Search Results (903)

Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus. Full article

Flower fragrance is a crucial ornamental and economic trait of Dendrobium chrysotoxum, and the most abundant and diverse aroma-active compounds are terpenes. Terpene synthase (TPS) is the ultimate enzyme for the biosynthesis of various types of terpenes, and TPS genes were identified as the key regulators governing the spatiotemporal release of volatile terpene compounds. Until recently, the TPS gene family in D. chrysotoxum has remained largely unexplored. Our study characterizes the TPS genes in D. chrysotoxum and identifies 37 DcTPS gene family members. It helped identify the DcTPS genes, gene characteristics, the phylogeny relationship, conserved motif location, gene exon/intron structure, cis-elements in the promoter regions, protein–protein interaction (PPI) network, tissue specific expression and verification of the expression across different flowering stages and floral organs. Three highly expressed DcTPS genes were cloned, and their functions were verified using a transient expressed in tobacco leaves. Further functional verification showed that the proteins encoded by these genes were enzymes involved in monoterpene synthesis, and they were all involved in the synthesis of linalool. This study comprehensively expatiates on the TPS gene family members in D. chrysotoxum for the first time. These data will help us gain a deeper understanding of both the molecular mechanisms and the effects of the TPS genes. Furthermore, the discovery that three TPS-b genes (DcTPS 02, 10, 32) specifically drive linalool-based scent in D. chrysotoxum, will provide new insights for expanding the TPS-b subfamily in orchids and identifying the linalool synthases contributing to orchid fragrance. Full article

The possible origin of four cultivated species of the genus Avena of different ploidy and different subgenome composition (A. strigosa, A. abyssinica, A. byzantina, and A. sativa) from possible wild species was investigated. The region of the internal transcribed spacer ITS1 and the 5.8S rRNA gene in the cultivated species was studied with next-generation sequencing (NGS), and the patterns of occurrence and distribution of the ribotypes were compared among them and with those of the wild species. According to these data diploid, A. strigosa is more closely related to the diploid A. hirtula than to polyploid oats, and it could have evolved independently of polyploid cultivated species. The tetraploid Avena abyssinica could be a cultivated derivative of A. vaviloviana. Two hexaploid cultivated species, A. byzantina and A. sativa, could have a different origin; A. sativa could be the cultivated form of A. fatua, whereas A. byzantina could originate independently. It was found that the oat species with the A and C subgenomes, even with strong morphological and karyological differences, could intercross and pass the further stages of introgression producing a new stable combination of genomes. Our data show that almost all species of Avena could form an introgressive interspecies complex. Full article

Background: The mitochondrial genome has been used for understanding higher-level phylogenetic relationships within Coccomorpha. we sequenced and analyzed the first mitochondrial genome of Xylococcus castanopsis Wu & Huang, 2017 to elucidate its genomic features and phylogenetic position. Methods: The complete mitogenome was assembled using NOVOPlasty and annotated with MITOS. We analyzed genome organization, codon usage, and tRNA structures. Phylogenetic relationships were reconstructed using 13 protein-coding genes from 19 scale insect species with Bayesian Inference and Maximum Likelihood methods. Result: The mitochondrial genome is 16,363 bp in size and contains the typical 37 mitochondrial genes, with an A + T content of 89.2%. All protein-coding genes start with the ATN and end with TAA/TAG or a single T- residue. Sixteen tRNAs exhibit the typical cloverleaf structure, while the remaining six lack either the dihydrouridine (DHU) or TΨC (T) arm. Gene rearrangements occur only in individual tRNAs and transpositions between the gene clusters trnS2-ND1 and trnL1-rrnL-trnV-rrnS. Phylogenetic analysis consistently place Xylococcidae as a sister group to all scale insects except Matsucoccidae. Conclusions: This study provides the first complete mitogenome for Xylococcidae, revealing characteristic gene rearrangements. Phylogenetic reconstruction resolves the phylogenetic position of Xylococcidae as a distinct lineage sister to all scale insects except Matsucoccidae, providing critical evolutionary insights. Full article

