tRNA Rearrangements Research Articles

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.

The complete mitochondrial genome of Hyotissasinensis (Bivalvia, Ostreoidea) indicates the genetic diversity within Gryphaeidae.

Different from the true oyster (family Ostreidae), the molecular diversity of the gryphaeid oyster (family Gryphaeidae) has never been sufficiently investigated. In the present study, the complete mitochondrial (mt) genome of Hyotissasinensis was sequenced and compared with those of other ostreoids. The total length of H.sinensis mtDNA is 30,385 bp, encoding 12 protein-coding-genes (PCGs), 26 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. The nucleotide composition and codon usage preference of H.sinensis mtDNA is similar to that of H.hyotis within the same genus. On the other hand, the presence of three trnM and three trnL genes of H.sinensis was not detected neither in H.hyotis nor other ostroid species. Another unique character of H.sinensis mtDNA is that both rrnS and rrnL have a nearly identical duplication. The PCG order of H.sinensis is identical to H.hyotis and the two congener species also share an identical block of 12 tRNA genes. The tRNA rearrangements mostly happen in the region from Cox1 to Nad3, the same area where the duplicated genes are located. The rearrangements within Gryphaeidae could be explained by a "repeat-random loss model". Phylogenetic analyses revealed Gryphaeidae formed by H.sinensis + H.hyotis as sister to Ostreidae, whereas the phylogenetic relationship within the latter group remains unresolved. The present study indicated the mitogenomic diversity within Gryphaeidae and could also provide important data for future better understanding the gene order rearrangements within superfamily Ostreoidea.

Comparative mitogenomes reveal diverse and novel gene rearrangements in the genus Meteorus (Hymenoptera: Braconidae).

Meteorus Haliday, 1835 is a cosmopolitan genus within Braconidae (Hymenoptera). They are koinobiont endoparasitoids of Coleoptera or Lepidoptera larvae. Only one mitogenome of this genus was available. Here, we sequenced and annotated three mitogenomes of Meteorus species, and found that the tRNA gene rearrangements in these mitogenomes were rich and diverse. Compared with the ancestral organization, only seven tRNAs (trnW, trnY, trnL2, trnH, trnT, trnP and trnV) were conserved and trnG had its own unique location in the four mitogenomes. This dramatic tRNA rearrangement was not observed in mitogenomes of other insect groups before. In addition, the tRNA cluster (trnA-trnR-trnN-trnS1-trnE-trnF) between nad3 and nad5 was rearranged into two patterns, i.e., trnE-trnA-trnR-trnN-trnS1 and trnA-trnR-trnS1-trnE-trnF-trnN. The phylogenetic results showed that the Meteorus species formed a clade within the subfamily Euphorinae, and were close to Zele (Hymenoptera, Braconidae, Euphorinae). In the Meteorus, two clades were reconstructed: M. sp. USNM and Meteorus pulchricornis forming one clade while the remaining two species forming another clade. This phylogenetic relationship also matched the tRNA rearrangement patterns. The diverse and phylogenetic signal of tRNA rearrangements within one genus provided insights into tRNA rearrangements of the mitochondrial genome at genus/species levels in insects.

Understanding the energetics of translation in bacterial and eukaryotic ribosomes.

Protein synthesis by the ribosome involves a wide range of large-scale conformational rearrangements. While structural methods have provided exquisite snapshots of this machine during function, and single-molecule methods have tracked transitions between stable conformations, the kinetics is ultimately controlled by free-energy barriers. To begin to probe these barriers and identify the interactions that are characteristic of the associated transition states, we are developing and applying a range of atomic-resolution models that employ simplified energetic representations (i.e. structure-based SMOG models). While early applications of these models illustrated the relationship between tRNA structure and kinetics, newer variants have allowed for larger-scale motions and ionic effects to be studied. As an example, recent efforts have shown how entropy contributes to the dynamics of subunit rotation in the yeast ribosome, where the “small” (∼1 MDa) subunit undergoes reversible ∼10-degree rotations. Similar strategies have elucidated the influence of key ribosomal proteins during hybrid-state formation in the human mitoribosome. In addition, recently developed explicit-ion models have shown that small changes in ionic concentrations can control rate-limiting free-energy barriers during tRNA rearrangements (e.g. accommodation) on the ribosome. Together, these efforts are uncovering the intricate balance of energetic factors that control translation across the kingdoms of life.

