tRNA Secondary Structures Research Articles

Characterization and phylogenetic analysis of the mitochondrial genome of Cylicostephanus longibursatus.

Cylicostephanus longibursatus is a common parasite in equine animals. Hosts infected by these nematodes might face disease or death. This study utilized next-generation sequencing technology to sequence the complete mitochondrial genome (mt genome) of C. longibursatus. Through bioinformatics techniques, the genomic base composition, codon usage, tRNA secondary structures, evolutionary relationships, and taxonomic status were analyzed. The results revealed that the mitochondrial genome of C. longibursatus is a double-stranded, 13,807-bp closed circular molecule with an AT content of 76.0%, indicating a clear preference for AT bases. The mitochondrial genome consisted of a total of 12 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 non-coding regions. Among the 12 protein-coding genes, TTG and ATT were the common start codons. TAA was the predominant termination codon, except for the ND3 and ND6 coding genes, and the COШ genes used TAG and "T" as termination codons, respectively. All tRNAs exhibited atypical clover-leaf secondary structures, except for tRNALys and tRNALeu2, where two tRNASer genes lacked DHU arms and DHU loops, tRNAmet lacked the TΨC-arm, tRNAIle lacked the TΨC-loop, and the remaining 16 tRNAs lacked the TΨC-arm and TΨC loop, which were substituted by the "TV-replacement loop". Phylogenetic analyses, based on the 12 protein-coding genes and utilizing maximum likelihood (ML) and Bayesian inference (BI) analyses, indicated that C. longibursatus did not form a monophyletic group with other Cylicostephanus but was instead more closely related to Cyathostomum. These research findings provide fundamental data for exploring the population classification and phylogeny of strongylid nematodes.

Mitochondrial tRNAAsn, tRNACys and tRNATyr encoding genes mutations landscape in colorectal cancer patient

The colorectal cancer (CRC) is one of the significant diseases implicated in high mortality rates in the world. Multi factors contributed in the cancer development and progression like tRNA encoding genes which have been linked with colorectal cancer. The present study aimed to report Mitochondrial tRNAAsn, tRNACys and tRNATyr encoding genes mutations landscape in colorectal cancer patients. A case control design depended on using PCR-sequencing of mtDNA region consisting of three tRNA genes. Data analysis was implemented using multiple alignment seq, tRNA secondary structure construction and phylogenic tree construction. The results showed that one case (female) was 25 years old and cancer stage T3N1MX has shown 6 mutations in tRNAAsn and 3 mutations in both tRNACys and tRNATyr while other samples did not show variations in the patients and control groups. The secondary structure of varied tRNAAsn, tRNACys and tRNATyr in this case might have been affected. The phylogenetic tree showed the conservative sequence of all CRC patients except the case that has a single cluster. The present finding concluded that there was non-association between tRNAAsn, tRNACys and tRNATyr encoding genes in mtDNA with colorectal cancer. One patient has mutations in tRNAs that may be affected in tRNA secondary structure and may be contributed for cancer progression.

Mitochondrial Genome Characteristics and Phylogenetic Analysis of Fulmekiola serrata (Kobus) (Thysanoptera: Thripidae)

Sugarcane thrips, Fulmekiola serrata (Kobus) (Thysanoptera: Thripidae), is a common foliar pest that infests sugarcane and is found throughout tropical and subtropical countries. In this study, we obtained and analyzed the complete mitochondrial genome of F. serrata for the first time and explored the phylogenetic relationships of the higher-order elements of Thysanoptera members at the mitochondrial level. The complete mitochondrial genome of F. serrata is 16,596 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 1 noncoding control region. A+T accounted for 75% of the total bases in the mitochondrial genome of F. serrata, revealing an obvious AT bias. Among the 13 PCGs, except for nad5, which had a start codon of TTG, the remaining genes had ATNs typical of insects (ATA, ATT, ATC, and ATG); nad1, nad2, nad3, and atp8 had incomplete termination codons of TA or T. The remaining nine PCGs were complete with the termination codon TAA. Of the 22 tRNA secondary structures, all were typical cloverleaf secondary structures except for trnS1, which was missing the DHU arm. Compared with the hypothetical ancestral gene arrangement of arthropods, F. serrata presented extensive gene rearrangement, with 23 translocated genes, 8 inverted genes, and 5 shuffled genes. Both maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees resulted in similar topologies: ((Thripidae + (Stenurothripidae + Aeolothripidae)) + Phlaeothripidae), with Thripidae, Aeolothripidae and Phlaeothripidae being monophyletic groups, whereas F. serrata is closely related to Thrips palmi, and the two are sister groups.

