Large Non-coding Region Research Articles

Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (Lynx canadensis).

Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms (SNPs) in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.

The complete mitochondrial genome of the rodent flea Nosopsyllus laeviceps: genome description, comparative analysis, and phylogenetic implications

BackgroundFleas are one of the most common and pervasive ectoparasites worldwide, comprising at least 2500 valid species. They are vectors of several disease-causing agents, such as Yersinia pestis. Despite their significance, however, the molecular genetics, biology, and phylogenetics of fleas remain poorly understood.MethodsWe sequenced, assembled, and annotated the complete mitochondrial (mt) genome of the rodent flea Nosopsyllus laeviceps using next-generation sequencing technology. Then we combined the new mitogenome generated here with mt genomic data available for 23 other flea species to perform comparative mitogenomics, nucleotide diversity, and evolutionary rate analysis. Subsequently, the phylogenetic relationship within the order Siphonaptera was explored using the Bayesian inference (BI) and maximum likelihood (ML) methods based on concentrated data for 13 mt protein-coding genes.ResultsThe complete mt genome of the rodent flea N. laeviceps was 16,533 base pairs (bp) in a circular DNA molecule, containing 37 typical genes (13 protein-coding genes, 22 transfer RNA [tRNA] genes, and two ribosomal RNA [rRNA] genes) with one large non-coding region (NCR). Comparative analysis among the order Siphonaptera showed a stable gene order with no gene arrangement, and high AT content (76.71–83.21%) with an apparent negative AT and GC skew except in three fleas Aviostivalius klossi bispiniformis, Leptopsylla segnis, and Neopsylla specialis. Moreover, we found robust evidence that the cytochrome c oxidase subunit 1 (cox1) gene was the most conserved protein-coding gene (Pi = 0.15, non-synonymous/synonymous [Ka/Ks] ratio = 0.13) of fleas. Phylogenomic analysis conducted using two methods revealed different topologies, but both results strongly indicated that (i) the families Ceratophyllidae and Leptopsyllidae were paraphyletic and were the closest to each other, and (ii) the family Ctenophthalmidae was paraphyletic.ConclusionsIn this study, we obtained a high-quality mt genome of the rodent flea N. laeviceps and performed comparative mitogenomics and phylogeny of the order Siphonaptera using the mt database. The results will enrich the mt genome data for fleas, lay a foundation for the phylogenetic analysis of fleas, and promote the evolutionary analysis of Siphonaptera.Graphical

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.

Mitogenomic Analysis and Phylogenetic Implications for the Deltocephaline Tribe Chiasmini (Hemiptera: Cicadellidae: Deltocephalinae).

