Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment.

The canonical stop codons of the nuclear genome of the trypanosomatid Blastocrithidia nonstop are recoded. Here, we investigated the effect of this recoding on the mitochondrial genome and gene expression. Trypanosomatids possess a single mitochondrion and protein-coding transcripts of this genome require RNA editing in order to generate open reading frames of many transcripts encoded as 'cryptogenes'. Small RNAs that can number in the hundreds direct editing and produce a mitochondrial transcriptome of unusual complexity. We find B. nonstop to have a typical trypanosomatid mitochondrial genetic code, which presumably requires the mitochondrion to disable utilization of the two nucleus-encoded suppressor tRNAs, which appear to be imported into the organelle. Alterations of the protein factors responsible for mRNA editing were also documented, but they have likely originated from sources other than B. nonstop nuclear genome recoding. The population of guide RNAs directing editing is minimal, yet virtually all genes for the plethora of known editing factors are still present. Most intriguingly, despite lacking complex I cryptogene guide RNAs, these cryptogene transcripts are stochastically edited to high levels.

Trypanosoma cruzi strain and starvation-driven mitochondrial RNA editing and transcriptome variability.

Trypanosoma cruzi is a unicellular protistan parasitic species that is comprised of strains and isolates exhibiting high levels of genetic and metabolic variability. In the insect vector, it is known to be highly responsive to starvation, a signal for progression to a life stage in which it can infect mammalian cells. Most mRNAs encoded in its mitochondrion require the targeted insertion and deletion of uridines to become translatable transcripts. This study defined differences in uridine-insertion/deletion RNA editing among three strains and established the mechanism whereby abundances of edited (and, thus, translatable) mitochondrial gene products increase during starvation. Our approach utilized our custom T-Aligner toolkit to describe transcriptome-wide editing events and reconstruct editing products from high-throughput sequencing data. We found that the relative abundance of mitochondrial transcripts and the proportion of mRNAs that are edited varies greatly between analyzed strains, a characteristic that could potentially impact metabolic capacity. Starvation typically led to an increase in overall editing activity rather than affecting a specific step in the process. We also determined that transcripts CR3, CR4, and ND3 produce multiple open reading frames that, if translated, would generate different proteins. Finally, we quantitated the inherent flexibility of editing in T. cruzi and found it to be higher relative to that in a related trypanosomatid lineage. Over time, new editing domains or patterns could prove advantageous to the organism and become more widespread within individual transcriptomes or among strains.

Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae.

BACKGROUND: Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group. RESULTS: We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis. Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy. CONCLUSIONS: The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.

Novel Biocompatible Magnetoelectric MnFe2 O4 Core@BCZT Shell Nano-Hetero-Structures with Efficient Catalytic Performance.

Magnetoelectric (ME) small-scale robotic devices attract great interest from the scientific community due to their unique properties for biomedical applications. Here, novel ME nano hetero-structures based on the biocompatible magnetostrictive MnFe2 O4 (MFO) and ferroelectric Ba0.85 Ca0.15 Zr0.1 Ti0.9 O3 (BCZT) are developed solely via the hydrothermal method for the first time. An increase in the temperature and duration of the hydrothermal synthesis results in increasing the size, improving the purity, and inducing morphology changes of MFO nanoparticles (NPs). A successful formation of a thin epitaxial BCZT-shell with a 2-5 nm thickness is confirmed on the MFO NPs (77 ± 14 nm) preliminarily treated with oleic acid (OA) or polyvinylpyrrolidone (PVP), whereas no shell is revealed on the surface of pristine MFO NPs. High magnetization is revealed for the developed ME NPs based on PVP- and OA-functionalized MFO NPs (18.68 ± 0.13 and 20.74 ± 0.22 emu g-1 , respectively). Moreover, ME NPs demonstrate 95% degradation of a model pollutant Rhodamine B within 2.5 h under an external AC magnetic field (150 mT, 100 Hz). Thus, the developed biocompatible core-shell ME NPs of MFO and BCZT can be considered as a promising tool for non-invasive biomedical applications, environmental remediation, and hydrogen generation for renewable energy sources.