Complete mitochondrial genome of the terrestrial isopod Cubaris murina Brandt, 1833: new family gene order and novel tRNA secondary structures

ABSTRACT Among isopods (order Isopoda), species belonging to the suborder Oniscidea are the most successful colonisers of terrestrial habitats and the largest family in this order is Armadillidae. In this study, the complete mitochondrial genome of an armadillid isopod, Cubaris murina, was assembled and characterised in detail for the first time. The gene order and secondary structure of transfer RNA (tRNA) genes were compared among isopods. The 14,212-bp-long mitogenome consists of 13 protein-coding genes, 20 tRNAs, two ribosomal RNAs, and four non-coding regions (NCRs), each longer than 100 bp. Two tRNA genes (trnG and trnI) were missing and several other tRNA genes exhibited secondary structures that departed from the typical cloverleaf pattern. Deletions and nucleotide insertions in the T- and D-arms and mismatches in the acceptor stem were commonly observed in these tRNAs. Notably, the mitogenome of C. murina exhibited a new gene order containing four tRNA rearrangements, and differences in the location of the NCRs were detected when compared to those reported for other isopods, including oniscid species. Interestingly, the second NCR had a similar number of secondary structures and repetitive elements to those reported in the control region of other crustaceans. The novel gene order, tRNA secondary structures, and NCR organisation reported herein for the mitogenome of C. murina confirms the hyper-variability of mitochondrial genomes in isopods. This study is the first to characterise in detail the mitogenome of the invasive isopod C. murina, belonging to the species-rich family Armadillidae within the Isopoda, and advances our understanding of mitochondrial genome architecture in isopods.

First complete mitochondrial genome of Pselliophora (Diptera, Tipulidae): genome description and phylogenetic implications

Pselliophora is widely distributed in Eurasia and China. To explore the characteristics of the mitogenome of Pselliophora and reveal phylogenetic relationships, the mitogenome of Pselliophora bifascipennis Brunetti, 1911 was sequenced and annotated. This is the first complete mitochondrial genome in this genus. Its mitogenome is 15821 bp in length, containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Nucleotide compositions of its whole mitogenome are 39.09% for A, 38.49% for T, 13.42% for C, and 9.01% for G. Consistent with previous observations of Tipulidae species, the mitogenome of Pselliophora bifascipennis is highly conserved in gene size, organization and codon usage, and secondary structures of tRNAs. Most tRNAs have the typical clover-leaf structure. The control region is 1006 bp long with an A + T content of 92.7%. Phylogenetic tree analysis using the sequences of the mitochondrial genomes of Pselliophora bifascipennis and other Tipulidae species showed that Pselliophora bifascipennis is closely related to Tanyptera hebeiensis. These two species are grouped on the same branch, which is in accordance with the traditional morphological classification. The results of this study lay a foundation for screening molecular markers of mitochondrion for molecular identification and genetic structure research in Tipulidae species.

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae).

Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.

Complete Mitogenome of "Pumpo" (Bos taurus), a Top Bull from a Peruvian Genetic Nucleus, and Its Phylogenetic Analysis.

The mitochondrial genome of Pumpo (Bos taurus), a prominent breed contributing to livestock farming, was sequenced using the Illumina HiSeq 2500 platform. Assembly and annotation of the mitochondrial genome were achieved through a multifaceted approach employing bioinformatics tools such as Trim Galore, SPAdes, and Geseq, followed by meticulous manual inspection. Additionally, analyses covering tRNA secondary structure and codon usage bias were conducted for comprehensive characterization. The 16,341 base pair mitochondrial genome comprises 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis places Pumpo within a clade predominantly composed of European cattle, reflecting its prevalence in Europe. This comprehensive study underscores the importance of mitochondrial genome analysis in understanding cattle evolution and highlights the potential of genetic improvement programs in livestock farming, thus contributing to enhanced livestock practices.

