Phylogeny Reconstruction Research Articles

The First Complete Chloroplast Genome Sequence of Secale strictum subsp. africanum Stapf (Poaceae), the Putative Ancestor of the Genus Secale.

Secale strictum ssp. africanum (synonym Secale africanum), a putative ancestor of the genus Secale, has been classified within Secale strictum, although recent phylogenetic studies suggest that it represents a distinct species. This study reports the first complete chloroplast genome of S. africanum, highlighting its structure, genetic composition, and phylogenetic relationships within Secale and related Triticiceae species. Phylogeny reconstruction based on the maximum-likelihood method reveals notable genetic similarity between S. strictum and S. africanum, supporting their genetic and phylogenetic distinction. Here, we assembled the complete, annotated chloroplast genome sequence of Secale strictum ssp. africanum. The genome is 137,068 base pair (bp) long. It is the first complete chloroplast genome that can be used as a reference genome for further analysis. The genome can be accessed on GenBank with the accession number OQ700974. This work sheds light on the evolutionary history of Secale and contributes to our understanding of chloroplast genomics in cereal ancestors, with potential applications in improving cereal crop resilience, advancing breeding strategies, and informing conservation efforts for genetic diversity.

Comprehensive phylogenetic analysis of newly detected rodent adenoviruses sheds light on ancient host-switches.

Here we provide a comprehensive update on the diversity and genetic relatedness of adenoviruses occurring in rodents. Extensive PCR screenings revealed the presence of adenoviral DNA in samples originating from representatives of 17 rodent species from four different suborders of Rodentia. Distinct sequences of 28 different adenoviruses were obtained from the positive samples. Out of these, 20 were from hitherto unknown, putative novel adenoviruses, whereas 6 were variants of previously published murine adenoviruses. Additionally, two known viruses, guinea pig adenovirus 1 and squirrel adenovirus 1 were also detected. By PCR and primer walking, we determined the sequence of a considerable part of the genomic DNA of squirrel adenovirus 1, detected in red squirrel (Sciurus vulgaris) samples from Germany previously. We annotated the almost complete genome sequence of a novel mastadenovirus found by data mining in the bulk data of the Ord's kangaroo rat (Dipodomys ordii) genome project. We revisited the sequence of the gene of E1B 19 K protein of mouse adenovirus 3. In contrast to the prototype strain, where a truncated version of this gene has been found, in our sample of mouse adenovirus 3, it seemed to be intact. Based on phylogeny reconstructions, all rodent adenoviruses clustered in the genus Mastadenovirus. Interestingly, however, there wasn't a common monophyletic clade encompassing every adenovirus of rodent origin. Instead, three major lineages were observed. Because two lineages contained viral sequences deduced from samples of three suborders, and one consisted almost exclusively of adenoviruses from the family Muridae, we hypothesize there has been a long-term coevolution with the rodent hosts, as a result of possible ancient host-switch events. Several putative viruses appeared in distinct branches further away from the three clades. Thus, the evolutionary past of the adenoviruses of rodents remains to be studied further.

The vertebrate small leucine-rich proteoglycans: amplification of a clustered gene family and evolution of their transcriptional profile in jawed vertebrates.

Small Leucine-Rich Proteoglycans (SLRPs) are a major family of vertebrate proteoglycans. In bony vertebrates, SLRPs have a variety of functions from structural to signaling and are found in extracellular matrices, notably in skeletal tissues. However, there is little or no data on the diversity, function and expression patterns of SLRPs in cartilaginous fishes, which hinders our understanding of how these genes evolved with the diversification of vertebrates, in particular regarding the early events of whole genome duplications that shaped gnathostome and cyclostome genomes. We used a selection of chromosome-level assemblies of cartilaginous fish and other vertebrate genomes for phylogeny and synteny reconstructions, allowing better resolution and understanding of the evolution of this gene family in vertebrates. Novel SLRP members were uncovered together with specific loss events in different lineages. Our reconstructions support that the canonical SLRPs have originated from different series of tandem duplications that preceded the extant vertebrate last common ancestor, one of them even preceding the extant chordate last common ancestor. They then further expanded with additional tandem and whole-genome duplications during the diversification of extant vertebrates. Finally, we characterized the expression of several SLRP members in the small-spotted catshark Scyliorhinus canicula and from this, inferred conserved and derived SLRP expression in several skeletal and connective tissues in jawed vertebrates.