Two complete mitochondrial genomes in Scolopendra and a comparative analysis of tRNA rearrangements in centipedes.

Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been reached on the phylogeny of Chilopoda based on morphological traits, recent analyses based on molecular data exhibited differences in results. The mitochondrial genome sequences of S. morsitans and S. hainanum were obtained by next-generation sequencing. S. morsitans contains 13 PCGs, two rRNAs, 11 tRNAs, and one CR. whereas S. hainanum contains 12 PCGs, of which ATP8 remains unpredicted, two rRNAs, 14 tRNAs, and one CR. An obvious tRNA rearrangement was found in the genus Scolopendra. S. morsitans exhibited a loss of trnW, trnC, trnI, trnK, trnD, trnA, trnN, trnQ, trnF, trnT, trnS, trnL, and trnV, and a repeat of trnR and trnL. S. hainanum exhibited a loss of trnQ, trnC, trnW, trnI, trnD, trnQ, trnP, and trnV. Phylogenetic analyses of centipedes based on 12 PCGs supported the sister relationship between the orders Geophilomorpha and Lithobiomorpha and a close relationship between Scolopendra dehaani and S. hainanum. The new mitogenomes determined in this study provide new genomic resources for gene rearrangements and contribute to the understanding of the evolution of gene rearrangement in Chilopoda.

Mitochondrial Genomes Yield Insights into the Basal Lineages of Ichneumonid Wasps (Hymenoptera: Ichneumonidae).

We obtained four mitochondrial genomes of Odontocolon sp., Xorides funiuensis, Euceros kiushuensis and Euceros serricornis, which represent the first two representatives from subfamily Eucerotinae and Xoridinae (Ichneumonidae), respectively. All of the 4 newly sequenced mitochondrial genomes contain 13 protein-coding genes (PCGs) and most 24 RNA genes. Furthermore, they all have novel tRNA rearrangement patterns comparing with published mitogenomes in Ichneumonidae. For the tRNA cluster trnI-trnQ-trnM, X. funiuensis is shuffled as trnM-trnI-trnQ with trnQ inversed, while Odontocolon sp. with a remote translocation of trnK, shuffling as trnI-trnM-trnQ. E. kiushuensis and E. serricornis shared the same cluster trnQ-trnY-trnW-trnC. Finally, we reconstructed the phylogenetic relationships among the sequenced subfamilies of Ichneumonidae based on nucleotides and amino acids sequences of 13 PCGs in mitochondrial genomes, and the results of both the maximum likelihood and Bayesian inference analyses highly support that Eucerotinae is the basal ichneumonid lineage rather than Xoridinae.

The complete mitochondrial genome of Aconurella prolixa (Lethierry 1885) (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini)

The complete mitochondrial genome of the widespread leafhopper species Aconurella prolixa (Hemiptera: Cicadellidae: Deltocephalinae: Chiasmini) was obtained via next-generation sequencing. This mitochondrial genome is 14,832 bp in length with the 37 classical eukaryotic mitochondrial genes and a control region. All 13 protein-coding genes (PCGs) are initiated with ATN, except ND5 uses TTG as the start codon, and terminate with TAA or TAG with the exception of COX2 and ND4 which use a single T residue as the stop codon. Twenty-one of the 22 transfer RNA (tRNAs) genes have the typical clover-leaf structure except for trnS1. Unlike some other species of deltocephalinae, no tRNA rearrangements were detected. The monophyly of Cicadellidae and Deltocephalinae, as well as the monophyly of Chiasmini, with a sister relationship between A. prolixa and (Exitianus indicus + Nephotettix cincticeps) is supported by Bayesian inference phylogenetic analyses based on 13 PCGs.