Molecular characterization of a novel Spiruromorpha species in wild Chinese pangolin by mitogenome sequence analysis.

Pangolins are susceptible to a variety of gastrointestinal nematodes due to their burrowing lifestyle and feeding habits, and few parasitic nematodes have been reported. Here, a Chinese pangolin with old wounds on its leg and tail was rescued from the Heyuan City, Guangdong Province. The cox1 and SSU rRNA of the worms from the intestine of the Chinese pangolin had the highest sequence identity of 89.58% and 97.95% to the species in the infraorder Spiruromorpha. The complete mitogenome of the worm was further assembled by next-generation sequencing, with a size of 13,708 bp and a GC content of 25.6%. The worm mitogenome had the highest sequence identity of 78.56% to that of Spirocerca lupi, sharing the same gene arrangement with S. lupi and some species in other families under Spiruromorpha. However, the mitogenome between the worm and S. lupi showed differences in codon usage of PCGs, sequences of NCR, and tRNA secondary structures. Phylogenetic analysis showed that the worm mitogenome was clustered with S. lupi in the family Thelaziidae to form a separate branch. However, it is still difficult to identify the worm in the family Thelaziidae because the species in the family Thelaziidae are confused, specifically S. lupi and Thelazia callipaeda in the family Thelaziidae were separated and grouped with species from other families. Thus, the parasitic nematode from the Chinese pangolin may be a novel species in Spiruromorpha and closely related to S. lupi. This study enriches the data on gastrointestinal nematodes in the Chinese pangolin.

Complete mitochondrial genomes of patients from Thailand with cardiovascular diseases.

Several previous studies have reported that both variation and haplogroups of mitochondrial (mt) DNA were associated with various kinds of diseases, including cardiovascular diseases, in different populations, but such studies have not been carried out in Thailand. Here, we sequenced complete mtDNA genomes from 82 patients diagnosed with three types of cardiovascular disease, i.e., Hypertrophic Cardiomyopathy (HCM) (n = 26), Long Q-T Syndrome (LQTS) (n = 7) and Brugada Syndrome (BrS) (n = 49) and compared these with 750 previously published mitogenome sequences from interviewed normal individuals as a control group. Both patient and control groups are from the same geographic region of northeastern Thailand. We found 9, 2, and 5 novel mutations that were not both damaging and deleterious in HCM, LQTS, and BrS patients, respectively. Haplogroup R9c was significantly associated with HCM (P = 0.0032; OR = 62.42; 95%CI = 6.892-903.4) while haplogroup M12b was significantly associated with LQTS (P = 0.0039; OR = 32.93; 95% CI = 5.784-199.6). None of the haplogroups was found to be significantly associated with BrS. A significantly higher density of mtDNA variants in the rRNA genes was found in patients with HCM and BrS (P < 0.001) than in those with LQTS or the control group. Effects of detected SNPs in either protein coding or tRNA genes of all the mitogenome sequences were also predicted. Interestingly, three SNPs in two tRNA genes (MT-TA m.5618T>C and m.5631G>A heteroplasmic variants in two BrS patients and MT-TQ m.4392C>T novel homoplasmic variant in a HCM patient) were predicted to alter tRNA secondary structure, possibly leading to abnormal tRNA function.

The Characterization and Phylogenetic Implications of the Mitochondrial Genomes of Antheminia varicornis and Carpocoris purpureipennis (Hemiptera: Pentatomidae)

