, which 23 are located on the majority Chain. The nucleotide composition shows evidently bias (A, C, G, and T was 43.8, 14.8, 10.1, and 31.3%, respectively) with an overall AT content of 75.2%. All PCGs are initiated by ATN codons, among them ATG is the most preferred. Eleven PCGs use a common stop codon of TAA or TAG, whereas the remaining two were terminated with single T as incomplete stop codon. The phylogenetic relationships based on Bayes method showed that U. multispinosa is closely related to Compsorhipis davidiana, which is in accordance with its traditional morphological classification.

The insulin-like growth factor 2 gene in mammals: Organizational complexity within a conserved locus.

The secreted protein, insulin-like growth factor 2 (IGF2), plays a central role in fetal and prenatal growth and development, and is regulated at the genetic level by parental imprinting, being expressed predominantly from the paternally derived chromosome in mice and humans. Here, IGF2/Igf2 and its locus has been examined in 19 mammals from 13 orders spanning ~166 million years of evolutionary development. By using human or mouse DNA segments as queries in genome analyses, and by assessing gene expression using RNA-sequencing libraries, more complexity was identified within IGF2/Igf2 than was annotated previously. Multiple potential 5’ non-coding exons were mapped in most mammals and are presumably linked to distinct IGF2/Igf2 promoters, as shown for several species by interrogating RNA-sequencing libraries. DNA similarity was highest in IGF2/Igf2 coding exons; yet, even though the mature IGF2 protein was conserved, versions of 67 or 70 residues are produced secondary to species-specific maintenance of alternative RNA splicing at a variable intron-exon junction. Adjacent H19 was more divergent than IGF2/Igf2, as expected in a gene for a noncoding RNA, and was identified in only 10/19 species. These results show that common features, including those defining IGF2/Igf2 coding and several non-coding exons, were likely present at the onset of the mammalian radiation, but that others, such as a putative imprinting control region 5’ to H19 and potential enhancer elements 3’ to H19, diversified with speciation. This study also demonstrates that careful analysis of genomic and gene expression repositories can provide new insights into gene structure and regulation.

Deep transcriptome profiling sheds light on key players in nucleus implantation induced immune response in the pearl oyster Pinctada martensii

Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Here we determined the complete mitogenome sequence of Chiromantes eulimene (Brachyura: Sesarmidae) for the first time. The total length is 15,894 bp and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, as well as a putative control region. The genome composition is highly A + T biased (75.5%), and exhibits a negative AT-skew (−0.017) and GC-skew (−0.206). All of the 13 PCGs are initiated by the start codon ATN, with an exception (GTG) in ND1. The typical stop codon (TAA or TAG) is detected in ten PCGs, whereas the remaining three PCGs (COI, COII and Cyt b) terminate by an incomplete T. The gene order in C. eulimene mitogenome was rearranged compared with that of the ancestor of Decapoda. The gene order of F-ND5-H changed to H-F-ND5. Like other sesarmid crabs, the I-Q-M gene cluster in the pancrustacean ground pattern became Q-I-M order in C. eulimene genome. Tandem duplication-random loss model and slipped-strand mispairing mechanism are determined as most likely to explain the observed gene rearrangements. Phylogenetic analysis places all Sesarmidae species into one group. Almost all families except Xanthidae, Gecarcinidae and Homolidae form a monophyletic clade and the polyphyly of Eriphioidea, Ocypodoidea and Grapsoidea is well supported. These results will help to better understand the gene rearrangements and evolutionary position of C. eulimene and lay a foundation for further phylogenetic studies of Brachyura.

Comparative analyses of the three complete mitochondrial genomes from forensic important beetle genus Dermestes with phylogenetic relationships

Necrophagous Dermestes species have high forensic importance in relation to the estimation of elapsed time since death or death season. To further supplement the genome-level features for related species, the complete mitochondrial genome (mitogenome) of Dermestes species D. essellatocollis, D. frischii and D. coarctatus are amplified, sequenced, annotated, analyzed, and compared with other twelve species of the infraorder Bostrichoidea. The mitochondrial genomes were typical circular molecules with 16,218, 15,873 and 15,873 bp in length, respectively. They included 13 protein coding genes, two rRNAs, and 22 tRNAs, as well as the putative control region. The gene orders and orientations are identical to those of other recorded bostrichiformian species and had the ancestral insect gene composition. Furthermore, phylogenetic analyses based on all the mitochondrial protein coding genes for 13 Bostrichoidea and 16 outgroup taxa were performed using Bayesian and Maximum Likelihood analyses. The inferred trees indicate that the genus Dermestes is monophyletic. The monophyly of infraorder Bostrichiformia is not supported. This study provides genomic data for mitochondrial genome library of the genus Dermestes to investigate evolutionary and systematic studies.