The grassland leafhopper tribe Chiasmini (Cicadellidae: Deltocephalinae) presently comprises 324 described species worldwide, with the highest species diversity occurring in the Nearctic region but a greater diversity of genera occurring in the Old World. In China, this tribe comprises 39 described species in 11 genera, but the fauna remains understudied. The complete mitogenomes of three species of this tribe have been sequenced previously. In order to better understand the phylogenetic position of Chiasmini within the subfamily Deltocephalinae and to investigate relationships among Chiasmini genera and species, we sequenced and analyzed the complete mitogenomes of 13 species belonging to seven genera from China. Comparison of the newly sequenced mitogenomes reveals a closed circular double-stranded structure containing 37 genes with a total length of 14,805 to 16,269 bp and a variable number of non-coding A + T-rich regions. The gene size, gene order, gene arrangement, base composition, codon usage, and secondary structure of tRNAs of the newly sequenced mitogenomes of these 13 species are highly conserved in Chiasmini. The ATN codon is commonly used as the start codon in protein-coding genes (PCGs), except for ND5 in Doratura sp. and ATP6 in Nephotettix nigropictus, which use the rare GTG start codon. Most protein-coding genes have TAA or TAG as the stop codon, but some genes have an incomplete T stop codon. Except for the tRNA for serine (trnS1(AGN)), the secondary structure of the other 21 tRNAs is a typical cloverleaf structure. In addition to the primary type of G-U mismatch, five other types of tRNA mismatches were observed: A-A, A-C, A-G, U-C, and U-U. Chiasmini mitochondrial genomes exhibit gene overlaps with three relatively stable regions: the overlapping sequence between trnW and trnC is AAGTCTTA, the overlapping sequence between ATP8 and ATP6 is generally ATGATTA, and the overlapping sequence between ND4 and ND4L is generally TTATCAT. The largest non-coding region is the control region, which exhibits significant length and compositional variation among species. Some Chiasmini have tandem repeat structures within their control regions. Unlike some other deltocephaline leafhoppers, the sequenced Chiasmini lack mitochondrial gene rearrangements. Phylogenetic analyses of different combinations of protein-coding and ribosomal genes using maximum likelihood and Bayesian methods under different models, using either amino acid or nucleotide sequences, are generally consistent and also agree with results of prior analyses of nuclear and partial mitochondrial gene sequence data, indicating that complete mitochondrial genomes are phylogenetically informative at different levels of divergence within Chiasmini and among leafhoppers in general. Apart from Athysanini and Opsiini, most of the deltocephaline tribes are recovered as monophyletic. The results of ML and BI analyses show that Chiasmini is a monophyletic group with seven monophyletic genera arranged as follows: ((Zahniserius + (Gurawa + (Doratura + Aconurella))) + (Leofa + (Exitianus + Nephotettix))).

Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences.

Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.

Comparative mitogenomic and evolutionary analysis of Lycaenidae (Insecta: Lepidoptera): Potential association with high-altitude adaptation.

Harsh environments (e.g., hypoxia and cold temperatures) of the Qinghai-Tibetan Plateau have a substantial influence on adaptive evolution in various species. Some species in Lycaenidae, a large and widely distributed family of butterflies, are adapted to the Qinghai-Tibetan Plateau. Here, we sequenced four mitogenomes of two lycaenid species in the Qinghai-Tibetan Plateau and performed a detailed comparative mitogenomic analysis including nine other lycaenid mitogenomes (nine species) to explore the molecular basis of high-altitude adaptation. Based on mitogenomic data, Bayesian inference, and maximum likelihood methods, we recovered a lycaenid phylogeny of [Curetinae + (Aphnaeinae + (Lycaeninae + (Theclinae + Polyommatinae)))]. The gene content, gene arrangement, base composition, codon usage, and transfer RNA genes (sequence and structure) were highly conserved within Lycaenidae. TrnS1 not only lacked the dihydrouridine arm but also showed anticodon and copy number diversity. The ratios of non-synonymous substitutions to synonymous substitutions of 13 protein-coding genes (PCGs) were less than 1.0, indicating that all PCGs evolved under purifying selection. However, signals of positive selection were detected in cox1 in the two Qinghai-Tibetan Plateau lycaenid species, indicating that this gene may be associated with high-altitude adaptation. Three large non-coding regions, i.e., rrnS-trnM (control region), trnQ-nad2, and trnS2-nad1, were found in the mitogenomes of all lycaenid species. Conserved motifs in three non-coding regions (trnE-trnF, trnS1-trnE, and trnP-nad6) and long sequences in two non-coding regions (nad6-cob and cob-trnS2) were detected in the Qinghai-Tibetan Plateau lycaenid species, suggesting that these non-coding regions were involved in high-altitude adaptation. In addition to the characterization of Lycaenidae mitogenomes, this study highlights the importance of both PCGs and non-coding regions in high-altitude adaptation.

