Analysis Of Molecular Data Research Articles

Relating Invasibility and Invasiveness: Case Study of Impatiens parviflora

Data on alien species show that plant invasions are caused by a complex combination of characteristics of invasive species (invasiveness) and characteristics of invaded environment (invasibility).Impatiens parviflorais one of Europe’s top invasive species. The present study aimed to evaluate molecular diversity of populations of highly invasive in LithuaniaI. parvifloraby applying several DNA markers and relating genetic parameters to abiotic and biotic environment. For sampling, urban forests, riparian forests, and agrarian shrublands were selected. Three different DNA-based techniques, Simple Sequence Repeats (SSR), Inter Simple Sequence Repeat (ISSR) markers, and Random Amplified Polymorphic DNA (RAPD), were used for detecting genetic variation between 21 populations. All population individuals were monomorphic and homozygotic for four loci and heterozygotic for one locus by SSR analysis. Hierarchical analyses of molecular variance at ISSR and RAPD loci revealed significant differentiation of populations depending on geographic zones of the country. Bayesian Structure analyses of molecular data demonstrated existence of many genetic clusters and this finding is in support to multiple introduction of the species. The polymorphism extent at ISSR loci was positively correlated with the total coverage of herbaceous plant species. The coverage byI. parviflorawas negatively correlated with the total number of herbaceous species and light in the sites. Our results indicate that Lithuanian sites withI. parvifloramight be distinguished by high soil nutrient levels. According to the principal component analysis, the coverage byI. parviflorawas a more important variable of populations compared to molecular data or parameters of abiotic environment. In conclusion, complexity of invasibility and invasiveness factors determine the variability ofI. parviflorasites, including genetic traits, coverage of invasive species and conditions of environment that were significant and interrelated.

Phylogeny, origin and diversification of the Dasylirion genus based on matK and rbcL sequences

AbstractThe Dasylirion genus is highly represented in the arid and semi-arid regions of Mexico and USA, playing important ecological and economical roles. Inferring the evolutionary patterns of this group will eventually facilitate understanding biological phenomena and outlining conservation and usage strategies. We performed a molecular phylogenetic analysis based on two chloroplast DNA regions: maturase-K gene (matK) and the large subunit of ribulose-1,5-bisphosphate carboxylase gene (rbcL). We constructed a phylogenetic tree by maximum likelihood with GTR as the sequence substitution model and a relaxed clock, inferred diversification patterns by lineage through time and explored the diversification rates of Dasylirion by the Yule model. The study included 11 species of the genus, which represent 50% of all its known species. We used two calibration points to date the tree, one based on fossil records of Acorus gramineus, and the other on the estimated stem age of the Yucca genus. The combined sequences of the two partial genes comprised 1455 bp and 18 polymorphic sites. We estimated an average substitution rate of 0.0005 nucleotide per million years for the concatenated DNA sequences. The molecular dating analysis estimated that the Dasylirion genus appeared more than 5.46 million years ago, with a rate of diversification of 0.0466 net speciation events per million years. The estimated age represents a lower bound, since not all Dasylirion species are included. These findings are consistent with other origin and diversification hypotheses for arid-land Asparagaceae in the Mexican highlands as a result of geomorphological events in North America.

Unraveling the evolutionary history of the snakefly family Inocelliidae (Insecta: Raphidioptera) through integrative phylogenetics.