Vicariance and dispersal events inferred from mitochondrial genomes and nuclear genes (18S, 28S) shaped global Cryptocercus distributions

Cryptocercus Scudder, a genus of wingless, subsocial cockroaches, has low vagility but exhibits a disjunct distribution in eastern and western North America, and in China, South Korea and the Russian Far East. This distribution provides an ideal model for testing hypotheses of vicariance through plate tectonics or other natural barriers versus dispersal across oceans or other natural barriers. We sequenced 45 samples of Cryptocercus to resolve phylogenetic relationships among members of the genus worldwide. We identified four types of tRNA rearrangements among samples from the Qin-Daba Mountains. Our maximum-likelihood and Bayesian phylogenetic trees, based on mitochondrial genomes and nuclear genes (18S, 28S), strongly supported six major lineages of Cryptocercus, which displayed a clear geographical distribution pattern. We used Bayesian molecular dating to estimate the evolutionary timescale of the genus, and reconstructed Cryptocercus ancestral ranges using statistical dispersal-vicariance analysis (S-DIVA) in RASP. Two dispersal events and six vicariance events for Cryptocercus were inferred with high support. The initial vicariance event occurred between American and Asian lineages at 80.5 Ma (95% credibility interval: 60.0–104.7 Ma), followed by one vicariance event within the American lineage 43.8 Ma (95% CI: 32.0–57.5 Ma), and two dispersal 31.9 Ma (95% CI: 25.8–39.5 Ma), 21.7 Ma (95% CI: 17.3–27.1 Ma) plus four vicariance events c. 29.3 Ma, 27.2 Ma, 24.8 Ma and 16.7 Ma within the Asian lineage. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these woodroaches.

The complete mitochondrial genome of Hemathlophorus brevigenatus Wei, 2005 (Hymenoptera: Tenthredinidae) with phylogenetic analysis

The mitochondrial genome of Hemathlophorus brevigenatus Wei, 2005 collected from Huanggang Mountain of China is described using the NGS approach. The length of the sequence is 15,452 bp containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The overall A + T content is 79.5%. tRNA rearrangements occur in the MQI cluster. Phylogenetic analysis of H. brevigenatus resolved it in a clade with Allantus togatus in Allantinae which provides new evidence for the phylogeny of Tenthredinidae.

The complete mitochondrial genome of Bombus filchnerae (Hymenoptera: Apidae) and phylogenetic analysis

Here, we report the complete mitochondrial genome (mitogenome) of Bombus filchnerae (Hymenoptera: Apidae). The genome size of B. filchnerae was 18,553 bp with 88.7% A + T content, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an AT-rich control region (D-loop). tRNA rearrangement was observed in this mitochondrial genome when compared to those of other bumblebee species (e.g. Bombus breviceps and Bombus asiaticus). All the 13 PCGs initiated with typical ATN codons. Among them, 11 PCGs terminated with TAA, only nad4 and nad5 with incomplete stop codon TA and T, respectively. All the 22 tRNAs can be folded into typical cloverleaf structure, except for trnS1, whose dihydrouridine (DHU) arm forms a simple loop. The phylogenetic analysis based on the concatenated nucleotide sequences of all 13 PCGs indicated that B. filchnerae showed the closest relationship with Bombus pascuorum, forming a mono clade of the subgenus Thoracobombus, with well-resolved relationships among nine Bombus subgenera.

Mitochondrial Phylogenomics of Tenthredinidae (Hymenoptera: Tenthredinoidea) Supports the Monophyly of Megabelesesinae as a Subfamily.