The mitochondrial genome (mitogenome) has been widely used for structural comparisons and phylogenetic analyses of Hemiptera groups at different taxonomic levels. However, little is known about the mitogenomic characteristics of species from Antheminia and Carpocoris, two morphologically similar genera in the Pentatomidae family, and their phylogenetic relationships need to be further confirmed. In this study, the mitogenomes of Antheminia varicornis (Jakovlev, 1874) and Carpocoris purpureipennis (De Geer, 1773) were sequenced and analyzed. Coupled with previously published mitogenomes of Pentatomidae, we performed a phylogenetic analysis. The mitogenomes of A. varicornis and C. purpureipennis are conserved in terms of genomic structure, base composition, codon usage, and tRNA secondary structure. Each mitogenome contains the typical 37 genes and a control region and all genes are arranged in the same order as in the ancestral insect mitogenome. Nucleotide composition is highly biased with the third codon in PCGs displaying the highest A + T content. Phylogenetic analysis strongly supports the sister relationship between A. varicornis and C. purpureipennis. The phylogenetic trees show a strong support for the monophyly of Asopinae and Phyllocephalinae, while the monophyly of Pentatominae and Podopinae was rejected. Our study enriches the mitochondrial genome database of the genera Antheminia and Carpocoris and provides a valuable resource for further phylogenetic and evolutionary analyses of the Pentatomidae.

The First Complete Mitochondrial Genome of the Genus Pachycondyla (Formicidae, Ponerinae) and Insights into the Phylogeny of Ants.

Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the "poneroid" clade and the "formicoid" clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the "formicoid" clade.

Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes.

Some species of the Hyrcanus group are vectors of malaria in China. However, the member species are difficult to identify accurately by morphology. The development of sequencing technologies offers the possibility of further studies based on the complete mitochondrial genome. In this study, samples of mosquitoes of the Hyrcanus group were collected in China between 1997 and 2015. The mitochondrial genomes of ten species of the Hyrcanus group were analyzed, including the structure and base composition, codon usage, secondary structure of tRNA, and base difference sites in protein coding regions. Phylogenetic analyses using maximum-likelihood and Bayesian inference were performed based on mitochondrial genes and complete mitochondrial genomes The mitochondrial genome of 10 Hyrcanus group members ranged from 15,403 bp to 15,475 bp, with an average 78.23% (A + T) content, comprising of 13 PCGs (protein coding genes), 22 tRNAs, and 2 rRNAs. Site differences between some closely related species in the PCGs were small. There were only 36 variable sites between Anopheles sinensis and Anopheles belenrae for a variation ratio of 0.32% in all PCGs. The pairwise interspecies distance based on 13 PCGs was low, with an average of 0.04. A phylogenetic tree constructed with the 13 PCGs was consistent with the known evolutionary relationships. Some phylogenetic trees constructed by single coding regions (such as COI or ND4) or combined coding regions (COI + ND2 + ND4 + ND5 or ND2 + ND4) were consistent with the phylogenetic tree constructed using the 13 PCGs. The phylogenetic trees constructed using some coding genes (COII, ND5, tRNAs, 12S rRNA, and 16S rRNA) differed from the phylogenetic tree constructed using PCGs. The difference in mitochondrial genome sequences between An. sinensis and An. belenrae was very small, corresponding to intraspecies difference, suggesting that the species was in the process of differentiation. The combination of all 13 PCG sequences was demonstrated to be optimal for phylogenetic analysis in closely related species.

Correlation of mitochondrial tRNA variants with coronary heart disease in a Chinese pedigree

To explore the correlation of mitochondrial DNA (mtDNA) variants and coronary heart disease (CHD) in a Chinese pedigree and the possible molecular mechanisms. A Chinese pedigree featuring matrilineal inheritance of CHD who visited Hangzhou First People's Hospital in May 2022 was selected as the study subject. Clinical data of the proband and her affected relatives was collected. By sequencing the mtDNA of the proband and her pedigree members, candidate variants were identified through comparison with wild type mitochondrial genes. Conservative analysis among various species was conducted, and bioinformatics software was used to predict the impact of variants on the secondary structure of tRNA. Real-time PCR was carried out to determine the copy number of mtDNA, and a transmitochondrial cell line was established for analyzing the mitochondrial functions, including membrane potential and ATP level. This pedigree had contained thirty-two members from four generations. Among ten maternal members, four had CHD, which yielded a penetrance rate of 40%. Sequence analysis of proband and her matrilineal relatives revealed the presence of a novel m.4420A>T variant and a m.10463T>C variant, both of which were highly conserved among various species. Structurally, the m.4420A>T variant had occurred at position 22 in the D-arm of tRNAMet, which disrupted the 13T-22A base-pairing, while the m.10463T>C variant was located at position 67 in the acceptor arm of tRNAArg, a position critical for steady-state level of the tRNA. Functional analysis revealed that patients with the m.4420A>T and m.10463T>C variants exhibited much fewer copy number of mtDNA and lower mitochondrial membrane potential (MMP) and ATP contents (P < 0.05), which were decreased by approximately 50.47%, 39.6% and 47.4%, respectively. Mitochondrial tRNAMet 4420A>T and tRNAArg 10463T>C variants may underlay the maternally transmitted CHD in this pedigree, which had shown variation in mtDNA homogeneity, age of onset, clinical phenotype and other differences, suggesting that nuclear genes, environmental factors and mitochondrial genetic background have certain influence on the pathogenesis of CHD.