Inocelliidae is one of the two extant families of the holometabolan order Raphidioptera (snakeflies), with the modern fauna represented by seven genera and 44 species. The evolutionary history of the family is little-known. Here we present the first phylogenetic and biogeographical analyses based on a worldwide sampling of taxa and datasets combined with morphological characters and mitochondrial genomes, aiming to investigate the intergeneric phylogeny and historical biogeography of Inocelliidae. The phylogenetic inference from the combined analysis of morphological and molecular data recovered the sister-group relationship between a clade of (Negha + Indianoinocellia) + Sininocellia and a clade of Fibla + the Inocellia clade (interiorly nested by Amurinocellia and Parainocellia). Amurinocellia stat.r. and Parainocellia stat.r. et emend.n. are relegated to subgeneric status within Inocellia, whereas a newly erected subgenus of Inocellia, Epinocellia subgen.n., accommodates the former Parainocellia burmana (U. Aspöck and H. Aspöck, 1968) plus a new species Inocellia (Epinocellia) weii sp.n. Further, the Inocellia crassicornis group constitutes the nominotypical subgenus Inocellia stat.n., but the Inocellia fulvostigmata group is paraphyletic. Diversification within Inocelliidae is distinguished by an Eocene divergence leading to extant genera and a Miocene radiation of species. A biogeographical scenario depicts how the diverse inocelliid fauna from East Asia could have originated from western North America via dispersal across the Beringia during the early Tertiary, and how the Miocene ancestors of Inocellia could have accomplished long-distance dispersals via the Tibet-Himalayan corridor or eastern Palaearctic to western Palaearctic. Our results shed new light specifically on the evolution of Inocelliidae and, in general, the Raphidioptera.

Phylogenetic phytogeography of selected groups of seagrasses (Monocotylendoneae - Alismatales) based on analysing of genes 5.8S rRNA and RuBisCo large subunit

Seagrasses are representatives of the families Cymodoceaceae, Posidoniaceae, Zosteraceae, Hydrocharitaceae (Monocotylendoneae - Alismatales), adapted to growing in seawaters and all their important life circle events are taking place under the water including pollination and distribution of diasporas. Seagrasses are widespread in the littoral areas of the World Ocean, except for Antarctica, and play an important ecosystem role. Due to the insufficiently studied history of dispersal and formation of modern seagrasses habitats, we carried out a phylogenetic analysis of representatives of the families Cymodoceaceae (Amphibolis, Halodule, Syringodium, Cymodocea, and Thalassodendron), Posidoniaceae (Posidonia), Zosteraceae (Zostera, and Phyllospadix), and Hydrocharitaceae (Enhalus, Halophila, and Thalassia). The cladograms constructed based on molecular data analysis of the 5.8S ribosomal RNA and ribulose–1,5–bisphosphate carboxylase/oxygenase large subunit genes are used as the basis for reconstructing the history of dispersal of the studied taxa. It is found that the main stages of dispersal of selected groups of seagrasses took place in the Late Cretaceous period. The main track of historical distribution is largely predetermined by the modern ranges of almost all genera of seagrasses, stretches from the southwestern waters of eastern Gondwana to the northwestern waters of the Eurasian part of Laurasia. The main route of movement of diasporas and seagrasses populations was the Tethys water area, which was modified in the Late Mesozoic and early Cenozoic. It was revealed that the main method of dispersal of seagrasses was long-distance dispersal, which is confirmed by both molecular genetic data and very fast (on a geological time scale) processes of penetration into new water areas, and analysis of the features of dissemination of modern representatives. An alternative vicar scenario was proposed only for the reconstruction of the formation of the Posidonia range.

Diatom Biodiversity and Speciation Revealed by Comparative Analysis of Mitochondrial Genomes

Diatoms (Bacillariophyta) constitute one of the most diverse and ecologically significant groups of phytoplankton, comprising 100,000–200,000 species in three classes Bacillariophyceae, Mediophyceae, and Coscinodiscophyceae. However, due to the limited resolution of common molecular markers including 18S rDNA, 28S rDNA, ITS, rbcL, and cox1, diatom biodiversity has not been adequately ascertained. Organelle genomes including mitochondrial genomes (mtDNAs) have been proposed to be “super barcodes” for distinguishing diatom species because of their rich genomic content, and the rapid progress of DNA sequencing technologies that has made it possible to construct mtDNAs with increasing throughout and decreasing cost. Here, we constructed complete mtDNAs of 15 diatom species including five Coscinodiscophyceae species (Guinardia delicatula, Guinardia striata, Stephanopyxis turris, Paralia sulcata, and Actinocyclus sp.), four Mediophyceae species (Hemiaulus sinensis, Odontella aurita var. minima, Lithodesmioides sp., and Helicotheca tamesis), and six Bacillariophyceae species (Nitzschia ovalis, Nitzschia sp., Nitzschia traheaformis, Cylindrotheca closterium, Haslea tsukamotoi, and Pleurosigma sp.) to test the practicality of using mtDNAs as super barcodes. We found that mtDNAs have much higher resolution compared to common molecular markers as expected. Comparative analysis of mtDNAs also suggested that mtDNAs are valuable in evolutionary studies by revealing extensive genome rearrangement events with gene duplications, gene losses, and gains and losses of introns. Synteny analyses of mtDNAs uncovered high conservation among species within an order, but extensive rearrangements including translocations and/or inversions between species of different orders within a class. Duplication of cox1 was discovered for the first time in diatoms in Nitzschia traheaformis and Haslea tsukamotoi. Molecular dating analysis revealed that the three diatom classes split 100 Mya and many diatom species appeared since 50 Mya. In conclusion, more diatom mtDNAs representing different orders will play great dividends to explore biodiversity and speciation of diatoms in different ecological regions.

