Tandem Repeat Units Research Articles

Characterization, Codon Usage Pattern and Phylogenetic Implications of the Waterlily Aphid Rhopalosiphum nymphaeae (Hemiptera: Aphididae) Mitochondrial Genome.

The water lily aphid, Rhopalosiphum nymphaeae, is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of R. nymphaeae was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of R. nymphaeae is 15,772 bp in length, with a high A+T content (84.34%). It contains 37 coding genes (13 protein-coding genes, 22 transport RNAs, and two ribosomal RNAs) and two non-coding regions (one control region and one repeat region). Enc-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of the protein-coding genes is mainly affected by natural selection. The evolution rate analysis (the ratio of nonsynonymous to synonymous, Ka/Ks) indicated that all the PCGs in R. nymphaeae are under a strong purifying selection. The control region has conserved structure elements, and two types of tandem repeat units exist. The length and sequence of the aphid-unique repeat region has high similarity with closely related species. Phylogenetic analyses determined by both maximum likelihood and Bayesian inference support the monophyly of Aphidinae, Aphidini, Aphidina, and Rhopalosiphina. However, the monophyly of the genera in Rhopalosiphina, such as Rhopalosiphum, is still not resolved. This study may help us to understand the phylogenetic relationship of aphids, and much more aphid data are needed in future studies.

Genotypic variation in the white spot syndrome virus detected from giant tiger shrimp (Penaeus monodon) in North Western and Eastern provinces of Sri Lanka

Shrimp farming in Sri Lanka accounting for 70 % of the exports in the field of aquaculture in Sri Lanka. However, it encounters substantial obstacles as a result of the white spot syndrome virus (WSSV) affecting the giant tiger shrimp (Penaeus monodon). This study focused on comprehending the current state of the disease and the genetic diversity present in the North Western and Eastern provinces in Sri Lanka. By extracting genomic DNA from the gills and pleopods of suspected infected shrimps and post-larvae, the study identified a high infection rate of at least 83 % (88/106), with varying incidence in sampled farms across regions. The analysis of the genome indicated distinct sizes of PCR products, suggesting the presence of variation in the tandem repeat units within the ORF94 region of the WSSV. Notably, the study discovered single nucleotide polymorphisms (SNPs) in Sri Lankan WSSV strains, which showed the change between T (Thymine) and G (Guanine) at the 48th site of the RU sequence, which is designated as K (keto) as indicated in the IUPAC code, indicating genetic diversity. Phylogenetic analysis suggested two distinct origins for Sri Lankan WSSVs, with possible links to North America and Mexico strains, highlighting a potential common source of outbreaks. This study emphasizes the intricate nature of WSSV infections in Sri Lanka and emphasizes the necessity for customized approaches to address this significant risk to the shrimp aquaculture industry.

Selected Lark Mitochondrial Genomes Provide Insights into the Evolution of Second Control Region with Tandem Repeats in Alaudidae (Aves, Passeriformes).

The control region (CR) regulates the replication and transcription of the mitochondrial genome (mitogenome). Some avian mitogenomes possess two CRs, and the second control region (CR2) may enhance replication and transcription; however, the CR2 in lark mitogenome appears to be undergoing loss and is accompanied by tandem repeats. Here, we characterized six lark mitogenomes from Alaudala cheleensis, Eremophila alpestris, Alauda razae, and Calandrella cinerea and reconstructed the phylogeny of Passerida. Through further comparative analysis among larks, we traced the evolutionary process of CR2. The mitochondrial gene orders were conserved in all published lark mitogenomes, with Cytb-trnT-CR1-trnP-ND6-trnE-remnant CR2 with tandem repeat-trnF-rrnS. Phylogenetic analysis revealed Alaudidae and Panuridae are sister groups at the base of Sylvioidea, and sporadic losses of CR2 may occur in their common ancestor. CR sequence and phylogeny analysis indicated CR2 tandem repeats were generated within CR2, originating in the ancestor of all larks, rather than inherited from CR1. The secondary structure comparison of tandem repeat units within and between species suggested slipped-strand mispairing and DNA turnover as suitable models for explaining the origin and evolution of these repeats. This study reveals the evolutionary process of the CR2 containing tandem repeat in Alaudidae, providing reference for understanding the evolutionary characteristics and dynamics of tandem repeats.