The mitochondrial genome of Heterosentis pseudobagri (Wang & Zhang, 1987) Pichelin & Cribb, 1999 reveals novel aspects of tRNA genes evolution in Acanthocephala

BackgroundAcanthocephala is a clade of obligate endoparasites whose mitochondrial genomes (mitogenomes) and evolution remain relatively poorly understood. Previous studies reported that atp8 is lacking from acanthocephalan mitogenomes, and that tRNA genes often have nonstandard structures. Heterosentis pseudobagri (Arhythmacanthidae) is an acanthocephalan fish endoparasite for which no molecular data are currently available, and biological information is unavailable in the English language. Furthermore, there are currently no mitogenomes available for Arhythmacanthidae.MethodsWe sequenced its mitogenome and transcriptome, and conducted comparative mitogenomic analyses with almost all available acanthocephalan mitogenomes.ResultsThe mitogenome had all genes encoded on the same strand and unique gene order in the dataset. Among the 12 protein-coding genes, several genes were highly divergent and annotated with difficulty. Moreover, several tRNA genes could not be identified automatically, so we had to identify them manually via a detailed comparison with orthologues. As common in acanthocephalans, some tRNAs lacked either the TWC arm or the DHU arm, but in several cases, we annotated tRNA genes only on the basis of the conserved narrow central segment comprising the anticodon, while the flanking 5’ and 3’ ends did not exhibit any resemblance to orthologues and they could not be folded into a tRNA secondary structure. We corroborated that these are not sequencing artefacts by assembling the mitogenome from transcriptomic data. Although this phenomenon was not observed in previous studies, our comparative analyses revealed the existence of highly divergent tRNAs in multiple acanthocephalan lineages.ConclusionsThese findings indicate either that multiple tRNA genes are non-functional or that (some) tRNA genes in (some) acanthocephalans might undergo extensive posttranscriptional tRNA processing which restores them to more conventional structures. It is necessary to sequence mitogenomes from yet unrepresented lineages and further explore the unusual patterns of tRNA evolution in Acanthocephala.

Comparative analysis of mitochondrial genomes reveals family-specific architectures and molecular features in scorpions (Arthropoda: Arachnida: Scorpiones)

Scorpions are a group of arachnids with great evolutionary success that comprise more than 2,000 described species. Mitochondrial genomes have been little studied in this clade. We describe and compare different scorpion mitochondrial genomes and analyze their architecture and molecular characteristics. We assembled eight new scorpion mitochondrial genomes from transcriptomic datasets, annotated them, predicted the secondary structures of tRNAs, and compared the nucleotide composition, codon usage, and relative synonymous codon usage of 16 complete scorpion mitochondrial genomes. Lastly, we provided a phylogeny based on all mitochondrial protein coding genes. We characterized the mitogenomes in detail and reported particularities such as dissimilar synteny in the family Buthidae compared to other scorpions, unusual tRNA secondary structures, and unconventional start and stop codons in all scorpions. Our comparative analysis revealed that scorpion mitochondrial genomes exhibit different architectures and features depending on taxonomic identity. We highlight the parvorder Buthida, particularly the family Buthidae, as it invariably exhibited different mitogenome features such as synteny, codon usage, and AT-skew compared to the parvorder Iurida that included the rest of the scorpion families we analyzed in this study. Our results provide a better understanding of the evolution of mitogenome features and phylogenetic relationships in scorpions.

Complete mitochondrial genome of Cyclopelta obscura (Lepeletier & Serville, 1825) (Hemiptera: Pentatomoidea: Dinidoridae) and phylogenetic analysis of Pentatomoidea species.