MOLECULAR CHARACTERIZATION OF THREE SPECIES OF PRAYING MANTIDS (DICTYOPTERA; MANTODEA) FROM SINDH, PAKISTAN

In the present experiment, sequencing of three species of mantodea belonging to the family Mantidae is conducted in iBOL (International Barcode of Life) University of Guelph, Canada. In this study cytochrome oxidase subunit I (CO1) gene data set is represented on various of Mantodea viz Mantis religiosa Linne, Archimantis latistyla Serville, Sphodromantis lineola Burmeister, Sphodromantis viridis Forskal, Blepharosis mendica Fabricius, Hierodula patellifera Serville, Rivetina baetica Rambur, Empusa unicornis Saussure and Statilia maculate Thunberg, shipped to iBOL Canada, for molecular data analyses, but only three species blasted results were got. Earlier many species and their sibling species were misidentified on morphological examination. However, in the present study molecular characteristics (DNA-based) species assignments has made it possible to overcome these doubts.

A meta-analysis of genetic divergence versus phenotypic plasticity in walnut cultivars (Juglans regia L.)

Persian walnut (Juglans regia L.), is very auspicious plant species of Iran from both economical and food points of views. Both wildly grown as well as cultivated forms of this plant species are scattered in different geographical regions of the country and are a valuable source for edible nut as well as job employment. Scattered published data on genetic diversity of this important plant species are mainly based on different molecular data analyses; therefore a meta-analysis of the same cultivars based on several different molecular markers including DNA-sequences and multi-locus markers was conducted to provide a detailed insight on genetic structure of walnuts. The results indicated a moderated genetic variability of about 40 percent in the studied cultivars; however these cultivars are genetically differentiated as revealed by Fst and AMOVA. HGT analyses revealed that the cultivars phylogeny differs to some degree by different markers and therefore a heat map was constructed to reveal the cultivars relationships based on combined molecular data. A higher Pst value was obtained compared to that of Fst genetic differentiation, therefore, it seems that local adaptation and selection have played role in the walnut cultivars’ morphological divergence. LFMM analysis identified some adaptive multi-locus alleles in the studied walnut cultivars.

Fine-scale diversity in Rhodocybe mellea (Entolomataceae, Basidiomycota), with a description of a new variety and notes on sclerotia formation in Rhodocybe

This study investigates morphological and genetic diversity in Rhodocybe mellea, after a new record of this species in the Brazilian Atlantic Forest. Phylogenetic analysis of molecular data (nrITS and nrLSU) and pairwise genetic distances, provide support for the recognition of cryptic lineages within R. mellea co-occurring in the Neotropics. We propose Rhodocybe mellea var. depressa as morphologically characterized by its depressed pileus, conspicuous sclerobasidia, small flexuous-cylindrical pseudocystidia, and a smooth cutis pileipellis. In addition, we also determine the position of nrITS sequences of some sclerotium-forming fungi collected in the same area, and confirm the genus Rhodocybe as a producer of this survival structure. Our findings provide unique information on Rhodocybe in South America, and highlight the relevance of approaches that address fine-scale diversity for fungal taxonomy.