India and Sri Lanka are known to exhibit high levels of biological diversity with many endemic taxa, such as the enigmatic scorpion genus Charmus Karsch, 1879. Members of this genus are rarely encountered in the field and are also known to be morphologically very similar, which impedes their systematic assessment. Our dedicated efforts towards sampling the members of the genus resulted in the collection of important material, which allowed us to carry out a thorough systematic revision of the genus using an integrated taxonomic approach. We propose several taxonomic changes based on the results of a detailed morphological study supported by molecular data. Charmus indicus Hirst, 1915 is synonymized with Charmus laneus Karsch, 1879, owing to the lack of morphological differences and low genetic divergence between the two taxa. We designate a neotype for Charmus sinhagadensis Tikader and Bastawade, 1983, and describe a new species from Sirumalai (Tamil Nadu, India). Moreover, we provide the first molecular phylogeny of Charmus based on Cytochrome c Oxidase subunit I (COI), 16S rRNA (16S) and 28S rRNA (28S) genes. The phylogenetic position of the genus within the family Buthidae C. L. Koch, 1837 is also tested using an independent genome-wide dataset (Ultraconserved Elements). Topological congruence and discrepancies between the phylogenies generated with Sanger sequences and the Ultraconserved Elements are commented on, and the reliability of these datasets when evaluating phylogenetic relationships at different hierarchical levels is further discussed. Full article

In order to examine the phylogeny and evolutionary history of the subfamily Notodontinae (Noctuoidea: Notodontidae), a molecular systematic study was conducted, mainly based on mitochondrial protein-coding genes (PCGs) generated by high-throughput sequencing, including 57 species belonging to 37 genera, together with 64 other species within Notodontidae and 14 outgroups, with the dataset comprising 10,980 bp of nucleotide sequences. An individual dataset of orthologous genes (OGs) comprising 589 loci (919,493 bp in total) was utilized as a supporting analysis for the result from the mitochodrial dataset. In this study, the monophyly of Notodontinae was well supported, with the internal clades consisting of three tribes—Stauropini, Notodontini, and Fentoniini—and supporting evidence found in the male genital characteristics. Furthermore, Neodrymoniaini Kobayashi, 2016 syn. nov. was synonymized with Fentoniini Matsumura, 1929. Divergence time estimation for Notodontinae, conducted using phylogenetic results across five fossil calibration points, suggested that Notodontinae originated around 22.71 Ma, and the most recent common ancestor of Stauropini and Fentoniini diverged between 24.44 and 20.23 Ma, followed by the emergence of Stauropini between 23.83 and 19.53 Ma. Then, Notodontini diverged around 23.60–19.10 Ma, with the youngest tribe, Fentoniini, dividing in 21.70–16.63 Ma. In summary, this study provided a robust foundation for classification within the terminal clades of Notodontidae and laid the groundwork for further research on phylogenetic relationships across the whole family. Full article

Background/Aims: Ledrinae comprises about 460 described species across five tribes and represents an early-branching, morphologically distinctive lineage of leafhoppers, yet its intra-subfamilial relationships remain ambiguous owing to limited mitogenomic sampling. Here, we sequence and annotate the complete mitochondrial genome of Petalocephala arcuata—only the 18th Ledrinae mitogenome—to broaden taxon coverage within the genus and furnish critical molecular data for rigorously testing Ledrinae monophyly and refining tribal and genus level phylogenetic hypotheses. Methods: In this study, we sequenced and annotated the complete mitochondrial genome of P. arcuata via Illumina sequencing and de novo assembly, and reconstructed the phylogeny of 62 Cicadellidae species using maximum likelihood and Bayesian inference methods. Results: The 14,491 bp circular mitogenome of P. arcuata contains 37 genes with 77.4% A+T. All PCGs use ATN start codons except ND5 (TTG), and codon usage is A or U biased. Of 22 tRNAs, only trnS1 lacks a DHU arm, while the others adopt the canonical cloverleaf structure. Bayesian inference and maximum likelihood analyses produced broadly congruent topologies with mostly high nodal support, recovering Ledrinae as monophyletic and clustering all Petalocephala species into a well-supported clade. Conclusions: In this study, we enriched the molecular resources for the genus Petalocephala by sequencing, annotating, and analyzing the complete mitochondrial genome of P. arcuata. Phylogenetic reconstructions based on these genomic data align closely with previous morphological diagnoses, further confirming the monophyly of the genus Petalocephala. Full article