Characteristics and Comparative Analysis of Mitochondrial Genomes of the Aphid Genus Hyalopterus Koch (Hemiptera: Aphididae: Aphidinae).

Using Illumina sequencing technology, we generated complete mitochondrial genomes (mitogenomes) of three constituent species of the aphid genus Hyalopterus Koch, Hyalopterus amygdali (Blanchard), Hyalopterus arundiniformis Ghulamullah, and Hyalopterus pruni (Geoffroy). The sizes of the Hyalopterus mitogenomes range from 15,306 to 15,410 bp, primarily due to variations in the length of non-coding regions. The Hyalopterus mitogenomes consist of 37 coding genes arranged in the order of the ancestral insect mitogenome, a control region, and a repeat region between trnE and trnF. According to the COI-based analysis, one previously reported mitogenome of H. pruni should be assigned to H. arundiniformis. The gene order, nucleotide composition, and codon usage in the Hyalopterus mitogenomes are highly conserved and similar to those of other species of Aphidinae. The tandem repeat units differ in nucleotide composition, length, and copy number across three Hyalopterus species. Within the widespread Eurasian species H. arundiniformis, variation in repeat units among different geographic populations is observed, indicating that the repeat region may provide valuable insights for studying the intraspecific diversification of aphids. Phylogenetic analyses based on 28 complete mitogenomes of Aphidinae supported the monophyly of Aphidinae, Aphidini, Macrosiphini, and two subtribes of Aphidini. Hyalopterus was monophyletic. H. amygdali and H. pruni formed a sister group, while H. arundiniformis was placed basally. Characterization of the mitogenomes of Hyalopterus provides valuable resources for further comparative studies and for advancing our understanding of the aphid mitogenome architecture.

A genome-wide spectrum of tandem repeat expansions in 338,963 humans

The Genome Aggregation Database (gnomAD), widely recognized as the gold-standard reference map of human genetic variation, has largely overlooked tandem repeat (TR) expansions, despite the fact that TRs constitute ∼6% of our genome and are linked to over 50 human diseases. Here, we introduce the TR-gnomAD (https://wlcb.oit.uci.edu/TRgnomAD), a biobank-scale reference of 0.86 million TRs derived from 338,963 whole-genome sequencing (WGS) samples of diverse ancestries (39.5% non-European samples). TR-gnomAD offers critical insights into ancestry-specific disease prevalence using disparities in TR unit number frequencies among ancestries. Moreover, TR-gnomAD is able to differentiate between common, presumably benign TR expansions, which are prevalent in TR-gnomAD, from those potentially pathogenic TR expansions, which are found more frequently in disease groups than within TR-gnomAD. Together, TR-gnomAD is an invaluable resource for researchers and physicians to interpret TR expansions in individuals with genetic diseases.

Variation within major internal repeats ofKSHV invivo.

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi's sarcoma (KS), yet the viral genetic factors that lead to the development of KS in KSHV-infected individuals have not been fully elucidated. Nearly, all previous analyses of KSHV genomic evolution and diversity have excluded the three major internal repeat regions: the two origins of lytic replication, internal repeats 1 and 2 (IR1 and IR2), and the latency-associated nuclear antigen (LANA) repeat domain (LANAr). These regions encode protein domains that are essential to the KSHV infection cycle but have been rarely sequenced due to their extended repetitive nature and high guanine and cytosine (GC) content. The limited data available suggest that their sequences and repeat lengths are more heterogeneous across individuals than in the remainder of the KSHV genome. To assess their diversity, the full-length IR1, IR2, and LANAr sequences, tagged with unique molecular identifiers (UMIs), were obtained by Pacific Biosciences' single-molecule real-time sequencing (SMRT-UMI) from twenty-four tumors and six matching oral swabs from sixteen adults in Uganda with advanced KS. Intra-host single-nucleotide variation involved an average of 0.16 per cent of base positions in the repeat regions compared to a nearly identical average of 0.17 per cent of base positions in the remainder of the genome. Tandem repeat unit (TRU) counts varied by only one from the intra-host consensus in a majority of individuals. Including the TRU indels, the average intra-host pairwise identity was 98.3 per cent for IR1, 99.6 per cent for IR2 and 98.9 per cent for LANAr. More individuals had mismatches and variable TRU counts in IR1 (twelve/sixteen) than in IR2 (two/sixteen). There were no open reading frames in the Kaposin coding sequence inside IR2 in at least fifty-five of ninety-six sequences. In summary, the KSHV major internal repeats, like the rest of the genome in individuals with KS, have low diversity. IR1 was the most variable among the repeats, and no intact Kaposin reading frames were present in IR2 of the majority of genomes sampled.