Cyclopelta obscura is a crop pest, which mainly damages legumes, especially Robinia pseudoacacia and Cercis chinensis. In recent years, many mitochondrial and nuclear DNA sequences of C. obscura have been sequenced and used for phylogenetic inference. However, the complete mitogenome has not been reported yet and studies on the phylogenetic relationships within Dinidoridae are rare. In this study, we sequenced the mitogenome of C. obscura and conducted comparative mitogenomic analyses of seven Dinidoridae species based on several different factors. The length of the mitogenome is 15,426 bp, which includes 37 typical mitochondrial genes (13 protein-coding genes (PCGs), 22 tRNAs, and 2 rRNAs) and a control region (796 bp long), as well as 13 intergenic spacers and 8 overlapping regions. Most PCGs of C. obscura began with the classical start codon ATN, while cox1 and nad4l used TTG, and nad1 used GTG. The Dinidoridae mitogenomes are highly conserved in terms of nucleotide composition, the codon usage of PCGs, and the secondary structure of tRNA. Phylogenetic analysis based on four datasets with two methods recovered the Dinidoridae as a monophyletic group with strong support values. All results indicate that Dinidoridae formed a sister group to Tessaratomidae, and (Tessaratomidae + Dinidoridae) formed a sister group to Cydnidae in most of the phylogenetic trees. Additionally, seven species within the Dinidoridae, we observed the following relationship: (Eumenotes sp. + (Cyclopelta parva + C. obscura)) + ((Megymenum gracilicorne + Megymenum brevicorne) + (Coridius chinensis + Coridius brunneu)).

Comparative analysis of tRNA genes in the mitochondrial genome of Parasitidae (Parasitiformes: Mesostigmata)

ABSTRACT The mitochondrial genome of Parasitus fimetorum was sequenced to study the Parasitidae tRNA gene secondary structure in Parasitiformes. tRNAscan-SE and ARWEN identified and inferred the secondary structures of 22 tRNA genes of Parasitus fimetorum, which were compared to 22 tRNA genes in sequenced Parasitidae mitochondrial genomes. The results showed that most tRNA genes of Parasitidae had a typical cloverleaf secondary structure; the base substitutions or mismatches occurred during the folding process, and the stem region showed less base variation than the loop region, showing high conservation. The base composition showed a clear preference for A + T. Relative synonymous codon usage (RSCU) analysis showed that the third codon of tRNA genes in Parasitidae species preferred to use codons that ended with A or U. ENC-plot analysis showed that most genes were distributed under the standard curve, indicating that codon usage in Parasitidae species was more influenced by natural selection pressure. Phylogenetic analysis showed that Parasitidae is a monophyletic group. This study complements the research on mitochondrial tRNA genes in Parasitidae, which has far-reaching implications for understanding the importance of tRNA gene sequences and secondary structures in comparative genomics and facilitates further studies on the evolution of species in the Parasitidae.

Comparative analysis and phylogeny of mitochondrial genomes of Pentatomidae (Hemiptera: Pentatomoidea).

The Phyllocephalini is a group of herbivorous insects in Pentatomidae, which lack distinctive morphological characteristics and systematic studies. Up to now, there are only two complete mitochondrial genomes of Phyllocephalini have been reported. In this study, we sequenced and analyzed the complete mitochondrial genomes of three Phyllocephalini species, Gonopsis coccinea, Gonopsimorpha nigrosignata, and Chalcopis glandulosus, which were 16,534, 16,531, and 16,534bp in length, respectively. The mitochondrial genomes contained 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region. The gene arrangement was consistent with that of the putative ancestral insect, with no rearrangement. The cox1 gene of Pentatomidae showed the lowest evolutionary rate among the protein-coding genes, the mean genetic distance of species, genera, and subfamilies of Pentatomidae increased hierarchically based on cox1 gene. The 16S rRNA of Pentatomidae was more conserved than 12S rRNA in sequence and secondary structure. All tRNAs could be folded into a typical cloverleaf structure except trnS1. The stem region was more conserved than the loop region in the secondary structure of tRNAs within Pentatomidae. Gonopsis coccinea and Gonopsimorpha nigrosignata had one type of tandem repetition unit in the control region, while C. glandulosus had two types. The heterogeneity analysis of Pentatomidae showed that Phyllocephalinae was the most heterogeneous. Phylogenetic trees based on the newly obtain mitochondrial genomes along with other 50 mitochondrial genomes of Pentatomidae using Bayesian Inference and Maximum Likelihood strongly supported the following three relationships: (((Anaxilaus + (Plautia + Glaucias)) + (Nezara + Palomena)) + (Eysarcorini + Carpocorini)), (Hoplistoderini + (Menidini + Asopinae)), and ((Sephelini + Halyini) + (Caystrini + (Cappaeini + (Placosternum + Phyllocephalini)))). The relationships within Phyllocephalini were (Chalcopis + (Dalsira + (Gonopsimorpha + Gonopsis))). Our results provide valuable molecular data for further phylogenetic analyses of Pentatomidae.