Orchard: Building large cancer phylogenies using stochastic combinatorial search.

Phylogenies depicting the evolutionary history of genetically heterogeneous subpopulations of cells from the same cancer, i.e., cancer phylogenies, offer valuable insights about cancer development and guide treatment strategies. Many methods exist that reconstruct cancer phylogenies using point mutations detected with bulk DNA sequencing. However, these methods become inaccurate when reconstructing phylogenies with more than 30 mutations, or, in some cases, fail to recover a phylogeny altogether. Here, we introduce Orchard, a cancer phylogeny reconstruction algorithm that is fast and accurate using up to 1000 mutations. Orchard samples without replacement from a factorized approximation of the posterior distribution over phylogenies, a novel result derived in this paper. Each factor in this approximate posterior corresponds to a conditional distribution for adding a new mutation to a partially built phylogeny. Orchard optimizes each factor sequentially, generating a sequence of incrementally larger phylogenies that ultimately culminate in a complete tree containing all mutations. Our evaluations demonstrate that Orchard outperforms state-of-the-art cancer phylogeny reconstruction methods in reconstructing more plausible phylogenies across 90 simulated cancers and 14 B-progenitor acute lymphoblastic leukemias (B-ALLs). Remarkably, Orchard accurately reconstructs cancer phylogenies using up to 1,000 mutations. Additionally, we demonstrate that the large and accurate phylogenies reconstructed by Orchard are useful for identifying patterns of somatic mutations and genetic variations among distinct cancer cell subpopulations.

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.

DNA sequencing of multiple bulk samples from a tumor provides the opportunity to investigate tumor heterogeneity and reconstruct a phylogeny of a patient's cancer. However, since bulk DNA sequencing of tumor tissue measures thousands of cells from a heterogeneous mixture of distinct sub-populations, accurate reconstruction of the tumor phylogeny requires simultaneous deconvolution of cancer clones and inference of ancestral relationships, leading to a challenging computational problem. Many existing methods for phylogenetic reconstruction from bulk sequencing data do not scale to large datasets, such as recent datasets containing upwards of ninety samples with dozens of distinct sub-populations. We develop an approach to reconstruct phylogenetic trees from multi-sample bulk DNA sequencing data by separating the reconstruction problem into two parts: a structured regression problem for a fixed tree [Formula: see text], and an optimization over tree space. We derive an algorithm for the regression sub-problem by exploiting the unique, combinatorial structure of the matrices appearing within the problem. This algorithm has both asymptotic and empirical improvements over linear programming (LP) approaches to the problem. Using our algorithm for this regression sub-problem, we develop fastBE, a simple method for phylogenetic inference from multi-sample bulk DNA sequencing data. We demonstrate on simulated data with hundreds of samples and upwards of a thousand distinct sub-populations that fastBE outperforms existing approaches in terms of reconstruction accuracy, sample efficiency, and runtime. Owing to its scalability, fastBE enables both phylogenetic reconstruction directly from indvidual mutations without requiring the clustering of mutations into clones, as well as a new phylogeny constrained mutation clustering algorithm. On real data from fourteen B-progenitor acute lymphoblastic leukemia patients, fastBE infers mutation phylogenies with fewer violations of a widely used evolutionary constraint and better agreement to the observed mutational frequencies. Using our phylogeny constrained mutation clustering algorithm, we also find mutation clusters with lower distortion compared to state-of-the-art approaches. Finally, we show that on two patient-derived colorectal cancer models, fastBE infers mutation phylogenies with less violation of a widely used evolutionary constraint compared to existing methods.

TreeWave: command line tool for alignment-free phylogeny reconstruction based on graphical representation of DNA sequences and genomic signal processing

BackgroundGenomic sequence similarity comparison is a crucial research area in bioinformatics. Multiple Sequence Alignment (MSA) is the basic technique used to identify regions of similarity between sequences, although MSA tools are widely used and highly accurate, they are often limited by computational complexity, and inaccuracies when handling highly divergent sequences, which leads to the development of alignment-free (AF) algorithms.ResultsThis paper presents TreeWave, a novel AF approach based on frequency chaos game representation and discrete wavelet transform of sequences for phylogeny inference. We validate our method on various genomic datasets such as complete virus genome sequences, bacteria genome sequences, human mitochondrial genome sequences, and rRNA gene sequences. Compared to classical methods, our tool demonstrates a significant reduction in running time, especially when analyzing large datasets. The resulting phylogenetic trees show that TreeWave has similar classification accuracy to the classical MSA methods based on the normalized Robinson-Foulds distances and Baker’s Gamma coefficients.ConclusionsTreeWave is an open source and user-friendly command line tool for phylogeny reconstruction. It is a faster and more scalable tool that prioritizes computational efficiency while maintaining accuracy. TreeWave is freely available at https://github.com/nasmaB/TreeWave.