The complete mitochondrial genome of Triplax ainonia Lewis, 1877 (Coleoptera: Erotylidae)

The beetle Triplax ainonia Lewis, 1877 is a serious pest of cultivated the mushroom Pleurotus ostreatus in China. The complete mitochondrial genome of this species was reported for the first time in this study. The mitogenome was 17,555 bp in length and had a base composition of 39.4% A, 36.1% T, 8.7% G and 15.3% C, which indicated that the base composition was AT-biased. Similar to other species of Coleoptera, the mitogenome of T. ainonia contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA unit genes, and a large noncoding region. Phylogenetic analysis based on mitogenomes suggested that the family Erotylidae was a monophyletic group.

Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination.

Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.

Intraspecific variation in the mitochondrial genomes of the black carpet beetle, Attagenus unicolor japonicus Reitter (1877) (Coleoptera: Dermestidae)

Dermestid beetles are economically important pests of various stored products but their genetic studies remain insufficient on contrary to their diversity and importance. In this study, the complete mitochondrial genome (mitogenome) of the black carpet beetle, Attagenus unicolor japonicus Reitter 1877, was reported and compared with the previously sequenced one. The two A. unicolor japonicus mitogenomes had an identical set of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes as well as a large non-coding control region. The new mitogenome was longer than the previous one due to its longer control region. A total of 126 variable sites were detected between the new and previous mitogenomes and most of them were found in PCGs. Synonymous mutations in PCGs frequently occurred on the third codon positions and did not change most translated amino acids. The phylogenetic results based on both the nucleotide dataset and amino acid dataset corresponded with previous molecular studies at both generic and subfamilial levels and helped to determine the correct identity of two misidentified or unidentified dermestid species from GenBank and previous studies.

The first complete mitochondrial genome of Matsucoccidae (Hemiptera, Coccoidea) and implications for its phylogenetic position.

The mitochondrial genome (mitogenome) has been extensively used to better understand the phylogenetic relationships within the hemipteran suborder Sternorrhyncha, but sequenced mitogenomes remain unavailable for the entire family Matsucoccidae to date. To address this, here we sequenced the complete mitogenome of Matsucoccusmatsumurae; the first for this family. The mitogenome is 15,360 bp in size and comprises the typical set of 37 mitochondrial genes and a large non-coding region (AT-rich region). Gene order, nucleotide composition and codon usage of protein-coding genes (PCGs) of M.matsumurae differ considerably from those of the other two sequenced Coccidae species. All PCGs were initiated by the ATN start codons and ended with the TAA/G or single T-- stop codons. Nine transfer RNA genes could be folded into typical clover-leaf secondary structures. The length and AT content of the ribosomal RNA genes are highly conserved in the Coccoidea mitogenomes. In contrast, the AT-rich control region is highly variable in size and in the number of tandem repeats. The sliding window analysis showed that the cox1 gene is the most conserved amongst the 13 PCGs, while the ratios of non-synonymous to synonymous substitution rates indicated that the evolution of this mitogenome has been dominated by positive selection. Phylogenetic analyses, based on nucleotide sequence data of 37 mitochondrial genes and amino acid sequence data of 13 PCGs using Bayesian Inference and Maximum Likelihood methods, showed that Matsucoccidae diverged before the Coccidae.

The Complete Mitochondrial Genome of Hyotissa hyotis (Bivalvia: Gryphaeidae) Reveals a Unique Gene Order within Ostreoidea