Simple SummaryTenthredinidae is the most speciose family of the paraphyletic ancestral grade Symphyta, including mainly phytophagous lineages. The subfamilial classification of this family has long been problematic with respect to their monophyly and/or phylogenetic placements. This article reports four complete sawfly mitogenomes of Cladiucha punctata, C. magnoliae, Megabeleses magnoliae, and M. liriodendrovorax for the first time. To investigate the mitogenome characteristics of Tenthredinidae, we also compare them with the previously reported tenthredinid mitogenomes. To explore the phylogenetic placements of these four species within this ecologically and economically important sawfly family, we perform the mitophylogenomics reconstruction and divergence time estimation analyses using a mitogenome dataset of 45 species of the superfamily Tenthredinoidea. Although these newly reported four species have currently classified in the subfamily of Allantinae, the obtained tree topology reveals the sister-group placement of Cladiucha and Megabeleses outside of Blennocampinae, Heterarthrinae, Tenthredininae, and the rest of Allantinae as a distinct lineage. In conjunction with the occurrence of morphological and molecular synapomorphic characters, apparent matches the reported divergence times of their host plants from Magnoliaceae—supporting the proposal of Megabelesesinae as a subfamily. This study represents a broad framework and valuable information for future research on this small subfamily.Tenthredinidae represents one of the external feeders of the most diverse superfamily, Tenthredinoidea, with diverse host plant utilization. In this study, four complete mitochondrial genomes (mitogenomes), those of Cladiucha punctata, Cladiucha magnoliae, Megabeleses magnoliae, and Megabeleses liriodendrovorax, are newly sequenced and comparatively analyzed with previously reported tenthredinid mitogenomes. The close investigation of mitogenomes and the phylogeny of Tenthredinidae leads us to the following conclusions: The subfamilial relationships and phylogenetic placements within Tenthredinidae are mostly found to be similar to the previously suggested phylogenies. However, the present phylogeny supports the monophyly of Megabelesesinae as a subfamily, with the sister-group placement of Cladiucha and Megabeleses outside of Allantinae. The occurrence of the same type of tRNA rearrangements (MQI and ANS1ERF) in the mitogenomes of Megabelesesinae species and the presence of apomorphic morphological characters also provide robust evidence for this new subfamily. The divergence and diversification times of the subfamilies appear to be directly related to colonization of the flowering plants following the Early Cretaceous. The origin time and diversification patterns of Megabelesesinae were also well matched with the divergence times of their host plants from Magnoliaceae.

Comparative mitogenomics and phylogenetics of the stinging wasps (Hymenoptera: Aculeata)

The stinging wasps (Hymenoptera: Aculeata) include diverse groups such as vespid wasps, ants and bees. Phylogenetic relationships among major lineages of stinging wasps have been inferred from molecular and morphological data. However, the genomic features of the mitochondrial genomes and their phylogenetic utility remain to be explored. In this study, we determined 23 mitochondrial genomes from the Aculeata. Four Mutillidae species showed relatively low A + T content compared to other species of the Aculeata (69.7%–77.4%). Eleven out of 44 species, mainly from the Chrysididae and the Pompilidae, showed reversals of GC skews. Gene rearrangements occurred across the species. Patterns of tRNA rearrangement were conserved in some groups, including the Chrysididae, Bethylidae, Pompilidae, Scolioidea and Vespoidea. Rearrangement of protein-coding genes were found in 12 out of 44 species of the Aculeata, including all four species from the Chrysididae, both species from the Bethylidae, one species from the Dryinidae, all three Scolioidea species and two Apoidea species. Phylogenetic inference showed a long branch in species with unusual genomic features, such as in the Mutillidae and Bethylidae. By excluding these species, we found paraphyly of the Chrysidoidea and a sister group relationship between the Formicoidea and Vespoidea. These results improve our understanding of the evolution of mitochondrial genomes in the Aculeata and, in general, the evolution across this subclade.

Mitogenome of Tolypocladium guangdongense.

Tolypocladium guangdongense is a high-value edible fungus with various medicinal and food safety properties. However, its evolutionary and genetic information is still limited. Mitochondrial genomes are potential models for molecular evolution and phylogenetic studies. In this study, we sequenced the complete mitogenome of T. guangdongense, demonstrating circular sequence of 46,102 bp, containing 14 standard protein-coding genes (PCGs), 2 ribosomal RNA subunit genes, and 28 tRNA genes. Phylogenetic analysis based on mitochondrial genes indicated that T. guangdongense was clustered into the Tolypocladium genus with high support value, based on the core PCG dataset. In addition, rps3 is also a suitable marker in the phylogenetic analysis in Hypocreales. Gene rearrangement analysis indicated that the gene order of PCGs was highly consistent in Hypocreales, and tRNA rearrangement events occurred in most species of Hypocreales; however, the rearrangement rates were not taxonomically correlated. Divergence time estimation based on the old fossil record and previous reports revealed that T. guangdongense originated approximately in the middle Cenozoic (42 Mya, 95% highest posterior density interval: 43-116) with the Tolypocladium genus differentiation. Our results provided more mitogenomic information of T. guangdongense and shed new insights into evolution of the Tolypocladium genus. KEY POINTS: • The general and unique features of T. guangdongense mitogenome are firstly reported. • Phylogenetic analysis further verified the taxonomic status of T. guangdongense. • Divergence time estimation provides more evolutionary information of T. guangdongense.

Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea)

Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.