The principle of ecological and molecular consensus in reconstructed plague microbe <i>Yersinia pestis</i> phylogeny

In the second half of the 20th century, through the efforts of scientists from many countries, a coherent theory of natural plague foci (sylvatic plague) was formulated, attempted to describe the history of the origin and evolution of the causative agent of plague infection, the microbeYersinia pestis. But the accumulated knowledge in this regard remained extremely limited. Envisioned by the modern phylogenetics, the methods of phylogenetic constructions in the pregenomic time were rather primitive, “manual”, characteristic of early empirico-intuitive Haeckel phylogenetics. Since the beginning of the 21st century, the introduction of genomic methodologies in the study of the plague pathogen allowed to detail the intraspecific diversity (subspecies, genovariants) of this particularly dangerous pathogen at the level of geographical and local populations (individual natural foci) around the world and to bring the diagnostics and description of intraspecific diversity to a high degree of perfection. Two important discoveries were made. First, the direct ancestor of the plague microbe was reliably established, it turned out to be the causative agent of intestinal infection — Far Eastern scarlet-like fever (Y. pseudotuberculosis0:1b). Secondly, the evolutionary youth of the plague pathogen was shown, the “molecular clock” showed the time of its divergence from the ancestral population no earlier than 30 thousand years ago. Thus, the root of the phylogenetic tree ofY. pestiswas fully characterized. Nevertheless, molecular genetic (MG) achievements do not yet allow to reveal the secrets of its phylogeny, i.e. the origin and sequence of world expansion. The most important reason is the high dependence of the MG of phylogeny reconstructions on the choice of evolutionary model for the analyzed characters: the model of neutral evolution is traditionally accepted, but its adequacy in relation toY. pestisphylogeny is questioned by many well-known ecological (in the broad sense) facts. At the same time, MG achievements contributed to the creation of an ecological (ECO) approach based on the provisions of the theory of natural plague foci in an updated version, according to which the plague pathogen is an evolutionarily young pathogen descended from a psychrophilic pseudotuberculous ancestor. The presumptive ECO scenario has no obvious natural-scientific and historical contradictions and can serve as a null hypothesis for improving the MG methodology of phylogenetic constructions for plague and other similar microbes. It is suggested that the creation of a real phylogeny of the plague microbe is possible only based on integration of MG and ECO approaches.

Detectability of Varied Hybridization Scenarios Using Genome-Scale Hybrid Detection Methods

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This phenomenon has led to the development of methods to infer these varied hybridization events, both methods that reconstruct networks directly, as well as summary methods that predict individual hybridization events from a subset of taxa. However, a lack of empirical comparisons between methods – especially those pertaining to large networks with varied hybridization scenarios – hinders their practical use. Here, we provide a comprehensive review of popular summary methods: TICR, MSCquartets, HyDe, Patterson’s D-Statistic (ABBA-BABA), D3, and Dp. TICR and MSCquartets are based on quartet concordance factors gathered from gene tree topologies and HyDe, Patterson’s D-Statistic, D3, and Dp use site pattern frequencies to identify hybridization events between sets of three taxa. We then use simulated data to address questions of method accuracy and ideal use scenarios by testing methods against complex networks which depict gene flow events that differ in depth (timing), quantity (single vs. multiple, overlapping hybridizations), and rate of gene flow (γ). We find that deeper or multiple hybridization events may introduce noise and weaken the signal of hybridization, leading to higher relative false negative rates across all methods. Despite some forms of hybridization eluding quartet-based detection methods, MSCquartets displays high precision in most scenarios. While HyDe results in high false negative rates when tested on hybridizations involving extinct or unsampled ghost lineages, HyDe is the only method able to identify the direction of hybridization, distinguishing the source parental lineages from recipient hybrid lineages. Lastly, we test the methods on a dataset of ultraconserved elements from the bee subfamily Nomiinae, finding possible hybridization events between clades which correspond to regions of poor support in the species tree estimated in a previous study.