Tereancistrum is a common genus of Neotropical monopisthocotylans; however, information on its diversity and phylogeny remains limited. In this study, we describe four new species of Tereancistrum parasitizing the gills of Prochilodus brevis (Characiformes: Prochilodontidae) from a weir in the state of Ceará, Brazil. Tereancistrum spiralocirrum n. sp. and Tereancistrum scleritelongatum n. sp. are characterized by a dextro-ventral vaginal pore and a Y-shaped dorsal bar. Notably, Tereancistrum spiralocirrum n. sp. is the first species in the genus to possess a male copulatory organ (MCO) with multiple rings (16 to 18). In contrast, Tereancistrum ancistrum n. sp. and Tereancistrum kritskyi n. sp. are distinguished by a sinistral vaginal pore, a sclerotized MCO in the form of a coiled tube with slightly more than one clockwise ring, and an accessory piece that is non-articulated with the base of the MCO. However, Tereancistrum ancistrum n. sp. is unique in lacking a dorsal bar. Sequences of the LSU rDNA obtained from seven species of Tereancistrum parasitizing P. brevis and Leporinus piau, along with published sequences of other Dactylogyridae members, were included in the molecular analyses. Phylogenetic reconstructions supported the monophyly of Tereancistrum. Full article

Surveys were conducted in the village of Shamgona in the Samegrelo Region of West Georgia, and two nematode species belonging to the Oscheius genus and a population of Heterorhabditis bacteriophora were isolated. Integrative diagnosis, combining morphology, PCA, sequencing and phylogeny, was carried for Oscheius sp. from the soil of hazelnut orchard. This population shows high similarity at morphological and morphometrical levels with O. cyrus from Iran, and the main distinctive features with O. cyrus from Iran are the presence of eight lateral lines and males. Sequence and phylogenetic analyses by using ITS, D2–D3 expansion domains of the 28S rRNA gene, the partial 18S rRNA gene, and the mitochondrial COI confirmed the identification as O. cyrus. A second population of Oscheius sp. and H. bacteriophora was characterized only at the molecular and phylogenetic level. The phylogenetic analyses, based on ITS and D2–D3 expansion domains, revealed the occurrence of O. insectivorus in Georgia grouping with O. insectivorus sequences with high support. The phylogenetic trees of H. bacteriophora, based on D2–D3 expansion domains, ITS, the partial 18S rRNA gene, and mitochondrial COI confirmed the high variability among geographical populations. The present study reports on the occurrence of two species of Oscheius in Georgia for the first time. Full article

The genus Travassosius Khalil, 1922, the smallest genus in the subfamily Trichostrongylinae (family Trichostrongylidae), primarily infects the only two extant beaver species worldwide and can be lethal in severe infections. However, the mitochondrial genome evolution of Travassosius remains poorly understood, and its phylogenetic placement within Trichostrongylinae is still unresolved. In this study, we applied both morphological techniques (differential interference contrast microscopy) and molecular tools (nuclear ITS2 and mitochondrial genome) to examine T. rufus Khalil, 1922. Specimens were collected from the Sino-Mongolian beaver, a subspecies of the Eurasian beaver native to the Ulungur River Basin in northern Xinjiang, China. This work presents the first complete mitochondrial genome sequence and annotation of T. rufus, and it is also the first mitochondrial genome reported for the genus Travassosius. The mitochondrial genome of T. rufus measures 13,646 bp and contains 36 genes, including 12 protein-coding genes (PCGs) (excluding atp8), 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis based on amino acid sequences of 12 mitochondrial PCGs strongly supports the distinctiveness of the genus Travassosius. Additionally, T. rufus appears to be closely related to Nematodirus within Trichostrongylinae. This study also addresses the possible consequences of parasitic infection for the Sino-Mongolian beaver and offers a scientific foundation for conserving this endangered subspecies and managing parasitic diseases in its population. Full article