Mitogenomic and nuclear ribosomal transcription unit datasets support the synonymy of Paragonimus iloktsuenensis and P. ohirai (Paragonimidae: Platyhelminthes).

The complete mitogenome (mtDNA) of nominal Paragonimus iloktsuenensis (Paragonimidae: Trematoda) and the nuclear ribosomal transcription unit (rTU) coding region (rTU*: from 5'-terminus of 18S to 3'-terminus of 28S rRNA gene, excluding the external spacer region) of this species and of P. ohirai were obtained and used to further support the previously suggested synonymy of these taxa in the P. ohirai complex. The complete mitogenome of P. iloktsuenensis was 14,827bp long (GenBank: ON961029) and nearly identical to that of P. ohirai (14,818bp; KX765277), with a 99.12% nucleotide identity. The rTU* was 7543bp and 6932bp in these two taxa, respectively. All genes and spacers in the rTU were identical in length, with exception of the first internal transcribed spacer, which contained multiple tandem repeat units (6.7 for P. iloktsuenensis and 5.7 for P. ohirai). There was near 100% identity for the rTU genes. The phylogenetic topology inferred from the mtDNA and from individual gene regions (partial cox1 of 387bp and the ITS-2 of 282bp - 285bp) indicated a very close relationship consistent with synonymy of P. iloktsuenensis and P. ohirai. The datasets provided here will be useful for taxonomic reappraisal as well as studies of evolutionary and population genetics of the genus Paragonimus and family Paragonimidae.

First complete mitochondrial genome of Antheraea pernyi Guérin-Méneville 1855 (Lepidoptera: Saturniidae) from North Korea

This study reports the first complete mitochondrial genome of Antheraea pernyi Guérin-Méneville 1855 (Lepidoptera: Saturniidae) strain Dingzhou_1, a silkworm resource serving silk production in North Korea. The mitochondrial genome is circular with 15,573 bp in length encoding 37 typical mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes). The 553-bp A + T-rich region harbors a repeat region composed of 6 ∼ 38 bp tandem repeat units, as found in other known inbred strains from Chinese populations. The phylogenetic analysis clustered Dingzhou_1 from North Korea together with Chinese Liaoning population, suggesting that oak silkworm in North Korea might be introduced from her neighbor China Liaoning.

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.

Comparative analysis of the characteristics of Haplorchis taichui mitochondrial genome with Metagonimus yokogawai and its ribosomal transcription unit with H. pumilio (family Heterophyidae)