Phylogeographic analysis of Ligidium japonicum (Isopoda: Ligiidae) and its allied species reveals high biodiversity and genetic differentiation in the Kanto region, Japan

AbstractResearch of the diversity and evolutionary history of Japanese soil invertebrates is scarce. Molecular data analysis can help to elucidate species classifications and evolutionary processes. We analyzed the mitochondrial cytochrome oxidase subunit I (COI) and nuclear 28S rDNA genes and the morphology of the male pleopod 2 endopod of Ligidium japonicum and its allied species from 67 sites in Hokkaido, Honshu and Shikoku, where only L. japonicum is thought to occur. We found males of the L. japonicum complex with a pleopod 2 endopod morphology matching that of the L. japonicum syntype specimens, except for the number of denticles at the inner margin. There were also more than five species that differed morphologically from the L. japonicum complex, and most of these species had allopatric distributions despite the absence of obvious barriers. A time‐calibrated molecular phylogeny implied that the L. japonicum complex of the Kanto region first differentiated allopatrically in the mountains; this was followed by independent dispersal of three lineages to the Kanto Plain and Boso Peninsula, where secondary contact occurred. Two of the three sympatrically distributed L. japonicum complex lineages had a significant difference in the number of denticles at the inner margin of male pleopod 2 endopods. This variation implies the presence of cryptic species within the L. japonicum complex.

Rhipidocotyle husi n. sp. and three known species of Bucephalidae Poche, 1907 from the East Asian Region: morphological and molecular data.

AbstractMorphological data and the first molecular data are provided for four species of the trematode family Bucephalidae Poche, 1907 from marine and freshwater teleost fish species of East Asia. A new species, Rhipidocotyle husi n. sp., was isolated from Huso dauricus from the Amur River, Russia. Adult worms of this species were distinguished from their congeners Rhipidocotyle illense and Rhipidocotyle kovalai by morphological analysis. Three other known species were identified: Bucephalus skrjabini and Prosorhynchus cf. squamatus were detected in Siniperca chuatsi from the Amur River and in Myoxocephalus spp. from the Okhotsk Sea, Russia, respectively, while Prosorynchoides karvei was extracted from Strongylura strongylura from Halong Bay, Vietnam. The 28S ribosomal DNA (rDNA)-based phylogenetic analysis showed that the new species formed a shared polytomy clade with Rhipidocotyle fennica. Phylogenetic analysis of all available molecular data showed that four genera, namely Rhipidocotyle, Bucephalus, Prosorynchoides and Prosorhynchus, are para- or polyphyletic. Molecular-based phylogenetic analysis of morphologically validated bucephalid species indicated that three genera – Rhipidocotyle, Bucephalus and Prosorynchoides – were monophyletic. The genus Prosorhynchus maintained paraphyly, and P. cf. squamatus was more closely related to Dollfustrema spp. than to other Prosorhynchus spp. These findings do not exclude the possibility that representatives of Dollfustrema and P. cf. squamatus belong to the same genus.

Resolution of the Eremophila tietkensii (Scrophulariaceae) species complex based on congruence between morphological and molecular pattern analyses

Eremophila R.Br. comprises at least 238 species endemic to Australia, with many more having not yet been formally described. Three putative new taxa, namely, E. sp. Hamersley Range (K. Walker KW 136), E. sp. Calvert Range (A. A. Burbidge 738) and E. sp. Rudall River (P. G. Wilson 10512), were segregated from a broadly defined E. tietkensii F.Muell. & Tate by J. Hurter at the Western Australian Herbarium in 2012. Both E. sp. Hamersley Range and E. sp. Rudall River are listed as being of conservation concern in Western Australia, the former occurring in the Pilbara region in areas of prospective interest for mining development. We sought to determine whether these phrase-named entities should be formally described as new species, using multivariate analyses of morphometric and molecular data derived from specimens in the Western Australia Herbarium. Eremophila sp. Rudall River could not be adequately separated from E. tietkensii by either morphological or molecular data, and is here included within that species. By contrast, E. sp. Hamersley Range and E. sp. Calvert Range are clearly morphologically and genetically distinct. We thus describe them here as the new species E. naaykensii A.L.Curtis & K.R.Thiele and E. hurteri A.L.Curtis & K.R.Thiele. The recognition of these taxa will help inform their conservation prioritisation and subsequent management.