Human Bocavirus Circulating in Patients with Acute Gastroenteritis in Taiwan, 2018–2022

Human bocavirus (HBoV) has been identified as a viral agent with a global presence, especially in young patients with gastrointestinal infections. In this study, we aimed to evaluate the epidemiological patterns of the HBoVs associated with acute gastroenteritis (AGE) in Taiwan. A total of 2994 AGE fecal samples from several diarrhea outbreaks from 2018 to 2022 were analyzed. From the samples, 73 positive samples were detected in three different bocaviruses: 30 (41.1%) were from HBoV1; 37 (50.7%) were from HBoV2; and 6 (8.2%) were from HBoV3, revealing the respective prevalences in AGE of 1%, 1.2%, and 0.2%. HBoV1 and HBoV2 were the two major epidemic agents of HBoVs in Taiwan during this study period and have seasonal distinct patterns with an epidemic peak from October to the following March. Phylogeny reconstruction and evaluation were implemented in Mega X; the results revealed that most HBoV1 strains in Taiwan appeared to be closely related to those strains from other Asian countries. The HBoV2 exhibited substantial genetic diversity and the HBoV3 genes showed discordance of groups.

Soil nematode community profiling using reference-free mito-metagenomics

Nematodes are ubiquitous and diverse components of soil ecosystems worldwide. The 18S-based metabarcoding is known to have low species-level resolution and introduce bias in PCR. The mito-metagenomics (MMG) approach involves directly sequencing pooled samples, yields numerous mitochondrial reads that can be assembled into full or partial mitogenomes. This method circumvents the challenges associated with PCR-based metabarcoding and hold significant promise in biodiversity and phylogeny study. However, a reference database is typically required to extract mito-reads/contigs and provide taxonomic or phylogenetic context, thereby limiting its applicability. In this study, we introduced a novel reference-free pipeline for MMG assembly and diversity estimation. This pipeline has been integrated into a snakemake workflow, enabling the generation of output that is readily useable for phylogeny reconstruction in a single run. The performance tests have indicated that this new approach surpasses reference-based methods in soil nematode community profiling. We demonstrated that assembly quality improves with increasing sequencing depth, recommending an average of 1–2 Gb per species to achieve acceptable MMG assembly. Our pipeline presents an opportunity to create high-resolution phylogenies and assess diversity for poorly understood taxa, including neglected microscopic eukaryotes.

Morphology and taxonomic significance of the labrum in the flea beetle genus Chaetocnema Stephens, 1831 (Coleoptera, Chrysomelidae, Galerucinae, Alticini).

The structure of labrum or upper lip in adult Coleoptera is only minimally investigated and used in classification and phylogeny. This study investigates the morphology of the labrum in the flea beetle genus Chaetocnema Stephens, 1831 (Chrysomelidae, Galerucinae, Alticini) to assess and develop a terminology and identify potential morphological characters useful to delimitation of species and species groups as well as phylogeny reconstruction in leaf beetles.

A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor

Members of the plant specific family of C1-1i zincfinger transcriptionfactors (ZF-TFs), such as SUPERMAN, JAGGED, KNUCKLES or GIS,regulatediversedevelopmental processes including sexual reproduction. C1-1is consist of one zinc-finger and one to two EAR domains, connected by large intrinsically disordered regions (IDR). While the role of C1-i1 ZF-TFs in development processes is well known for some genes in Arabidopsis, rice or tomatoa comprehensive and broadphylogenetic background is lacking, yet knowledge of orthology is a requirement for a better understanding of C1-1i-Zf-TFs diverse roles in plants. Here, we provide a fine-grained and land plant wide classification of C1-1i sub-families and their known co-repressors TOPLESS and TOPLESS RELATED. Our work combines the identification of orthologous groups with Maximum-Likelihood phylogeny reconstructions and digital gene expression analyses mining high quality land plant genomes and transcriptomes to generate a comprehensive framework of C1-1i ZF-TF evolution. We show that C1-1i’s are low to moderate copy genesand that orthologous genesonly partiallyhaveconserved sub-family and life cycle stage dependent expression pattern across land plants while others are highly diverged. Our workprovides the phylogenetic framework for C1-1i ZF-TFs, s and strengthen C1-1 ZF-TFs as a potential model for IDR-research in plants.