Minute intestinal flukes, Haplorchis taichui and H. pumilio, belong to the family Heterophyidae (Trematoda: Platyhelminthes), which have been studied very limited, especially the molecular markers of the mitochondrial genomes (mtDNA) and the ribosome transcription units (rTU or rDNA). We have obtained the complete mitochondrial genome of H. taichui and the coding part of ribosome transcription unit of H. taichui and H. pumilio of Vietnam. Nucleotide and amino acid data were compared between H. taichui and Metagonimus yokogawai for genomic/gene composition, codon usage (skew/skewness), and tandem repeat units (TRU). The complete mtDNA of H. taichui (strain Htai-QT3-VN) with the length of 15,120 bp and M. yokogawai (15,258 bp; Korea; KC330755) contains 36 genes, including 12 protein-coding genes (cox1, cox2, cox3, nad1, nad2, nad3, nad4L, nad4, nad5, nad6, atp6 and cob), 2 ribosomal RNA genes (rRNA); 22 transfer RNA (tRNA or trn) and a noncoding region (NCR) between trnE and trnG, divided into 2 sub-regions containing 5 TRUs (182–183 bp/TRU). H. taichui (Vietnam and Laos) uses A = 19.56%, T = 39.71%, G = 28.34%, C = 12.39% (A + T is 59.27% ​​and G + C is 40.73%) for mtDNA construction, whose skew/skewness value at A+T is negative (–0,340) and G+C is positive (0.392); for 12 protein-coding genes (PCGs) is similar; but for the mito-ribosomal genes (MRGs, of 16S/rrnL and 12S/rrnS) it is less for A+T (57.22%) and more for G+C (42.78%). M. yokogawai had lower A+T (mtDNA/55.68%; PCGs/55.96%; MRGs/54.15%) and higher G+C usage rate than H. taichui. H. taichui of Vietnam and Laos has 10,164 bp encoding for 3,376 amino acids to construct 12 PCGs with the mostly used codons as Phenylalanine (Phe-TTT) and Leucine (Leu-TTG), and the leastly used codonsas Glutamine (Gln-CAA), Arginine (Arg-CGC). Additional condon, Thr-ACA/ACC can be added as the least used in M. yokogawai. The rTU (from 5 '18S to 3' 28S) of H. taichui (7,268 bp) and H. pumilio (7,416 bp) were identified with 5 genomic regions including 18S rDNA, ITS1, 5.8S rDNA, ITS2 and 28S rDNA. The 18S and 5.8S genes of both species were of the same length (1,992 bp for 18S, 160 bp for 5.8S), but different for 28S genes (3,875 bp for H. taichui and 3,870 bp for H. pumilio). ITS1 in H. taichui (797 bp) and ITS2 in H. pumilio (280 bp) do not contain TRUs, whilst ITS1 in H. pumilio (1,106 bp) contains 5 TRUs(136 bp for 3 TRU and 116 bp for 2 TRUs); and ITS2 in H. taichui (444 bp) contain 3 TRUs (83–85 bp/each).

TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner.

The Tandem Repeat Annotation Library (TRAL) focuses on analyzing tandem repeat units in genomic sequences. TRAL can integrate and harmonize tandem repeat annotations from a large number of external tools, and provides a statistical model for evaluating and filtering the detected repeats. TRAL version 2.0 includes new features such as a module for identifying repeats from circular profile hidden Markov models, a new repeat alignment method based on the progressive Poisson Indel Process, an improved installation procedure and a docker container. TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via vital-it.ch/software/tral.

Phylogenetic analyses of ribosomal transcription units from Haplorchis taichui and H. pumilio species of Heterophyidae (Platyhelminthes: Opisthorchiata)

Heterophyidiasis caused by minute intestinal flukes becomes of public concern in many countries worldwide. Haplorchis taichui and H. pumilio, belonging to the family Heterophyidae (Platyhelminthes: Trematoda) are two of many infecting humans and commonly found in Vietnam. Sequence study of these two small intestinal flukes is still very limited, hence we need more prospective markers for taxonomic identification and classification. This study provides complete coding sequence of the ribosomal transcription units (rTU) from H. taichui and H. pumilio (Vietnamese samples) and demonstrates the use of complete 28S rDNA sequences for phylogenetic analysis.The complete coding sequence of the rTU (from 5' 18S to 3' 28S), consisting of complete 18S, ITS-1, 5.8S, ITS2 and complete 28S rRNA genes and spacers, from H. taichui (7,268 bp) and H. pumilio (7,416 bp) from human hosts in Vietnam, were determined and annotated. The 18S and 5.8S genes of both species were of the same length (1,992 bp/18S, 160 bp/5.8S), but 28S genes differed (3,875 bp/H. taichui and 3,870 bp/H. pumilio). ITS-1 in H. taichui (797 bp) and ITS-2 in H. pumilio (280 bp) do not contain tandem repeat units (TRUs), while ITS-1 in H. pumilio (1,106 bp) contains 3 TRUs of 136 bp/each and 2 TRUs of 116 bp/each and ITS-2 in H. taichui (444 bp) contain 3 TRUs (83–85 bp/each). A phylogenetic tree inferred from the alignment of complete 28S rDNA sequences of 32 trematode strains/species, including 2 Vietnamese Haplorchis spp. and 24 species of 8 families in the suborders Xiphidiata (families Nanophyetidae, Paragonimidae, Collyriclidae), Opisthorchiata (Heterophyidae, Opisthorchiidae), and Echinostomata (Echinostomatidae, Fasciolidae). and Schistosoma japonicum of the family Schistosomatidae is used as an outgroup. The topology of the phylogenetic tree clearly confirmed the status of the Vietnamese H. taichui and H. pumilio species. These species gathered in a group (in the family Heterophyidae) clearly identified in the position of "sister” group to those in the family Opisthorchiidae (suborder Opisthorchiata, superfamily Opisthorchioidea).