Platinum(IV) Carbonato Complexes: Formation via the Addition of CO2 to the [Pt(OH)6]2- Anion and Generation of Platinum(IV) Oxide Nanoparticles for the Preparation of Catalysts.

A combination of multinuclear nuclear magnetic resonance spectroscopy and theoretical calculation based on density functional theory was used for a speciation study of Pt in solutions prepared either by the interaction of [Pt(OH)6]2- with gaseous CO2 in an alkaline solution of platinum(IV) hydroxide ([Pt(OH)4(H2O)2]) or by the dissolution of [Pt(OH)4(H2O)2] in an aqueous KHCO3 solution. The formed solutions contained coexisting Pt(IV) carbonato complexes with κ1- and κ2-coordination modes. The gradual condensation of mononuclear Pt species in such bicarbonate solutions resulted in the formation of PtO2 nanoparticles aggregating into a solid precipitate on prolonged aging. The deposition of PtO2 particles from bicarbonate solutions was adapted for the preparation of Pt-containing heterogeneous catalysts: bimetallic Pt-Ni catalysts were prepared using various supporting materials (CeO2, SiO2, and g-C3N4) and tested for the activity in hydrazine-hydrate decomposition. All prepared materials showed high selectivity with respect to H2 production from the hydrazine-hydrate with PtNi/CeO2 showing the highest rate of H2 evolution. In the long-range evaluation, the PtNi/CeO2 catalyst operating at 50 °C showed an exceptional turnover number value of 4600 producing hydrogen at a 97% selectivity level and with a mean turnover frequency value of about 470 h-1. In the case of the PtNi/g-C3N4 catalyst, for the first time, the photodriven decomposition of hydrazine-hydrate was shown to enhance the productivity of the catalyst by 40%.

Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events.

Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.

High-Loaded Copper-Containing Sol-Gel Catalysts for Furfural Hydroconversion.

In this study, the high-loaded copper-containing catalysts modified with Fe and Al were successfully applied for the hydroconversion of furfural to furfuryl alcohol (FA) or 2-methylfuran (2-MF) in a batch reactor. The synthesized catalysts were studied using a set of characterization techniques to find the correlation between their activity and physicochemical properties. Fine Cu-containing particles distributed in an amorphous SiO2 matrix, which has a high surface area, provide the conversion of furfural to FA or 2-MF under exposure to high pressure of hydrogen. The modification of the mono-copper catalyst with Fe and Al increases its activity and selectivity in the target process. The reaction temperature strongly affects the selectivity of the formed products. At a H2 pressure of 5.0 MPa, the highest selectivity toward FA (98%) and 2-MF (76%) was achieved in the case of 35Cu13Fe1Al-SiO2 at the temperature of 100 °C and 250 °C, respectively.

Dynamics of Podospora anserina Genome Evolution in a Long-Term Experiment.

The Podospora anserina long-term evolution experiment (PaLTEE) is the only running filamentous fungus study, which is still going on. The aim of our work is to trace the evolutionary dynamics of the accumulation of mutations in the genomes of eight haploid populations of P. anserina. The results of the genome-wide analysis of all of the lineages, performed 8 years after the start of the PaLTEE, are presented. Data analysis detected 312 single nucleotide polymorphisms (SNPs) and 39 short insertion-deletion mutations (indels) in total. There was a clear trend towards a linear increase in the number of SNPs depending on the experiment duration. Among 312 SNPs, 153 were fixed in the coding regions of P. anserina genome. Relatively few synonymous mutations were found, exactly 38; 42 were classified as nonsense mutations; 72 were assigned to missense mutations. In addition, 21 out of 39 indels identified were also localized in coding regions. Here, we also report the detection of parallel evolution at the paralog level in the P. anserina model system. Parallelism in evolution at the level of protein functions also occurs. The latter is especially true for various transcription factors, which may indicate selection leading to optimization of the wide range of cellular processes under experimental conditions.