Characterization of gut symbionts from wild-caught Drosophila and other Diptera: description of Utexia brackfieldae gen. nov., sp. nov., Orbus sturtevantii sp. nov., Orbus wheelerorum sp. nov, and Orbus mooreae sp. nov.

Non-culture based surveys show that the bacterial family Orbaceae is widespread in guts of insects, including wild Drosophila. Relatively few isolates have been described, and none has been described from Drosophila. We present the isolation and characterization of five strains of Orbaceae from wild-caught flies of the genera Drosophila (Diptera: Drosophilidae) and Neogriphoneura (Diptera: Lauxaniidae). Cells are generally rod-shaped, mesophilic, and measure 0.8-2.0 µm long by 0.3-0.5 µm wide. Optimal growth was observed under ambient atmosphere. Reconstruction of phylogenies from the 16S rRNA gene and from single-copy orthologs verify placement of these strains within Orbaceae. Cells exhibited similar fatty acid profiles to those of other Orbaceae. Strain lpD01T shared 74% average nucleotide identity (ANI) with its closest relatives Ca. Schmidhempelia bombi Bimp and Zophobihabitans entericus IPMB12T. Results from multiple genome-wide similarity comparisons indicate lpD01T should be classified as a novel species within a novel genus. The major respiratory quinone for lpD01T is ubiquinone Q-8. lpD02T, lpD03, lpD04T, and BiBT are more closely related to Orbus hercynius CN3T (76, 77, 76, and 77% ANI, respectively) than to other described Orbaceae. Genomic and phylogenetic analyses suggest that lpD03 and lpD04T belong to the same species and that lpD02T, lpD03/lpD04T, and BiBT are each novel species of the genus Orbus. The proposed names of these strains are Utexia brackfieldae gen. nov., sp. nov. (type strain lpD01T =NCIMB 15517T =ATCC TSD-399T), Orbus sturtevantii sp. nov (type strain lpD02T =NCIMB 15518T =ATCC TSD-400T), Orbus wheelerorum sp. nov. (type strain lpD04T =NCIMB 15520T =ATCC TSD-401T), and Orbus mooreae sp. nov (type strain BiBT=NCIMB 15516T =ATCC TSD-402T). The isolation and characterization of these strains expands the repertoire of culturable bacteria naturally associated with insects, including the model organism D. melanogaster.

Unique findings of <i>Phoma</i>-like fungi associated with soybean

Ascochyta leaf blight of soybean is a widespread disease caused by several closely related Phoma-like species, this disease often leads to significant crop losses. Among Phoma-like species from Didymellaceae family, the most frequently associated with symptomatic soybean tissues are species of the genera Boeremia and Didymella. Currently reliable species identification in Didymellaceae relies on polyphasic approach based on consolidated species concept and combined molecular phylogenetic, micromorphological and cultural features. At least three loci are commonly used for reconstruction of the molecular phylogeny of Didymellaceae: internal transcribed spacer (ITS) of the ribosomal DNA, partial RNA-polymerase II gene (rpb2), and β-tubulin (tub2). As a result of long-term phytosanitary monitoring of soybean crops, soybean leaves with symptoms of Ascochyta blight were collected from major soybean producing areas of Russia. From surface sterilized plant tissues more than 100 isolates of Phoma-like fungi were obtained and stored in the collection of pure cultures of the Laboratory of Mycology and Phytopathology (MF, All-Russian Institute of Plant Protection). Most of them, as a result of multilocus phylogenetic analysis, were identified as Boeremia and Didymella species. Eight isolates were identified as species of other genera, suspected to be rare findings. The aim of this study was to identify these eight isolates based on multilocus phylogenetic analysis, as well micromorphological, cultural, and pathogenicity data. Multilocus phylogenetic analysis has resulted in identification of all eight isolates to species level. Single isolate from the Ryazan region was Neoascochyta graminicola. Three other from three different districts of the Amur region were Remotididymella capsici. Two isolates from the Primorskiy territory and Amur region were Stagonosporopsis heliopsidis. Another two from two districts of the Amur region were S. stuijvenbergii. Pathogenicity tests have resulted in conclusion, that all studied isolates were not pathogenic for soybean leaves. Probably, these Phoma-like species are associate with soybean as saprophytes or endophytes. For all these Phoma-like species Glycine max was detected as substrate for the first time. Neoascochyta graminicola is widespread in Europe in association with Poaceae plants. There are only two findings of Remotididymella capsici in the world, both from leaves of Capsicum annuum. First finding was made in the former USSR in 1977 and was identified based on only morphological features. Second findings was collected in the Fiji and verified with multilocus phylogenetic analysis. Stagonosporopsis heliopsidis isolates were revealed in the USA, Canada, Netherlands and Russia and this fungus was believed to be specific for Asteraceae plants. Isolates of Stagonosporopsis stuijvenbergii are known only from soil in the Netherlands. Thus, such species as Neoascochyta graminicola and Stagonosporopsis stuijvenbergii were revealed in the Russia for the first time. Studied Remotididymella capsici isolates were first confirmed findings of this fungus in Russia. Additionally to detailed phylogenetic data, the manuscript is supplement with a detailed description of the cultural and micromorphological features of all species.