Taxonomy, phylogeny and identification of Chaetomiaceae with emphasis on thermophilic species.

Chaetomiaceae comprises phenotypically diverse species, which impact biotechnology, the indoor environment and human health. Recent studies showed that most of the traditionally defined genera in Chaetomiaceae are highly polyphyletic. Many of these morphology-based genera, such as Chaetomium, Thielavia and Humicola, have been redefined using multigene phylogenetic analysis combined with morphology; however, a comprehensive taxonomic overview of the family is lacking. In addition, the phylogenetic relationship of thermophilic Chaetomiaceae species with non-thermophilic taxa in the family is largely unclear due to limited taxon sampling in previous studies. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of genera and species belonging to Chaetomiaceae, including an extensive taxon sampling of thermophiles. A multigene phylogenetic analysis based on the ITS (internal transcribed spacers 1 and 2 including the 5.8S nrDNA), LSU (D1/D2 domains of the 28S nrDNA), rpb2 (partial RNA polymerase II second largest subunit gene) and tub2 (β-tubulin gene) sequences was performed on 345 strains representing Chaetomiaceae and 58 strains of other families in Sordariales. Divergence times based on the multi-gene phylogeny were estimated as aid to determine the genera in the family. Genera were delimited following the criteria that a genus must be a statistically well-supported monophyletic clade in both the multigene phylogeny and molecular dating analysis, fall within a divergence time of over 27 million years ago, and be supported by ecological preference or phenotypic traits. Based on the results of the phylogeny and molecular dating analyses, combined with morphological characters and temperature-growth characteristics, 50 genera and 275 species are accepted in Chaetomiaceae. Among them, six new genera, six new species, 45 new combinations and three new names are proposed. The results demonstrate that the thermophilic species fall into seven genera (Melanocarpus, Mycothermus, Remersonia, Thermocarpiscus gen. nov., Thermochaetoides gen. nov., Thermothelomyces and Thermothielavioides). These genera cluster in six separate lineages, suggesting that thermophiles independently evolved at least six times within the family. A list of accepted genera and species in Chaetomiaceae, together with information on their MycoBank numbers, living ex-type strains and GenBank accession numbers to ITS, LSU, rpb2 and tub2 sequences is provided. Furthermore, we provide suggestions how to describe and identify Chaetomiaceae species.

Identification of potential inhibitors for Hematopoietic Prostaglandin D2 synthase: Computational modeling and molecular dynamics simulations

To design a new therapeutic agent for Hematopoietic Prostaglandin D2 synthase (hPGDS), a set of 60 molecules with different molecular scaffolds were (range of pIC50 values are from 8.301 to 3.932) considered to create a pharmacophore model. Further, identification of potential hPGDS inhibitors were carried out by using virtual screening with different databases (from 15,74,182 molecules). The molecular screening was performed by using different sequential methods right from Pharmacophore based virtual screening, molecular docking, MM-GBSA studies and ADME property analysis. Based on the molecular screening and visual data analysis, 4 molecules were further subjected to molecular dynamics (MD) simulation study. Outcomes of the present study conclude with a new proposed molecule. Molecule SP1 show a good range of interaction with human hPGDS enzyme in comparison to the marketed compounds i.e., HQL-79, TFC-007, HPGDS inhibitor I and TAS-204.