The mitochondrial (mt) genome is an important tool when studying the evolution of metazoan animals. The oyster family Gryphaeidae, together with Ostreidae, is one of the two extant taxa of superfamily Ostreoidea. Up until now, the available mitochondrial genomes of oysters were all limited to family Ostreidae. In the present study, the first complete mtDNA of family Gryphaeidae represented by Hyotissa hyotis was sequenced and compared with other available ostreoid mtDNA. The mtDNA of H. hyotis is 22,185 bp in length, encoding 13 protein-coding-genes (PCGs), two ribosomal RNA (rRNA) and 23 transfer RNA (tRNA) genes. Within all the intergenic regions that range from 2 to 1528 bp, two large non-coding regions were identified. The first large non-coding region, located between Cox1 and trnA, contains 1528 nucleotides, while the second one is 1191 bp in length and positioned between Cytb and Nad2. The nucleotide composition of the whole mtDNA is A + T biased, accounting for 59.2%, with a negative AT skew value of −0.20 and a positive GC skew value of 0.33. In contrast to the mtDNA of Ostreidae, neither the split of rrnL nor rrnS was detected in that of H. hyotis. The duplication of trnW of H. hyotis was also discovered for the first time within Ostreoidea. The gene order of H. hyotis is quite different from those of ostreids, indicating extensive rearrangements within superfamily Ostreoidea. The reconstructed phylogeny supported H. hyotis as sister to Ostreidae, with the latter clade formed by Ostrea + (Saccostrea + Crassostrea). This study could provide important information for further understanding the mitochondrial evolution of oysters.

A Novel Mitochondrial Genome Fragmentation Pattern in the Buffalo Louse Haematopinus tuberculatus (Psocodea: Haematopinidae).

Sucking lice are obligate ectoparasites of mammalian hosts, causing serious public health problems and economic losses worldwide. It is well known that sucking lice have fragmented mitochondrial (mt) genomes, but many remain undetermined. To better understand patterns of mt genome fragmentation in the sucking lice, we sequenced the mt genome of the buffalo louse Haematopinus tuberculatus using next-generation sequencing (NGS). The mt genome of H. tuberculatus has ten circular minichromosomes containing a total of 37 genes. Each minichromosome is 2.9-5.0 kb long and carries one to eight genes plus one large non-coding region. The number of mt minichromosomes of H. tuberculatus (ten) is different from those of congeneric species (horse louse H. asini, domestic pig louse H. suis and wild pig louse H. apri) and other sucking lice. Two events (gene translocation and merger of mt minichromosome) are observed in Haematopinus. Compared to other studies, our phylogeny generated from mt genome datasets showed a different topology, suggesting that inclusion of data other than mt genomes would be required to resolve phylogeny of sucking lice. To our knowledge, this is the first report of a ten mt minichromosomes genome in sucking lice, which opens a new outlook into unexplored mt genome fragmentation patterns in sucking lice.

Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae).

The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.

The complete mitochondrial genome of Hemiclepsis yangtzenensis (Clitellata: Glossiphoniidae)

We present the complete mitochondrial genome sequence of a recently described new leech species named Hemiclepsis yangtzenensis Yang & Bolotov 2021 collected in central China. The mitochondrial genome is 14,984 bp in length and consists of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, all of which are encoded on a single strand. It exhibited a strong A + T bias of 72.87%. There is a large non-coding region (614 bp) located between the tRNA-Arg and tRNA-His genes, wherein we identified 40 short dispersed repeats, 13–22 bp long, 8 of which were direct, 20 inverted, and 12 palindromic. Phylogenetic analysis of 20 Hirudinea mitogenome sequences resolved monophyletic Glossiphoniidae, and H. yangtzenensis formed a sister lineage with Glossiphonia concolor.

Mitochondrial genomes of 10 Mantidae species and their phylogenetic implications.