Sulfuric Acid Solutions of [Pt(OH)4(H2O)2]: A Platinum Speciation Survey and Hydrated Pt(IV) Oxide Formation for Practical Use.

The systematic study of the platinum speciation in sulfuric acid solutions of platinum (IV) hydroxide {[Pt(OH)4(H2O)2], HHPA} was performed with the use of a combination of methods. Depending on the prevailing Pt form, the three regions of H2SO4 concentration were marked: (1) up to 3 M H2SO4 forms unstable solutions gradually generating the PtO2·xH2O particles; (2) 4-12 M H2SO4, where the series of mononuclear aqua-sulfato complexes ([Pt(SO4)n(H2O)6-n]4-2n, where n = 0···4) dominate; and (3) 12 M and above, where, along with [Pt(SO4)n(H2O)6-n]4-2n species, the polynuclear Pt(IV) species and complexes with a bidentate coordination mode of the sulfato ligand are formed. For the first time, the salts of the aqua-hydroxo Pt(IV) cation [Pt(OH)2(H2O)4]SO4 (triclinic and monoclinic phases) were isolated and studied with a combination of methods, including the single-crystal X-ray diffraction. The formation of PtO2·xH2O particles in sulfuric acid solutions (1-3 M) of HHPA and their spectral characteristics and morphology were studied. The deposition of PtO2·xH2O was highlighted as a convenient method to prepare various Pt-containing heterogeneous catalysts. This possibility was illustrated by the preparation of Pt/g-C3N4 catalysts, which show an excellent performance in catalytic H2 generation under visible light irradiation with a quantum efficiency up to 5% and a rate of H2 evolution up to 6.2 mol·h-1 per gram of loaded platinum.

Effect of Phosphorus Precursor, Reduction Temperature, and Support on the Catalytic Properties of Nickel Phosphide Catalysts in Continuous-Flow Reductive Amination of Ethyl Levulinate.

Levulinic acid and its esters (e.g., ethyl levulinate, EL) are platform chemicals derived from biomass feedstocks that can be converted to a variety of valuable compounds. Reductive amination of levulinates with primary amines and H2 over heterogeneous catalysts is an attractive method for the synthesis of N-alkyl-5-methyl-2-pyrrolidones, which are an environmentally friendly alternative to the common solvent N-methyl-2-pyrrolidone (NMP). In the present work, the catalytic properties of the different nickel phosphide catalysts supported on SiO2 and Al2O3 were studied in a reductive amination of EL with n-hexylamine to N-hexyl-5-methyl-2-pyrrolidone (HMP) in a flow reactor. The influence of the phosphorus precursor, reduction temperature, reactant ratio, and addition of acidic diluters on the catalyst performance was investigated. The Ni2P/SiO2 catalyst prepared using (NH4)2HPO4 and reduced at 600 °C provides the highest HMP yield, which reaches 98%. Although the presence of acid sites and a sufficient hydrogenating ability are important factors determining the pyrrolidone yield, the selectivity also depends on the specific features of EL adsorption on active catalytic sites.

Tetranitratopalladate(II) Salts with Tetraalkylammonium Cations: Structural Aspects, Reactivity, and Applicability toward Palladium Deposition for Catalytic Applications.