The EurOPDX Data Portal: an open platform for patient-derived cancer xenograft data sharing and visualization

BackgroundPatient-derived xenografts (PDX) mice models play an important role in preclinical trials and personalized medicine. Sharing data on the models is highly valuable for numerous reasons – ethical, economical, research cross validation etc. The EurOPDX Consortium was established 8 years ago to share such information and avoid duplicating efforts in developing new PDX mice models and unify approaches to support preclinical research. EurOPDX Data Portal is the unified data sharing platform adopted by the Consortium.Main bodyIn this paper we describe the main features of the EurOPDX Data Portal (https://dataportal.europdx.eu/), its architecture and possible utilization by researchers who look for PDX mice models for their research. The Portal offers a catalogue of European models accessible on a cooperative basis. The models are searchable by metadata, and a detailed view provides molecular profiles (gene expression, mutation, copy number alteration) and treatment studies. The Portal displays the data in multiple tools (PDX Finder, cBioPortal, and GenomeCruzer in future), which are populated from a common database displaying strictly mutually consistent views.(Short) ConclusionEurOPDX Data Portal is an entry point to the EurOPDX Research Infrastructure offering PDX mice models for collaborative research, (meta)data describing their features and deep molecular data analysis according to users’ interests.

The ecological responses of bacterioplankton during a Phaeocystis globosa bloom in Beibu Gulf, China highlighted by integrated metagenomics and metatranscriptomics

The interaction between bacteria and phytoplankton during bloom events is complicated throughout the developmental processes of algal blooms. The detailed ecological roles of bacterioplankton during algal blooms still need to be investigated comprehensively. With the assistance of omics techniques, the composition and function of bacterioplankton were studied during the blooming and recession periods of Phaeocystis globosa in the Beibu Gulf, China. The transcriptionally active taxa of Vibrio, which correlated with most functional genes, were enriched in the blooming period, whereas the active microbial groups, such as Erythrobacter and Candidatus puniceispirillum, increased significantly in the recession period of the P. globosa bloom. The transcriptional analyses indicated the blooming and recession periods of P. globosa had different impacts on the function of bacterioplankton, including shifts in expression of specific metabolic pathways for variable nutritional utilization and their advantage in bacterial motility, quorum sensing, and extracellular secretion. Overall, the integrated field investigation and in-depth analysis of molecular data highlighted the difference of bacterial community during the outbreak and collapse stages of P. globosa bloom, and provided fundamental data for better understanding of the bacterial community in response to blooming and recession of the P. globosa bloom.

SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data.

MotivationSingle-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate variants calls remains challenging.ResultsWe introduce SmMIP-tools, a comprehensive computational method that promotes the detection of single nucleotide variants and short insertions and deletions from smMIP-based sequencing. Our approach delivered near-perfect performance when benchmarked against a set of known mutations in controlled experiments involving DNA dilutions and outperformed other commonly used computational methods for mutation detection. Comparison against clinically approved diagnostic testing of leukaemia patients demonstrated the ability to detect both previously reported variants and a set of pathogenic mutations that did not pass detection by clinical testing. Collectively, our results indicate that increased performance can be achieved when tailoring data processing and analysis to its related technology. The feasibility of using our method in research and clinical settings to benefit from low-cost smMIP technology is demonstrated.Availability and implementationThe source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). Raw sequencing data generated in this study have been submitted to the European Genome-Phenome Archive (EGA; https://ega-archive.org) and can be accessed under accession number EGAS00001005359.Supplementary information Supplementary data are available at Bioinformatics online.

How Gas-Solid Interaction Matters in Graphene-Doped Silica Aerogels.

It was interesting to experimentally find that the thermal insulation of silica aerogels was improved by doping graphene sheets with high heat conductivity. The underlying mechanism is investigated in the present work from the perspective of gas-solid interaction using a comprehensive analysis of molecular dynamics (MD) simulations, theoretical modeling, and experimental data. The MD-modeled small pores are demonstrated to effectively represent big pores in silica aerogels because of similar heat conduction physics, because it is found that adsorption does not contribute to gas heat conduction. Meanwhile, based on the experimentally measured density, the porous structures are schematically re-engineered using molecular modeling for the first time. The evaluated pore size distributions numerically present a consistency with available experimental data. Inspired by the visualization of the 3D pore structure, we proposed a graphene/silica/nitrogen model to evaluate the role of graphene in heat conduction: it can not only reduce effective gas collision (impede heat transport) but also enhance the gas-solid coupling effect. The former is dominant because of the high porosity, leading to an improvement in thermal insulation. The competition between them can be the reason for the "trade-off" phenomenon in the graphene doping effect in the available experiment.

