Tool For Phylogenetic Analysis Research Articles

An update on the status of direct testing for Treponema pallidum subspecies pallidum for the laboratory diagnosis of syphilis in Canada

Background: In Canada, the recent resurgence of infectious syphilis and rising rates of congenital syphilis have renewed interest in direct detection methods for the laboratory diagnosis of syphilis. The Canadian Public Health Laboratory Network (CPHLN) has previously published a series of guidelines for the diagnosis of syphilis in Canada, including the use of direct tests. In the decade since those guidelines were published, laboratory practice has changed. Methods: This systematized review combined a literature search (MEDLINE) of methods for direct detection of Treponema pallidum with an informal survey of current testing practices in Canadian public health laboratories. Results: Direct testing methods have favourable performance characteristics for detection of early syphilis and congenital cases. Although no government licensed commercial nucleic acid amplification test (NAAT) for syphilis is available in Canada, laboratory-developed tests have been implemented in multiple Canadian jurisdictions. Clinical specimens with the highest yield of positive NAAT results for syphilis include genital ulcers, skin lesions, and oral swabs from primary and secondary syphilis patients. For investigation of congenital syphilis, nasopharyngeal, placenta, umbilical cord, blood, and skin lesions are specimens of choice for direct detection of T. pallidum by NAAT. Conclusions: This update on the status of direct testing highlights the importance of NAAT for the detection of T. pallidum, the reduced role of microscopy-based methods, and the emergence of DNA and genome sequencing as tools for phylogenetic analysis and molecular epidemiology.

Phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things).

Phylogenetic comparative methods comprise the general endeavor of using an estimated phylogenetic tree (or set of trees) to make secondary inferences: about trait evolution, diversification dynamics, biogeography, community ecology, and a wide range of other phenomena or processes. Over the past ten years or so, the phytools R package has grown to become an important research tool for phylogenetic comparative analysis. phytools is a diverse contributed R library now consisting of hundreds of different functions covering a variety of methods and purposes in phylogenetic biology. As of the time of writing, phytools included functionality for fitting models of trait evolution, for reconstructing ancestral states, for studying diversification on trees, and for visualizing phylogenies, comparative data, and fitted models, as well numerous other tasks related to phylogenetic biology. Here, I describe some significant features of and recent updates to phytools, while also illustrating several popular workflows of the phytools computational software.

Development and validation of genome-wide SSR molecular markers of Tapes dorsatus.

Tapes dorsatus is an economically important benthic animal in the Beibu Gulf of China. However, the deficiency of microsatellite markers has hindered the study of its genetics. The development of microsatellite markers will provide useful tools for genetic improvement, variety identification, phylogenetic analysis and resource conservation. Within the genome sequence, 145,008 simple sequence repeats (SSRs) were identified, and 29,691 primer pairs were designed successfully. A total of 100 primer pairs were randomly synthesized for testing, and 93 primers yielded products. Sixty highly polymorphic primers were used to reveal the genetic diversity of 50 T. dorsatus individuals. The average number of alleles (Na) of the population was 10.40; the average number of effective alleleswas 6.16, the average expected heterozygosity (He) was 0.82, and the average polymorphic information contentwas 0.80. The genetic structure of the population was detected, by which the population could be divided into three subpopulations. We identified 145,008 SSRs in the genome of T. dorsatus and designed 29,691 primer pairs in this study. Of 100 synthesized primers, 60 were highly polymorphic and used to reveal the genetic diversity and structure of the population. The SSR markers identified here will provide useful tools and a foundation for genetic diversity, linkage mapping and molecular marker-aided breeding in T. dorsatus.

An evolution strategy approach for the balanced minimum evolution problem.

The Balanced Minimum Evolution (BME) is a powerful distance based phylogenetic estimation model introduced by Desper and Gascuel and nowadays implemented in popular tools for phylogenetic analyses. It was proven to be computationally less demanding than more sophisticated estimation methods, e.g. maximum likelihood or Bayesian inference while preserving the statistical consistency and the ability to run with almost any kind of data for which a dissimilarity measure is available. BME can be stated in terms of a nonlinear non-convex combinatorial optimization problem, usually referred to as the Balanced Minimum Evolution Problem (BMEP). Currently, the state-of-the-art among approximate methods for the BMEP is represented by FastME (version 2.0), a software which implements several deterministic phylogenetic construction heuristics combined with a local search on specific neighbourhoods derived by classical topological tree rearrangements. These combinations, however, may not guarantee convergence to close-to-optimal solutions to the problem due to the lack of solution space exploration, a phenomenon which is exacerbated when tackling molecular datasets characterized by a large number of taxa. To overcome such convergence issues, in this article, we propose a novel metaheuristic, named PhyloES, which exploits the combination of an exploration phase based on Evolution Strategies, a special type of evolutionary algorithm, with a refinement phase based on two local search algorithms. Extensive computational experiments show that PhyloES consistently outperforms FastME, especially when tackling larger datasets, providing solutions characterized by a shorter tree length but also significantly different from the topological perspective. The software and the data are available at https://github.com/andygaspar/PHYLOES.