As one of the four primary evolutionary groups within myriapods, centipedes (Chilopoda) comprise approximately 3150 valid species. Recent molecular studies have begun to elucidate the phylogeny and time to divergence in Chilopoda; yet, identifying scutigeromorphs at the species level remains a notoriously challenging task. In this study, we obtained seven new complete mitogenomes of Thereuopoda clunifera (Wood, 1862) to investigate the phylogeny and divergence times of Chilopoda. Both maximum likelihood (ML) and Bayesian inference (BI) analyses recovered the relationship of (Scutigeromorpha + (Scolopendromorpha + (Lithobiomorpha + Geophilomorpha))). For Scutigeromorpha, seven newly sequenced mitogenomes of T. clunifera were divided into four distinct clades. Divergence time estimates suggest that the basal split of Chilopoda occurred during the Middle Ordovician period, with the origins of Scolopendromorpha, Lithobiomorpha, and Geophilomorpha dating to the Devonian period. Factors such as warm climates, coevolution between predator and prey, and the rifting of the Hainan Island may have driven the diversification of Scutigeromorpha. Based on genetic distance, the delimitation of molecular species, phylogenetic relationships, and divergence time analyses, we identified three cryptic species that existed within T. clunifera. This exceptionally high degree of hidden diversity can be ascribed to the morphological stasis that has occurred since the Paleozoic era and taxonomic impediment. Full article

Infectious bronchitis virus (IBV) is a chicken pathogen present in commercial poultry farms worldwide. It is classified within the species Avian coronavirus, genus Gammacoronavirus. As with other members of the family Coronaviridae, it has a single positive-sense RNA genome with 27.6 Kb and presents viral particles with a typical crown-like aspect due to the spike (S) transmembrane glycoprotein. IBV has a remarkable capacity for genetic recombination and mutation, resulting in many genotypes and antigenic variants over evolutionary time. Currently, it is classified into nine genetic types (GI to GIX) and 41 (1 to 41) lineages disseminated worldwide. In South America, IBV was first identified in early commercial poultry production ventures in Brazil in the 1950s. Since then, this virus has been frequently detected in commercial South American poultry farms, being classified into serotypes in the first decades and genotypes more recently. IBVs of the Massachusetts (Mass) serotype were initially detected and vaccine strains of this serotype were used extensively on commercial poultry farms. Other serotypes/genotypes were identified later, with almost all of them classified in the current genetic type I (GI). In addition, five GI lineages (GI-1, -11, -13, -16, and -23) have been associated with the main infectious bronchitis outbreaks in the continent, with some variations in the occurrence according to the countries and the period of time. Molecular epidemiological surveillance of IBV genetic types and lineages is necessary to anticipate potential outbreaks, revealing patterns of viral evolution and dissemination, as well as to guide the selection of appropriate vaccine strains and immunization programs. Full article