This article aims to present a phylogenetic evaluation of Mantidae based on a mitochondrial genome (mitogenome) data set. The mitogenome of 10 Mantidae species were sequenced using next-generation sequencing. The length of nine the complete mitogenomes ranged from 15,371 bp in Tenodera aridifolia to 16,063 bp in Hierodula longa. Mantidae mitogenomes have 37 genes and control region with two exceptions: five trnR copies in Statilia maculata, and H. zhangi was incomplete missing trnI, trnQ, trnM and a portion of the control region. There was a large noncoding region (LNC) between trnM and nad2 in H. chinensis, H. longa, H. maculata and Titanodula sp. Most of protein-coding genes (PCGs) used the typical start ATN codon and TAA/TAG stop codons. All tRNAs fold into the typical clover-leaf secondary structure except trnS1 which lacks a dihydrouracil (DHU) arm. Nucleotide diversity and Ka/Ks analysis of 13 PCGs showed that atp8 had the highest variability and fastest evolutionary rate. Phylogenetic relationships among 42 Mantidae species were reconstructed using the 13 PCGs and two rRNA genes using Bayesian Inference (BI) and Maximum Likelihood (ML) methods. Of the seven mantid subfamilies included in this analysis, only four had multiple exemplars, and of those only Mantinae and Vatinae formed monophyletic groups in BI and ML trees. Consistent with previous studies, the monophyly of the Hierudulinae and Tenoderinae were not been supported. The present results imply that it is necessary to combine nuclear molecular markers and external characteristic to understand the phylogenetic relationships within Mantidae.

The investigation of intraspecific characteristics and comparative analyses of the complete mitochondrial genome of Stegobium paniceum (Linnaeus, 1758) (Coleoptera: Ptinidae) assembled from public NGS raw reads of the black truffle, Tuber melanosporum.

Due to the rapid development of NGS technologies, a huge amount of NGS raw reads have been accumulated in public repositories, such as the Short Read Archive of NCBI. We successfully rescued the complete mitochondrial genome of Stegobium paniceum, a drug store beetle, from public NGS raw reads of truffle generated from the whole genome project. The circular mitogenome of S. paniceum is 15,474 bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 803 bp. Intraspecific transfer RNAs structure and sequence variations were investigated and simple sequence repeats identified from three S. paniceum mitochondrial genomes were compared showing their diversities as fundamental data to utilize them in various aspects including developing efficient molecular markers in the family, Ptinidae. Phylogenetic analysis of 23 Bostrichoidea mitochondrial genomes presented better species identification based on phylogenetic analyses and the optimal options for constructing phylogenetic trees based on Bostrichoidea mitochondrial genomes. Our results present not only utilization of public NGS raw read sequences but also intraspecific features of S. paniceum mitochondrial genomes and comparative analysis of Bostrichoidea mitochondrial genomes in various aspects.

Determination of the complete mitochondrial genome of Lardoglyphus konoi (Acari: Astigmata)

The mitochondrial genome of Lardoglyphus konoi was 14,269 bp long and consisted of 37 genes including 22 transfer RNAs, 13 protein-coding genes and 2 ribosomal RNA genes. All the 13 protein-coding genes had complete start/stop codons. Most inferred tRNAs were extremely truncated and the T- or D-arm was missing. The position of two rRNAs and the largest non-coding region were separated by tRNAs. The Bayesian phylogenetic tree indicated that L. konoi was closely related to Carpoglyphus lactis.

Structural Features and Phylogenetic Implications of 11 New Mitogenomes of Typhlocybinae (Hemiptera: Cicadellidae).