Inference of chromosome selection parameters and missegregation rate in cancer from DNA-sequencing data

Aneuploidy is frequently observed in cancers and has been linked to poor patient outcome. Analysis of aneuploidy in DNA-sequencing (DNA-seq) data necessitates untangling the effects of the Copy Number Aberration (CNA) occurrence rates and the selection coefficients that act upon the resulting karyotypes. We introduce a parameter inference algorithm that takes advantage of both bulk and single-cell DNA-seq cohorts. The method is based on Approximate Bayesian Computation (ABC) and utilizes CINner, our recently introduced simulation algorithm of chromosomal instability in cancer. We examine three groups of statistics to summarize the data in the ABC routine: (A) Copy Number-based measures, (B) phylogeny tip statistics, and (C) phylogeny balance indices. Using these statistics, our method can recover both the CNA probabilities and selection parameters from ground truth data, and performs well even for data cohorts of relatively small sizes. We find that only statistics in groups A and C are well-suited for identifying CNA probabilities, and only group A carries the signals for estimating selection parameters. Moreover, the low number of CNA events at large scale compared to cell counts in single-cell samples means that statistics in group B cannot be estimated accurately using phylogeny reconstruction algorithms at the chromosome level. As data from both bulk and single-cell DNA-sequencing techniques becomes increasingly available, our inference framework promises to facilitate the analysis of distinct cancer types, differentiation between selection and neutral drift, and prediction of cancer clonal dynamics.

SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies

BackgroundSimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation.ResultsHere, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool.ConclusionSimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca, where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at https://github.com/UdeS-CoBIUS/SimSpliceEvol.

The genomic trajectory of ovarian high-grade serous carcinoma can be observed in STIC lesions.

Ovarian high-grade serous carcinoma (HGSC) originates in the fallopian tube, with secretory cells carrying a TP53 mutation, known as p53 signatures, identified as potential precursors. p53 signatures evolve into serous tubal intraepithelial carcinoma (STIC) lesions, which in turn progress into invasive HGSC, which readily spreads to the ovary and disseminates around the peritoneal cavity. We recently investigated the genomic landscape of early- and late-stage HGSC and found higher ploidy in late-stage (median 3.1) than early-stage (median 2.0) samples. Here, to explore whether the high ploidy and possible whole-genome duplication (WGD) observed in late-stage disease were determined early in the evolution of HGSC, we analysed archival formalin-fixed paraffin-embedded (FFPE) samples from five HGSC patients. p53 signatures and STIC lesions were laser-capture microdissected and sequenced using shallow whole-genome sequencing (sWGS), while invasive ovarian/fallopian tube and metastatic carcinoma samples underwent macrodissection and were profiled using both sWGS and targeted next-generation sequencing. Results showed highly similar patterns of global copy number change between STIC lesions and invasive carcinoma samples within each patient. Ploidy changes were evident in STIC lesions, but not p53 signatures, and there was a strong correlation between ploidy in STIC lesions and invasive ovarian/fallopian tube and metastatic samples in each patient. The reconstruction of sample phylogeny for each patient from relative copy number indicated that high ploidy, when present, occurred early in the evolution of HGSC, which was further validated by copy number signatures in ovarian and metastatic tumours. These findings suggest that aberrant ploidy, suggestive of WGD, arises early in HGSC and is detected in STIC lesions, implying that the trajectory of HGSC may be determined at the earliest stages of tumour development. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Direct whole-genome sequencing of HIV-1 for clinical drug-resistance analysis and public health surveillance