Characterization of the complete mitochondrial genome of a barklouse, Lepinotus sp. (Psocodea: Trogiomorpha: Trogiidae)

Barklice in the genus Lepinotus (Psocoptera: Trogiidae) are small, soft-bodied stored-product pests that are difficult to control. We sequenced and annotated the mitochondrial (mt) genome of Lepinotus sp. The mt genome of Lepinotus sp. is 16,299 bp in size with 74.4% A + T content. The gene order was highly conserved in some of the Trogimorpha barklice. Two types of tandem repeat units were identified in CR of Lepinotus sp. The phylogenetic analysis showed that Trogiidae species was the sister group to Lepidopsocidae barklice, and the suborder Troctomorpha was polyphyletic.

Mitochondrial genomes of eight Scelimeninae species (Orthoptera) and their phylogenetic implications within Tetrigoidea.

Scelimeninae is a key member of the pygmy grasshopper community, and an important ecological indicator. No mitochondrial genomes of Scelimeninae have been reported to date, and the monophyly of Scelimeninae and its phylogenetic relationship within Tetrigidae is still unclear. We sequenced and analyzed eight nearly complete mitochondrial genomes representing eight genera of Scelimeninae. These mitogenomes ranged in size from 13,112 to 16,380 bp and the order of tRNA genes between COII and ATP8 was reversed compared with the ancestral order of insects. The protein-coding genes (PCGs) of tetrigid species mainly with the typical ATN codons and most terminated with complete (TAA or TAG) stop codons. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene within Tetrigidae, while COI was the most conserved. The longest intergenic spacer (IGS) region in the mitogenomes was always found between tRNASer(UCN) and ND1. Additionally, tandem repeat units were identified in the longest IGS of three mitogenomes. Maximum likelihood (ML) and Bayesian Inference (BI) analyses based on the two datasets supported the monophyly of Tetriginae. Scelimeninae was classified as a non-monophyletic subfamily.

Identification and characterization of a Babesia bigemina thrombospondin-related superfamily member, TRAP-1: a novel antigen containing neutralizing epitopes involved in merozoite invasion

BackgroundThrombospondin-related anonymous protein (TRAP) has been described as a potential vaccine candidate for several diseases caused by apicomplexan parasites. However, this protein and members of this family have not yet been characterized in Babesia bigemina, one of the most prevalent species causing bovine babesiosis.MethodsThe 3186-bp Babesia bigemina TRAP-1 (BbiTRAP-1) gene was identified by a bioinformatics search using the B. bovis TRAP-1 sequence. Members of the TRAP and TRAP-related protein families (TRP) were identified in Babesia and Theileria through a search of the TSP-1 adhesive domain, which is the hallmark motif in both proteins. Structural modeling and phylogenetic analysis were performed with the identified TRAP proteins. A truncated recombinant BbiTRAP-1 that migrates at approximately 107 kDa and specific antisera were produced and used in Western blot analysis and indirect fluorescent antibody tests (IFAT). B-cell epitopes with neutralizing activity in BbiTRAP-1 were defined by enzyme-linked immunosorbent assays (ELISA) and invasion assays.ResultsThree members of the TRAP family of proteins were identified in B. bigemina (BbiTRAP-1 to -3). All are type 1 transmembrane proteins containing the von Willebrand factor A (vWFA), thrombospondin type 1 (TSP-1), and cytoplasmic C-terminus domains, as well as transmembrane regions. The BbiTRAP-1 predicted structure also contains a metal ion-dependent adhesion site for interaction with the host cell. The TRP family in Babesia and Theileria species contains the canonical TSP-1 domain but lacks the vWFA domain and together with TRAP define a novel gene superfamily. A variable number of tandem repeat units are present in BbiTRAP-1 and could be used for strain genotyping. Western blot and IFAT analysis confirmed the expression of BbiTRAP-1 by blood-stage parasites. Partial recognition by a panel of sera from B. bigemina-infected cattle in ELISAs using truncated BbiTRAP-1 suggests that this protein is not an immunodominant antigen. Additionally, bovine anti-recombinant BbiTRAP-1 antibodies were found to be capable of neutralizing merozoite invasion in vitro.ConclusionsWe have identified the TRAP and TRP gene families in several Babesia and Theileria species and characterized BbiTRAP-1 as a novel antigen of B. bigemina. The functional relevance and presence of neutralization-sensitive B-cell epitopes suggest that BbiTRAP-1 could be included in tests for future vaccine candidates against B. bigemina.Graphical