A series of salts (R4N)2[Pd(NO3)4] (R = CH3, C2H5, n-C3H7; 1-3) were synthesized in high yield from a nitric acid solution of palladium. The salts were characterized by a combination of physicochemical methods, and their crystal structures were determined by X-ray diffraction. The conformation of the [Pd(NO3)4]2- anion was studied in detail using crystal structure data and density functional theory calculations. A combination of nonhygroscopicity and stability under normal conditions, together with thermolability, high solubility in various solvents, and the lability of nitrato ligands, makes salts 1-3 valuable starting materials for the synthesis of Pd compounds and the preparation of Pd-containing catalysts. In this work, these applications were illustrated by the synthesis of heteroleptic Pd(II) nitrato complexes with N-donor ligands and the preparation of Pd0.1Ni0.9/SiO2 catalysts, which worked well in H2 generation from hydrazine hydrate. Generally, it was shown that up to several weight percent of Pd can be deposited on various oxide/hydroxide supports using a straightforward chemisorption procedure from acetone solutions of 1-3.

Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool.

RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3' to 5' on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded. Thus, analysis of kinetoplastid mitochondrial transcriptomes has proven frustratingly complex. Here we present our analysis of Leptomonas pyrrhocoris mitochondrial cDNA deep sequencing reads using T-Aligner, our new tool which allows comprehensive characterization of RNA editing, not relying on targeted transcript amplification and on prior knowledge of final edited products. T-Aligner implements a pipeline of read mapping, visualization of all editing states and their coverage, and assembly of canonical and alternative translatable mRNAs. We also assess T-Aligner functionality on a more challenging deep sequencing read input from Trypanosoma cruzi. The analysis reveals that transcripts of cryptogenes of both species undergo very complex editing that includes the formation of alternative open reading frames and whole categories of truncated editing products.

Aging Induces Profound Changes in sncRNA in Rat Sperm and These Changes Are Modified by Perinatal Exposure to Environmental Flame Retardant.

Advanced paternal age at fertilization is a risk factor for multiple disorders in offspring and may be linked to age-related epigenetic changes in the father's sperm. An understanding of aging-related epigenetic changes in sperm and environmental factors that modify such changes is needed. Here, we characterize changes in sperm small non-coding RNA (sncRNA) between young pubertal and mature rats. We also analyze the modification of these changes by exposure to environmental xenobiotic 2,2',4,4'-tetrabromodiphenyl ether (BDE-47). sncRNA libraries prepared from epididymal spermatozoa were sequenced and analyzed using DESeq 2. The distribution of small RNA fractions changed with age, with fractions mapping to rRNA and lncRNA decreasing and fractions mapping to tRNA and miRNA increasing. In total, 249 miRNA, 908 piRNA and 227 tRNA-derived RNA were differentially expressed (twofold change, false discovery rate (FDR) p ≤ 0.05) between age groups in control animals. Differentially expressed miRNA and piRNA were enriched for protein-coding targets involved in development and metabolism, while piRNA were enriched for long terminal repeat (LTR) targets. BDE-47 accelerated age-dependent changes in sncRNA in younger animals, decelerated these changes in older animals and increased the variance in expression of all sncRNA. Our results indicate that the natural aging process has profound effects on sperm sncRNA profiles and this effect may be modified by environmental exposure.

Tetraalkylammonium Salts of Platinum Nitrato Complexes: Isolation, Structure, and Relevance to the Preparation of PtO x/CeO2 Catalysts for Low-Temperature CO Oxidation.

A series of tetraalkylammonium salts with anionic platinum nitrato complexes (Me4N)2[Pt2(µ-OH)2(NO3)8] (1), (Et4N)2[Pt2(µ-OH)2(NO3)8] (2), ( n-Pr4N)2[Pt2(µ-OH)2(NO3)8] (3b), ( n-Pr4N)2[Pt(NO3)6] (3a), and ( n-Bu4N)2[Pt(NO3)6] (4) were isolated from nitric acid solutions of [Pt(H2O)2(OH)4] in high yield. The structures of salts 2, 3a, 3b, and 4, prepared for the first time, were characterized by X-ray diffraction. The sorption of [Pt(NO3)6]2- and [Pt2(µ-OH)2(NO3)8]2- complexes onto the ceria surface from acetone solutions of salts 4 and 1 was examined. The dimeric anion was shown to quickly and irreversibly chemisorb onto the CeO2 carrier, selectively transforming into Pt(II) centers after thermal treatment, becoming active in the low-temperature CO oxidation reaction ( T50% = 110 °C at a space velocity of 240 000 h-1). By contrast, the homoleptic complex [Pt(NO3)6]2- did not interact with the ceria, which may be attributed to the substitutional inertness of the [Pt(NO3)6]2- anion. We believe that the strategy based on the sorption of polynuclear platinum nitrato complexes is an effective route to prepare ionic platinum species uniformly distributed on an oxide carrier for various catalytic applications.