Mitochondrial genomes and 28S rDNA contradict the proposed obsoletion of the order Tetraonchidea (Platyhelminthes: Monogenea)

Due to the incongruence of morphology-based hypotheses and scarcity of molecular data, validity of the order Tetraonchidea remains contentious. The only complete mitogenome currently available for the entire order is that of Paratetraonchoides inermis (Tetraonchoididae). To study the phylogeny of Tetraonchidea from mitogenomic perspective, we sequenced the first mitogenome for the family Tetraonchidae: Tetraonchus monenteron (Tetraonchidea). To get a nuclear-data perspective, we also sequenced nuclear 28S rDNA gene of both species. The mitogenome of T. monenteron does not have high A + T content, nor tRNA pseudo-genes, both of which were unique features reported in P. inermis. However, T. monenteron exhibits a unique gene order, with a large number of tRNA rearrangements in comparison to P. inermis and other monogeneans. Phylogenetic analyses conducted using Bayesian inference and maximum likelihood methods, complemented with partitioning, consistently support the sister-group relationship of T. monenteron (Tetraonchidae) and P. inermis (Tetraonchoididae). This is also partially supported by the 28S rDNA data and two morphologic apomorphies. This close relationship of Tetraonchidae and Tetraonchoididae challenges the latest major morphology-based classification, which proposed obsoletion of the Tetraonchidea order, and grouped Tetraonchoididae into the Gyrodactylidea clade. The validity of this order shall have to be further confirmed with more data.

Mitochondrial genomes of two diplectanids (Platyhelminthes: Monogenea) expose paraphyly of the order Dactylogyridea and extensive tRNA gene rearrangements

BackgroundRecent mitochondrial phylogenomics studies have reported a sister-group relationship of the orders Capsalidea and Dactylogyridea, which is inconsistent with previous morphology- and molecular-based phylogenies. As Dactylogyridea mitochondrial genomes (mitogenomes) are currently represented by only one family, to improve the phylogenetic resolution, we sequenced and characterized two dactylogyridean parasites, Lamellodiscus spari and Lepidotrema longipenis, belonging to a non-represented family Diplectanidae.ResultsThe L. longipenis mitogenome (15,433 bp) contains the standard 36 flatworm mitochondrial genes (atp8 is absent), whereas we failed to detect trnS1, trnC and trnG in L. spari (14,614 bp). Both mitogenomes exhibit unique gene orders (among the Monogenea), with a number of tRNA rearrangements. Both long non-coding regions contain a number of different (partially overlapping) repeat sequences. Intriguingly, these include putative tRNA pseudogenes in a tandem array (17 trnV pseudogenes in L. longipenis, 13 trnY pseudogenes in L. spari). Combined nucleotide diversity, non-synonymous/synonymous substitutions ratio and average sequence identity analyses consistently showed that nad2, nad5 and nad4 were the most variable PCGs, whereas cox1, cox2 and cytb were the most conserved. Phylogenomic analysis showed that the newly sequenced species of the family Diplectanidae formed a sister-group with the Dactylogyridae + Capsalidae clade. Thus Dactylogyridea (represented by the Diplectanidae and Dactylogyridae) was rendered paraphyletic (with high statistical support) by the nested Capsalidea (represented by the Capsalidae) clade.ConclusionsOur results show that nad2, nad5 and nad4 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in the Diplectanidae. The unique gene order pattern further suggests discontinuous evolution of mitogenomic gene order arrangement in the Class Monogenea. This first report of paraphyly of the Dactylogyridea highlights the need to generate more molecular data for monogenean parasites, in order to be able to clarify their relationships using large datasets, as single-gene markers appear to provide a phylogenetic resolution which is too low for the task.