Complete mitochondrial genome of a blue-tailed skink Plestiodon capito (Reptilia, Squamata, Scincidae) and comparison with other Scincidae lizards.

Vertebrate mitochondrial genomes (mitogenomes) are valuable for studying phylogeny, evolutionary genetics and genomics. To date, however, compared to other vertebrate groups, our knowledge about the mitogenomes of skinks (the family Scincidae), even of reptile, has been relatively limited. In the present study, we determined the complete mitogenome of a blue-tailed skink Plestiodon capito for the first time, and compared it with other skinks available in GenBank. The circular genome is 17,344bp long, showing a typical vertebrate pattern with 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region (CR). The gene organization, nucleotide composition, and codon usage are similar to those from skinks previously published. Twelve out of 13 PCGs initiates with canonical start codon (ATG), while COX1 starts with GTG. The codon usage analysis revealed a preferential use of the LeuCUN (Leu1), Pro, and Thr codons with the A/U ending. All tRNAs in P. capito were predicted to fold into typical clover-leaf secondary structure, except tRNA-Ser AGY. The secondary structures of 12S rRNA and 16S rRNA comprises 34 helices and 56 helices, respectively. The alignment of the Plesitodon species CRs exhibited high genetic variability and rich A + T content. Besides, variable types and numbers of tandem repeat units were also identified in the CR of Plestiodon. Phylogenetic analyses recovered P. capito as the sister species to P. tunganus; monophyly of the Scincidae is well supported. Our results will help to better understand structure and evolution of the mitochondrial DNA control region in reptiles as well as the evolutionary status of P. capito, and to lay foundation for further phylogenetic study of skinks in a mitogenomic framework.

Characterization of the Complete Mitochondrial Genome of Drabescus ineffectus and Roxasellana stellata (Hemiptera: Cicadellidae: Deltocephalinae: Drabescini) and Their Phylogenetic Implications.