Evolution of small and large ribosomal RNAs from accretion of tRNA subelements

tRNAs presumably accreted into modern ribosomal RNAs. Previous analyses showed similar secondary structures for ancient rRNA subelements and theoretical minimal RNA rings, candidate tRNA ancestors rationally designed from tRNA-unrelated principles. Here, analyses test which tRNA secondary structure subelements resemble ancient/recent rRNA subelements. Results show that ribosomal RNA subelements evolved from structures resembling 1. Upper half part of the tRNA secondary structure; and 2. Towards structures resembling (a) tRNA 5′ stem-loop hairpins in large rRNA subunit and (b) tRNA lower half part in small rRNA subunit (stop and start codons conservation model). tRNAs and rRNAs presumably originated from the tRNA upper half part including the acceptor stem. Modern split 5′ and 3′ tRNA genes (spliced at anticodons) apparently reproduce ancestral-like states, because the acceptor stem protocode suggests acceptor stems evolved from spliced anticodon-like stem-loop hairpins, strengthening central roles for acceptor stem CCA-addition at translation origins. The Root-Bernstein hypothesis on the existence of tRNA structural symmetries presumably reflects late 5’ tRNA stem-loop hairpin duplications, some integrating rRNAs. Analyses of tRNA subelements similarities with rRNA subelements suggest tRNAs evolved and re-evolved by different duplication-fusions, along different structural subdivision models. Hence, sequential/parallel processes, perhaps in the same ancestral organism(s) produced polyphyletic tRNAs. Results confirm RNA ring usefulness for understanding prebiotic and early life evolution, and their similarities with primordial protein coding and tRNA genes.

The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications.

Platygaster robiniae is economically important as a highly specific parasitoid of the invasive pest Obolodiplosis robiniae which was introduced into the Euro-Asia region in the last decade. Despite being a critical and specific parasitoid of the invasive pest O. robiniae and its use as an effective biocontrol agent, the absence of sequence information from P. robiniae have limited its genetic applications for pest management in forests. Mitochondrial (mt) genomes generally contain abundant nucleotide information and thus are helpful for understanding species history. Here, we sequenced the complete mt genome of P. robiniae using next generation sequencing, and annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 702 bp noncoding region. Comparative analysis indicated that this mt genome has a normal A + T content and codons use, however possessed both the expected and unique rearrangements. Ten tRNAs at four gene blocks COII-ATP8, COIII-ND3, ND3-ND5 and the A + T-rich region-ND2 were rearranged, including gene shuffles, transpositions and inversions. Notably, two genes tRNASer(UCN) and tRNALeu(CUN) had undergone long-range inversions, which is the first record of this rearrangement type in the superfamily Platygastroidea. The D-loops of both tRNAIle and tRNALeu(CUN) were absent from the tRNA secondary structure, which has not been reported from hymenopteran previously. Phylogenetic analysis based with the maximum likelihood and Bayesian methods showed that P. robiniae grouped with other species of Platygastridae, and that the superfamily Platygastridea is sister to the other Proctotrupomorpha superfamilies. Our tree strongly supports the monophyly of the five superfamilies of Proctotrupomorpha. This study discovered some unique characters of P. robiniae, and contributes to our understanding of genome rearrangements in the order Hymenoptera.