The Complete Mitochondrial Genome of Terapon jarbua (Centrarchiformes: Terapontidae) and Comparative Analysis of the Control Region among Eight Centrarchiformes Species

In this article, we determined and described the complete mitochondrial genome of Terapon jarbua, which is 16 664 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, one origin of replication on the light-strand (OL), and a putative control region (CR). The gene order and the base composition of T. jarbua mitogenome are similar to that of most other vertebrates. The overall base composition is 27.5% A, 26.0% T, 29.9% C, 16.6% G, respectively, with a slight AT bias (53.5%). All the protein-coding genes use the initiation codon ATG except COI use GTG. Most of them have TAA or TAG as the stop codon, except COII and ND4 use AGA, COIII and Cyt b use an incomplete stop codon TA and T, respectively. In order to further explore the structure of CR in Centrarchiformes, eight CR sequences from representative species were compared. Like that of other teleosts, the CR of the Centrarchiformes is also partitioned into three domains, including the termination associated sequence (TAS), the central conserved sequence blocks (CSB-E, D, B and A), and the conserved sequence blocks (CSB-2 and 3). We hope these results will provide consensus sequences of the conserved units of the CR in Centrarchiformes genomes, as well as useful molecular information for phylogenetic studies of Centrarchiformes.

The first complete mitochondrial genome of marigold pest thrips, Neohydatothrips samayunkur (Sericothripinae) and comparative analysis

Complete mitogenomes from the order Thysanoptera are limited to representatives of the subfamily Thripinae. Therefore, in the present study, we sequenced the mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome possesses the canonical 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs) as well as two putative control regions (CRs). The majority strand was 77.42% A + T content, and 22.58% G + C with weakly positive AT skew (0.04) and negative GC skew (−0.03). The majority of PCGs start with ATN codons as observed in other insect mitochondrial genomes. The GCG codon (Alanine) was not used in N. samayunkur. Most tRNAs have the typical cloverleaf secondary structure, however the DHU stem and loop were absent in trnV and trnS1, while the TΨC loop was absent in trnR and trnT. The two putative control regions (CR1 and CR2) show 99% sequence similarity indicated a possible duplication, and shared 57 bp repeats were identified. N. samayunkur showed extensive gene rearrangements, with 11 PCGs, 22 tRNAs, and two rRNAs translocated when compared to the ancestral insect. The gene trnL2 was separated from the ‘trnL2-cox2’ gene block, which is a conserved, ancestral gene order found in all previously sequenced thrips mitogenomes. Both maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees resulted in similar topologies. The phylogenetic position of N. samayunkur indicates that subfamily Sericothripinae is sister to subfamily Thripinae. More molecular data from different taxonomic groups is needed to understand thrips phylogeny and evolution.

Complete mitochondrial genome of the tomato leafminer Tuta absoluta (Lepidoptera: Gelechiidae)

The complete mitochondrial genome of the tomato leafminer Tuta absoluta was determined in this study. It is 15,290 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a putative control region. All the 13 PCGs were initiated with typical ATN start codons, except for cox1 with the CGA. These PCGs were terminated by the typical TAA codon or the incomplete T– – codon. The phylogenetic relationships based on neighbour-joining method revealed that T. absoluta is clustered with six Gelechiidae species, which agree with the conventional taxonomy.

Characterization of the complete mitochondrial genome of Pacific abalone Haliotis discus hannai

The complete mitochondrial genome of Pacific abalone Haliotis discus hannai, an economically valuable shellfish in China, was sequenced and analyzed. The mitogenome was 16,716 bp in length and contained 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a putative control region. The gene arrangement and orientation were identical with other Haliotis species. Phylogenetic tree was constructed based on 13 PCGs of 7 Haliotidae species to assess their phylogenetic relationship, the tree revealed that H. discus hannai was more closely to H. rufescens and H. iris.

Phylogenetic analysis of the complete mitochondrial genome of Dysomma anguillare (Anguilliformes, Synaphobranchidae)

The mitochondrial DNA (mtDNA) has been widely used as a suitable tool for phylogenetic studies among species, including molecular evolution, phylogenetics, population genetics, and comparative and evolutionary genomics. We described the complete mitogenome of Dysomma anguillare in this study. The mitogenome is 16,689 bp in length and contains 13 protein-coding genes (PCGs), 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and a putative control region (CR) and one origin of replication (OL) on the light-strand. Moreover, a phylogenetic tree based on the neighbor-joining method was constructed to explore the phylogenetic relationship of D. anguillare, which strongly supported it had the closest relationship with the Simenchelys parasitica. These results would provide comprehensive phylogenetic relationship within Gobionellinae and additional information for management for this species.

Characterization of complete mitochondrial genome of Evarcha coreana (Araneae: Salticidae)

The complete mitochondrial genome of a hunting spider Evarcha coreana was determined. The circular mitogenome is 14,333 bp in length (GenBank accession number MK381265), and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and a putative control region. The orientation and gene order of E. coreana are identical with other spider mitogenomes. The AT content of the overall base composition is 75.86%. Twenty-two genes were in the major strand and 15 genes were in minor strand. Five intergenic regions and 25 reading frame overlaps were found in the mitogenome of E. coreana. Seven tRNA genes lost the TΨC arm stems, whereas three tRNAs lacked the dihydrouracil (DHU) arm. The control region is 697 bp in length with an A + T content of 81.06%. ATA, ATT, TTA, and TTG were initiation codons, and TAA, TAG, and T were termination codons. Phylogenetic analysis was performed using 13 PCGs with other spiders of the family Salticidae and it was seen that E. coreana is closely related to Telamonia vlijmi and Plexippus paykulli.