Simple SummaryDrabescini comprises over 225 species and 46 genera with a highly diverse tribe of Deltocephalinae. These species serve as vectors of numerous agricultural plant pathogens and also transmit plant viruses to host plants. Previous phylogenetic analyses in this tribe mainly focused on morphological characters and were restricted to several gene fragments. Furthermore, the taxonomic status and phylogenetic relationships of this tribe need to be further studied. Therefore, the mitogenome may provide additional molecular evidence to reconstruct the phylogeny of this group and further elucidate relationships among major lineages. In this study, we sequenced and analyzed two newly complete mitogenomes including Drabescus ineffectus and Roxasellana stellata. These two mitogenomes contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and the non-coding structure called A + T-control region. The Drabescini mitogenomes are highly conserved in base content and composition, genome size and order, protein-coding genes and codon usage, and secondary structure of tRNAs. Phylogenetic analyses using Bayesian inference and maximum likelihood methods indicated strong support for the monophyly of Drabescini. These results provide the comprehensive framework and valuable data toward the future resolution of phylogenetic relationships in this tribe.To explore the mitogenome characteristics and shed light on the phylogenetic relationships and molecular evolution of Drabescini species, we sequenced and analyzed the complete mitochondrial genome of two species including Drabescus ineffectus and Roxasellana stellata. The complete mitogenomes of D. ineffectus and R. stellata are circular, closed and double-stranded molecules with a total length of 15744 bp and 15361 bp, respectively. These two newly sequenced mitogenomes contain the typical 37 genes. Most protein-coding genes (PCGs) began with the start codon ATN and terminated with the terminal codon TAA or TAG, with an exception of a special initiation codon of ND5, which started with TTG, and an incomplete stop codon T-- was found in the Cytb, COX2, ND1 and ND4. All tRNAs could be folded into the canonical cloverleaf secondary structure except for the trnS1, which lacks the DHU arm and is replaced by a simple loop. The multiple tandem repeat units were found in A + T-control region. The sliding window, Ka/Ks and genetic distance analyses indicated that the ATP8 presents a high variability and fast evolutionary rate compared to other PCGs. Phylogenetic analyses based on three different datasets (PCG123, PCG12R and AA) using both Bayesian inference (BI) and maximum likelihood (ML) methods showed strong support for the monophyly of Drabescini.

Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes.

Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.

Signals of selection in the mitogenome provide insights into adaptation mechanisms in heterogeneous habitats in a widely distributed pelagic fish

Oceans are vast, dynamic, and complex ecosystems characterized by fluctuations in environmental parameters like sea surface temperature (SST), salinity, oxygen availability, and productivity. Environmental variability acts as the driver of organismal evolution and speciation as organisms strive to cope with the challenges. We investigated the evolutionary consequences of heterogeneous environmental conditions on the mitogenome of a widely distributed small pelagic fish of Indian ocean, Indian oil sardine, Sardinella longiceps. Sardines were collected from different eco-regions of the Indian Ocean and selection patterns analyzed in coding and non-coding regions. Signals of diversifying selection were observed in key functional regions involved in OXPHOS indicating OXPHOS gene regulation as the critical factor to meet enhanced energetic demands. A characteristic control region with 38–40 bp tandem repeat units under strong selective pressure as evidenced by sequence conservation and low free energy values was also observed. These changes were prevalent in fishes from the South Eastern Arabian Sea (SEAS) followed by the Northern Arabian Sea (NAS) and rare in Bay of Bengal (BoB) populations. Fishes belonging to SEAS exhibited accelerated substitution rate mainly due to the selective pressures to survive in a highly variable oceanic environment characterized by seasonal hypoxia, variable SST, and food availability.

Self-Assembly of Topologically Networked Protein-Ti3C2Tx MXene Composites.

Hierarchical organization plays an important role in the stunning physical properties of natural and synthetic composites. Limits on the physical properties of such composites are generally defined by percolation theory and can be systematically altered using the volumetric filler fraction of the inorganic/organic phase. In natural composites, organic materials such as proteins that interact with inorganic filler materials can further alter the hierarchical order and organization of the composite via topological interactions, expanding the limits of the physical properties defined by percolation theory. However, existing polymer systems do not offer a topological parameter that can systematically modulate the assembly characteristics of composites. Here, we present a composite based on proteins and titanium carbide (Ti3C2Tx) MXene that manifests a topological network that regulates the organization, and hence physical properties, of these biomimetic composites. We designed, recombinantly expressed, and purified synthetic proteins consisting of polypeptides with repeating amino acid sequences (tandem repeats) that have the ability to self-assemble into topologically networked biomaterials. We demonstrated that the interlayer distance between MXene sheets can be controlled systematically by the number of tandem repeat units. We varied the filler fraction and number of tandem repeat units to regulate the in-plane and out-of-plane electrical conductivities of these composites. Once Ti3C2Tx MXene sheets are separated enough to facilitate formation of cross-links in our proteins with the number of tandem repeat units reaching 11, the linear I-V characteristics of the composites switched into nonlinear I-V curves with a distinct hysteresis for out-of-plane electron transport, while the in-plane I-V characteristics remained linear. This highlights the impact of synthetic protein templates, which can be designed to modulate electronic transport in composites both isotropically and anisotropically.