Simple SummaryTyphlocybinae is the smallest sized and most evolved leafhopper, body length 2–4 mm, forewing with four apical cells but lacking closed preapical cells. It comprises over 6000 species (Dietrich, 2013) distributed worldwide, making it the second largest group of Cicadellidae. Previous phylogenetic analyses in this subfamily were mainly based on morphological characters and were restricted to several gene fragments. To provide further insight into the relationships of its included tribes, complete mitogenomes of two Alebrini species (Shaddai acuminatus, Sobrala sp.), two Dikraneurini species (Dikraneura (Dikraneura) zlata, Robusta emeiensis), two Empoascini species (Alebroides salici, Empoasca serrata), two Erythroneurini species (Elbelus tripunctatus, Kaukania anser), two Typhlocybini species (Eupteryx (Eupteryx) adspersa, Eurhadina jarrary), and one Zyginellini species (Yangisunda tiani) are newly sequenced and comparatively analyzed. The mitogenomes comprise the typical set of 37 mitochondrial genes and a large non-coding region (A+T-rich region). The acceptor arm of trnR is the most inconstant among all the tRNAs, due to the acceptor arm comprising unpaired bases. Phylogenetic analyses using Bayesian inference and maximum likelihood methods produced a well-resolved framework of Typhlocybinae, showed the monophyly of Typhlocybinae and its inner tribes, except for Typhlocybini and Zyginellini combined. These results provide the valuable data toward the future study of the phylogenetic relationships in this subfamily.To explore the characteristics of mitogenomes and discuss the phylogenetic relationships and molecular evolution of the six tribes within Typhlocybinae, 11 complete mitogenomes are newly sequenced and comparatively analyzed. In all of these complete mitogenomes, the number and order of the genes are highly conserved in overall organization. The PCGs initiate with ATN/TTG/GTG and terminate with TAA/TAG/T. Almost all tRNAs are folded into the typical clover-leaf secondary structure. The control region is always variable in length and in numbers of multiple tandem repeat units. The atp8 and nad2 exhibits the highest evolution rate among all the PCGs. Phylogenetic analyses based on whole mitogenome sequences, with three different datasets, using both maximum likelihood and Bayesian methods, indicate the monophyly of Typhlocybinae and its inner tribes, respectively, except for Typhlocybini and Zyginellini that are paraphyletic. Finally, we confirm that Erythroneurini is a subtribe of Dikraneurini.

Global mapping of cancers: The Cancer Genome Atlas and beyond.

Cancer genomes have been explored from the early 2000s through massive exome sequencing efforts, leading to the publication of The Cancer Genome Atlas in 2013. Sequencing techniques have been developed alongside this project and have allowed scientists to bypass the limitation of costs for whole‐genome sequencing (WGS) of single specimens by developing more accurate and extensive cancer sequencing projects, such as deep sequencing of whole genomes and transcriptomic analysis. The Pan‐Cancer Analysis of Whole Genomes recently published WGS data from more than 2600 human cancers together with almost 1200 related transcriptomes. The application of WGS on a large database allowed, for the first time in history, a global analysis of features such as molecular signatures, large structural variations and noncoding regions of the genome, as well as the evaluation of RNA alterations in the absence of underlying DNA mutations. The vast amount of data generated still needs to be thoroughly deciphered, and the advent of machine‐learning approaches will be the next step towards the generation of personalized approaches for cancer medicine. The present manuscript wants to give a broad perspective on some of the biological evidence derived from the largest sequencing attempts on human cancers so far, discussing advantages and limitations of this approach and its power in the era of machine learning.

Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises (Mantodea: Mantidae): Translocation, duplication and pseudogenization

Gene rearrangements have been found in several mitochondrial genomes of Mantodea, located in the gene blocks CR-I-Q-M-ND2, COX1-K-D-ATP8 and ND3-A-R-N-S-E-F-ND5. We have sequenced one mitogenome of Amelidae (Yersinia mexicana) and six mitogenomes of Mantidae to discuss the mitochondrial gene rearrangement and the phylogenetic relationship within Mantidae. These mitogenomes showed rearrangements of tRNA genes except for Asiadodis yunnanensis and Hierodula zhangi. These novel gene rearrangements of Mantidae were primarily concentrated in the region of CR-I-Q-M-ND2, including gene translocation, duplication and pseudogenization. For the occurrences of these rearrangements, the tandem duplication-random loss (TDRL) model and slipped-strand mispairing model were suitable to explain. Large non-coding regions (LNCRs) located in the region of CR-I-Q-M-ND2 were detected in most Mantidae species, whereas some LNCRs had high similarity to the control region (CR). Both BI and ML phylogenetic analyses supported the monophyly of Mantidae and the paraphyly of Mantinae. The phylogenetic results with the gene order and the location of NCRs acted as forceful evidence that specific gene rearrangements and special LNCRs may be synapomorphies for several groups of mantises.