Complete mitochondrial genome of Macrosteles quadrimaculatus (Matsumura) (Hemiptera: Cicadellidae: Deltocephalinae) with a shared tRNA rearrangement and its phylogenetic implications

Comparative studies of leafhopper mitochondrial genomes suggest that genome rearrangements are very rare in these insects but that nucleotide sequences are informative of phylogenetic relationships at various levels of divergence. A recent study reported that tRNA cluster trnW-trnC-trnY is rearranged to trnC-trnW-trnY in the Aster Leafhopper, Macrosteles quadrilineatus, an economically important North American species. The complete mitochondrial genome of the East Asian species, Macrosteles quadrimaculatus, sequenced and annotated here for the first time, reveals that this species shares the same tRNA rearrangement, suggesting it is a genus-level trait. The entire mitogenome of M. quadrimaculatus is a circular molecule 15,734 bp in size comprising 37 genes and one control region, which is similar to other studied hemipteran mitogenomes. The whole mitogenome sequence shows heavily A + T biased nucleotide composition (77.7%) and moderately positive AT-skews (0.120). Except for the nad5 gene which starts with TTG and ends with incomplete codon T, all protein-coding genes begin with ATN codons and terminate with TAA. All tRNA genes have typical cloverleaf secondary structures, except for trnS1, in which dihydrouridine (DHU) stem is simplified to form a loop structure. Phylogenetic analysis based on nucleotide sequence datasets recovered Macrosteles as monophyletic and sister to the rest of Deltocephalinae.

Nearly complete mitogenome of hairy sawfly, Corynis lateralis (Brullé, 1832) (Hymenoptera: Cimbicidae): rearrangements in the IQM and ARNS1EF gene clusters

The Cimbicidae is a small family of the primitive and relatively less diverse suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genome (mitogenome) of hairy sawfly, Corynis lateralis (Hymenoptera: Cimbicidae) was sequenced using next generation sequencing and comparatively analysed with the mitogenome of Trichiosoma anthracinum. The sequenced length of C. lateralis mitogenome was 14,899bp with an A+T content of 80.60%. All protein coding genes (PCGs) are initiated by ATN codons and all are terminated with TAR or T- stop codon. All tRNA genes preferred usual anticodons. Compared with the inferred insect ancestral mitogenome, two tRNA rearrangements were observed in the IQM and ARNS1EF gene clusters, representing a new event not previously reported in Symphyta. An illicit priming of replication and/or intra/inter-mitochondrial recombination and TDRL seem to be responsible mechanisms for the rearrangement events in these gene clusters. Phylogenetic analyses confirmed the position of Corynis within Cimbicidae and recovered a relationship of Tenthredinoidea + (Cephoidea + Orussoidea) in Symphyta.

Complete mitochondrial genomes of Trisidos kiyoni and Potiarca pilula: Varied mitochondrial genome size and highly rearranged gene order in Arcidae.

We present the complete mitochondrial genomes (mitogenomes) of Trisidos kiyoni and Potiarca pilula, both important species from the family Arcidae (Arcoida: Arcacea). Typical bivalve mtDNA features were described, such as the relatively conserved gene number (36 and 37), a high A + T content (62.73% and 61.16%), the preference for A + T-rich codons, and the evidence of non-optimal codon usage. The mitogenomes of Arcidae species are exceptional for their extraordinarily large and variable sizes and substantial gene rearrangements. The mitogenome of T. kiyoni (19,614 bp) and P. pilula (28,470 bp) are the two smallest Arcidae mitogenomes. The compact mitogenomes are weakly associated with gene number and primarily reflect shrinkage of the non-coding regions. The varied size in Arcidae mitogenomes reflect a dynamic history of expansion. A significant positive correlation is observed between mitogenome size and the combined length of cox1-3, the lengths of Cytb, and the combined length of rRNAs (rrnS and rrnL) (P < 0.001). Both protein coding genes (PCGs) and tRNA rearrangements is observed in P. pilula and T. kiyoni mitogenomes. This analysis imply that the complicated gene rearrangement in mitochondrial genome could be considered as one of key characters in inferring higher-level phylogenetic relationship of Arcidae.

Capturing Transition States for tRNA Hybrid-State Formation in the Ribosome.

In order to quantitatively describe the energetics of biomolecular rearrangements, it is necessary to identify reaction coordinates that accurately capture the relevant transition events. Here, we perform simulations of A-site tRNA movement (∼20 Å) during hybrid-state formation in the ribosome and quantify the ability of interatomic distances to capture the transition state ensemble. Numerous coordinates are found to be accurate indicators of the transition state, allowing tRNA rearrangements to be described as diffusion across a one-dimensional free-energy surface. In addition to providing insights into the physical-chemical relationship between biomolecular structure and dynamics, these results can help enable single-molecule techniques to probe the free-energy landscape of the ribosome.