This study aimed to elucidate the mitochondrial genome organization of Chlorogomphus papilio and the phylogenetic relationships of Chlorogomphidae. We used the Illumina MiSeq sequencing platform to sequence the mitochondrial genome of C. papilio, which was subsequently assembled, annotated, and analyzed. Bayesian inference, maximum likelihood, and maximum parsimony methods were employed to construct the mitochondrial phylogenetic tree of 25 species of Chlorogomphidae based on 16S rRNA and cox1 genes. We observed that the mitochondrial genome of C. papilio is 15,251 bp in length and includes 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding control region. All PCGs start with a typical ATN codon. While cox1, cox2, cox3, and nad5 end with an incomplete termination codon (T), the remaining PCGs terminate with TAG. The secondary structure of the 22 tRNAs showed that only the trnS1 gene lacked the dihydrouracil arm (DHU arm), whereas the rest formed a typical cloverleaf structure. Additionally, 32 G-U mismatches were observed in the secondary structure. Phylogenetic analyses indicated that C. papilio and C. magnificus are sister species. Divergence time analyses indicated that Chlorogomphidae originated around 111.04 Ma, with C. papilio diverging from the common ancestor shared with C. magnificus approximately 58.51 Ma. This divergence is likely linked to the Paleocene–Eocene Thermal Maximum (PETM) and the tectonic uplift of the Himalayas, which created warm, humid habitats and contributed to geographic isolation. This study contributes to a better understanding of the mitochondrial genome and phylogeny of C. papilio, providing valuable molecular markers for further genetic studies. Full article

Background/Objectives: Aloa lactinea, class Insecta, order Lepidoptera, superfamily Noctuoidea, family Erebidae, and subfamily Arctiinae, is a polytrophic agricultural pest. However, there are still many sequences missing for Arctiinae from mitochondrial whole-genome sequences. Methods: In this study, we determined and analyzed the complete mitochondrial genome sequence of A. lactinea. Furthermore, based on the sequencing results, we used the Bayesian inference, maximum likelihood, and maximum reduction methods to analyze the phylogenies of 18 species of the Hypophora subfamily. Results: The mitochondrial genome was found to be a circular double-stranded DNA with a length of 15,380 bp and included 13 protein-coding genes (PCG_S), 22 tRNA genes, 2 rRNA genes, and one control region. With the exception of tRNA^Ser(AGC), all the tRNA genes could form conventional clover structures. There were 23 intergenic spacer regions with lengths of 1–52 bp and six gene overlaps with lengths of 1–8 bp. The control region was located between rrnS and tRNA^Met genes and comprised 303 bp and an AT content of 74.25%. Conclusions: The results showed that A. lactinea is closely related to Hyphantria cunea. Our results suggest that Syntomini is phylogenetically distinct from Arctiini and may warrant separate tribal status within Arctiinae. This study is dedicated to researching the mitochondrial genome and phylogenetic relationships of A. lactinea, providing a molecular basis for its classification. Full article

The living gymnosperms include about 1200 species in five major groups: cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes (conifers II). Molecular phylogenetic studies have yet to reach a unanimously agreed-upon relationship among them. Moreover, cytonuclear phylogenetic incongruence has been repeatedly observed in gymnosperms. We collated a comprehensive dataset from available genomes of 17 gymnosperms across the five major groups and added our own high-quality assembly of a species from Podocarpaceae (the second largest conifer family) to increase sampling width. We used these data to infer reconciled nuclear species phylogenies using two separate methods to ensure the robustness of our conclusions. We also reconstructed organelle phylogenomic trees from 42 mitochondrial and 82 plastid genes from 38 and 289 gymnosperm species across the five major groups, respectively. Our nuclear phylogeny consistently recovers the Ginkgo–cycads clade as the first lineage split from other gymnosperm clades and the Pinaceae as sister to gnetophytes (the Gnepines hypothesis). In contrast, the mitochondrial tree places cycads as the earliest lineage in gymnosperms and gnetophytes as sister to cupressophytes (the Gnecup hypothesis) while the plastomic tree supports the Ginkgo–cycads clade and gnetophytes as the sister to cupressophytes. We also examined the effect of mitochondrial RNA editing sites on the gymnosperm phylogeny by manipulating the nucleotide and amino acid sequences at these sites. Only complete removal of editing sites has an effect on phylogenetic inference, leading to a closer congruence between mitogenomic and nuclear phylogenies. This suggests that RNA editing sites carry a phylogenetic signal with distinct evolutionary traits. Full article