Fiber-Like Organization as a Basic Principle for Euchromatin Higher-Order Structure.

A detailed understanding of the principles of the structural organization of genetic material is of great importance for elucidating the mechanisms of differential regulation of genes in development. Modern ideas about the spatial organization of the genome are based on a microscopic analysis of chromatin structure and molecular data on DNA–DNA contact analysis using Chromatin conformation capture (3C) technology, ranging from the “polymer melt” model to a hierarchical folding concept. Heterogeneity of chromatin structure depending on its functional state and cell cycle progression brings another layer of complexity to the interpretation of structural data and requires selective labeling of various transcriptional states under nondestructive conditions. Here, we use a modified approach for replication timing-based metabolic labeling of transcriptionally active chromatin for ultrastructural analysis. The method allows pre-embedding labeling of optimally structurally preserved chromatin, thus making it compatible with various 3D-TEM techniques including electron tomography. By using variable pulse duration, we demonstrate that euchromatic genomic regions adopt a fiber-like higher-order structure of about 200 nm in diameter (chromonema), thus providing support for a hierarchical folding model of chromatin organization as well as the idea of transcription and replication occurring on a highly structured chromatin template.

Mitogenomic phylogeny resolves Cuneopsis (Bivalvia: Unionidae) as polyphyletic: The description of two new genera and a new species

AbstractFreshwater mussels are known to have two types of mitochondrial DNA (mtDNA) transmitted separately through oocytes and sperms, namely, maternal (F‐type) and paternal (M‐type) mtDNA. The additional suite of mitochondrial genes provides a great opportunity to resolve phylogenetically problematic relationships. East Asian freshwater mussels of the genus Cuneopsis were considered a compact group of taxa having wedge‐shaped shells. However, preliminary results from previous studies challenged the monophyly of Cuneopsis, and the exact phylogenetic relationships among Cuneopsis and its allied genera are yet to be determined with comprehensive species sampling. Here, we evaluated species boundaries in Cuneopsis based on COI barcoding and obtained 11 new F‐ and M‐type mitogenomes via genome skimming to elucidate the evolutionary history of Cuneopsis. COI barcode data supported the validity of all sampled six Cuneopsis species (missing C. kiangsiensis). Our mitochondrial phylogenomic analyses confirmed that the currently recognized genus Cuneopsis sensu lato was polyphyletic, recovering three well‐supported clades. Molecular dating analysis suggested Cuneopsis s.l. diversified at ~58.06 million years ago in the Paleogene. Hereby, we propose two new genera, that is, Arcuneopsis gen. nov. and Pseudocuneopsis gen. nov. Additionally, we report a new species, Pseudocuneopsis sichuanensis sp. nov., from Chengdu, Sichuan, China, and a newly recorded species from China, Cuneopsis demangei.

Melanodevriesia, a New Genus of Endolichenic Oleaginous Black Yeast Recovered from the Inner Mongolia Region of China

Black yeasts are a phylogenetically diverse group of ascomycetous fungi that may exist in both unicellular and mycelial morphs. This group of fungi contains numerous commercially significant species as well as others whose precise roles are unknown, such as endolichenic species. There is currently a paucity of data about endolichenic black yeast species. To bridge this gap, we surveyed China's Inner Mongolia Autonomous Region in July 2019. Several fungal species associated with diverse lichens were isolated during this survey. Among these were two isolates of a previously unknown species of oleaginous black yeast fromMycosphaerellales. Analyses of morphological and molecular data revealed that these two isolates were closely related toXenodevriesia strelitziicola(Xenodevriesiaceae), although with significant differences. As a result, we established the genusMelanodevriesia gen. nov.to describe this previously unknown species,Melanodevriesia melanelixiae sp. nov.In addition, we used Transmission Electron Microscopy to visualise the intracellular oil bodies metabolised by this fungus in its unicellular state. The black yeast species identified in this study may have a wide range of commercial applications. More research is needed to determine the chemical composition of the microbial oil synthesized by this fungus and whether it has commercial value.