BackgroundHuman Immunodeficiency virus type 1 (HIV-1) remains a significant global health threat partly due to its ability to develop resistance to anti-retroviral therapies. HIV-1 genotype and drug resistance analysis of the polymerase (pol) sequence is a mainstay of its clinical and public health management. However, as new treatments and resistances evolve, analysis methods must change accordingly. In this study, we outline the development and implementation of a direct whole-genome sequencing approach (dWGS) using probe-capture target-enrichment for HIV-1 genotype and drug resistance analysis. MethodsWe implemented dWGS and performed parallel pol Sanger sequencing for clinical samples, followed by comparative genotype and drug-resistance analysis. These HIV-1 WGS sequences were also utilised for a novel partitioned phylogenetic analysis. ResultsOptimised nucleic acid extraction and DNAse I treatment significantly increased HIV-1 whole-genome coverage and depth, and improved recovery of high-quality genomes from low viral load clinical samples, enabling routine sequencing of viral loads as low as 1000 copies/mL. Overall, dWGS was robust, accurate and more sensitive for detecting low-frequency variants at drug-resistance sites compared to Sanger sequencing. Analysis of multiple sequence regions improved phylogenetic reconstruction for recombinant HIV-1 sequences compared to analysis of pol sequence alone. ConclusionsThese findings demonstrate dWGS enhances HIV-1 drug-resistance analysis by quantitative variant detection and improves reconstruction of HIV-1 phylogenies compared to traditional pol sequencing. This work supports that HIV-1 dWGS is a viable option to replace Sanger sequencing for clinical and public health applications.

In silico analysis of a heme-thiolate peroxidase gene discovered in an ectomycorrhizal fungus of Carpathian primeval forest: implications for biotechnological applications

In this work, we focus on the identification of novel fungal peroxygenase gene belonging to the peroxidase-peroxygenase superfamily. We applied a metagenomic approach on soil samples from primeval forest and appropriate bioinformatics tools for analysis of obtained genomic DNA sequence. Peroxidases are ubiquitous metalloenzymes that are able to reduce reactive peroxides, mainly hydrogen peroxide, into water, whereas several substrates can be concomitantly oxidized during their catalytic reaction. Our purpose was to collect unique peroxygenase sequence data originating from a preserved biotope for a robust phylogenetic reconstruction of a particular gene family coding for highly versatile heme-thiolate peroxidases that has peculiar yet undiscovered representatives among ectomycorrhizal fungi. We identified unique DNA sequence, 812 bp long, from ectomycorrhizal Suillus species coding for a heme-thiolate peroxidase with 1 typical intron that appears distinctive for Carpathian forests. After translation in corresponding protein sequence 251 amino acids long we could identify typical signatures of this peroxygenase. On the proximal side of heme we found the conserved P-C-P triad responsible for efficient ligation of heme iron thus influencing the reactivity of this peroxidase. On the distal side we recognized the E-H-D-X-S-L motif for interaction with a stabilizing magnesium ion. Maximum likelihood reconstruction of protein phylogeny revealed with a high bootstrap support the presence of a monophyletic HTP4 clade originating in numerous Suillus representatives. Together with sister clades of edible Boletus and poisonous Paxillus containing diverse peroxygenases these newly discovered heme catalyst can be considered for application of oxyfunctionalization of organic molecules.

Phylogenetic position of <i>Polymorphus phippsi</i> Kostylew, 1922 and <i>Polymorphus magnus</i> Skrjabin, 1913 (Palaeacanthocephala, Polymorphidae) ascertained on the basis of molecular data

Polymorphidae is a family of acanthocephalans, obligatory parasites with a complex life cycle involving arthropods as intermediate hosts and vertebrates of different taxa as definitive hosts. The current taxonomy of Polymorphidae seems to be equivocal. Its type genus Polymorphus has been shown to be polyphyletic based on molecular data. We obtained partial sequences of 28S rDNA gene and cox1 mitochondrial gene of two species of this genus, Polymorphus phippsi and P. magnus, and used them in a reconstruction of the polymorphid phylogeny. As a result, P. magnus was included into the same clade as the type species of the genus, P. minutus, while P. phippsi appeared to be close to Profilicollis spp. The position of P. phippsi agrees with the polyphyly of Polymorphus but does not correspond to its taxonomic status based on described phenotypic characters.