The Influence of Cu and Al Additives on Reduction of Iron(III) Oxide: In Situ XRD and XANES Study.

The reduction of Fe-based nanocomposite catalysts doped with Al and Cu has been studied using in situ X-ray diffraction (XRD), in situ X-ray absorption near-edge structure (XANES), and temperature-programmed reduction (TPR) techniques. The catalysts have been synthesized by melting of iron, aluminum, and copper salts. According to XRD, the catalysts consist mainly of Fe2O3 and Al2O3 phases. Alumina is in an amorphous state, whereas iron oxide forms nanoparticles with the protohematite structure. The Al3+ cations are partially dissolved in the Fe2O3 lattice. Due to strong alumina-iron oxide interaction, the specific surface area of the catalysts increases significantly. TPR and XANES data indicate that copper forms highly dispersed surface CuO nanoparticles and partially dissolves in iron oxide. It has been shown that the reduction of iron(III) oxide by CO proceeds via two routes: a direct two-stage reduction of iron(III) oxide to metal (Fe2O3 → Fe3O4 → Fe) or an indirect three-stage reduction with the formation of FeO intermediate phases (Fe2O3 → Fe3O4 → FeO → Fe). The introduction of Al into Fe2O3 leads to a decrease in the rate for all reduction steps. In addition, the introduction of Al stabilizes small Fe3O4 particles and prevents further sintering of the iron oxide. The mechanism of stabilization is associated with the formation of Fe3- xAl xO4 solid solution. The addition of copper to the Fe-Al catalyst leads to the formation of highly dispersed CuO particles on the catalyst surface and a mixed oxide with a spinel-type crystalline structure similar to that of CuFe2O4. The low-temperature reduction of Cu2+ to Cu0 accelerates the Fe2O3 → Fe3O4 and FeO → Fe transformations but does not affect the Fe3O4 → FeO/Fe stages. These changes in the reduction properties significantly affect the catalytic performance of the Fe-based nanocomposite catalysts in the low-temperature oxidation of CO.

High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution.

Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.

Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters.

The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with those of other vertebrate species. In birds and mammals, the α- and ß-globin genes are segregated into separate clusters located on different chromosomes and organized into chromatin domains of different types, whereas in cold-blooded vertebrates, including Danio rerio, α- and ß-globin genes are organized into common clusters. The major globin gene locus of Danio rerio is of particular interest as it is located in a genomic area that is syntenic in vertebrates and is controlled by a conserved enhancer. We have found that the major globin gene locus of Danio rerio is structurally and functionally segregated into two spatially distinct subloci harboring either adult or embryo-larval globin genes. These subloci demonstrate different organization at the level of chromatin domains and different modes of spatial organization, which appears to be due to selective interaction of the upstream enhancer with the sublocus harboring globin genes of the adult type. These data are discussed in terms of evolution of linear and 3D organization of gene clusters in vertebrates.

A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling.

Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.

Extraordinary Genetic Diversity in a Wood Decay Mushroom.

Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10(-8) (95% CI: 1.1 × 10(-8) to 4.1 × 10(-8)) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics.

Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.

BACKGROUND: Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. RESULTS: We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50 Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100-10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. CONCLUSIONS: Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.