Pollen morphology of Ipomoea L. from Garhwal Himalaya, India

Pollen morphology serves as a valuable tool for identification, phylogenetic analysis and evolutionary studies. The present study aims to investigate the pollen morphology of 12 species of the genus Ipomoea L. (a diverse and economically important genus within the family Convolvulaceae) from Garhwal Himalaya, India. Fresh flower buds were collected from the study area and pollen preparation completed using the acetolysis method. The morphology of the pollen grains were examined using light microscopy and scanning electron microscopy. Pollen grains of all the studied species were apolar, spheroidal, pantoporate, subtectate with fine reticulation and echinate, but they differed from one another in their size, number of spines and pores, spine length and spine types. The size of grains ranged from 53.3 to 128.7 μm. Cluster analysis was performed based on pollen characters to show the relationship among the species; a key was prepared and is discussed. The observed variation in pollen morphological traits gives important taxonomic information that is useful for distinguishing Ipomoea species and establishing taxonomic and phylogenetic relationships.

Global mpox lineage discovery and rapid outbreak tracking with nanopore sequencing

Insufficient tracking of virus introduction, spread, and new lineage emergence for the human monkeypox (mpox) virus 1 (hMPXV1) outbreak of 2022 hindered epidemiological studies and public health response. hMPXV1 mutations accumulated unexpectedly faster than predicted. Thus, new variants with altered pathogenicity could emerge and spread without early detection. Whole genome sequencing addresses this gap when implemented but requires widely accessible and standardized methodologies to be effective both regionally and globally. Here we developed a rapid nanopore whole genome sequencing method complete with working protocols, from DNA extraction to phylogenetic analysis tools. Using this method, we sequenced 84 complete hMPXV1 genomes from Illinois, a Midwestern region of the United States, spanning the first few months of the outbreak. The resulting five-fold increase in hMPXV1 genomes from this region established two previously unnamed global lineages, several mutational profiles not seen elsewhere, multiple separate introductions of the virus into the region, and the likely emergence and spread of new lineages from within this region. These results demonstrate that a dearth of genomic sequencing of hMPXV1 slowed our understanding and response to the mpox outbreak. This accessible nanopore sequencing approach makes near real-time mpox tracking and rapid lineage discovery straightforward and creates a blueprint for how to deploy nanopore sequencing for genomic surveillance of diverse viruses and future outbreaks.

Ksak: A high-throughput tool for alignment-free phylogenetics.

Phylogenetic tools are fundamental to the studies of evolutionary relationships. In this paper, we present Ksak, a novel high-throughput tool for alignment-free phylogenetic analysis. Ksak computes the pairwise distance matrix between molecular sequences, using seven widely accepted k-mer based distance measures. Based on the distance matrix, Ksak constructs the phylogenetic tree with standard algorithms. When benchmarked with a golden standard 16S rRNA dataset, Ksak was found to be the most accurate tool among all five tools compared and was 19% more accurate than ClustalW2, a high-accuracy multiple sequence aligner. Above all, Ksak was tens to hundreds of times faster than ClustalW2, which helps eliminate the computation limit currently encountered in large-scale multiple sequence alignment. Ksak is freely available at https://github.com/labxscut/ksak.

Synergistic soil-less medium for enhanced yield of crops: a step towards incorporating genomic tools for attaining net zero hunger

Globally, industrial farming endangers crucial ecological mechanisms upon which food production relies, while 815 million people are undernourished and a significant number are malnourished. Zero Hunger aims to concurrently solve global ecological sustainability and food security concerns. Recent breakthroughs in molecular tools and approaches have allowed scientists to detect and comprehend the nature and structure of agro-biodiversity at the molecular and genetic levels, providing us an advantage over traditional methods of crop breeding. These bioinformatics techniques let us optimize our target plants for our soil-less medium and vice versa. Most of the soil-borne and seed-borne diseases are the outcomes of non-treated seed and growth media, which are important factors in low productivity. The farmers do not consider these issues, thereby facing problems growing healthy crops and suffering economic losses. This study is going to help the farmers increase their eco-friendly, chemical residue-free, quality yield of crops and their economic returns. The present invention discloses a synergistic soil-less medium that consists of only four ingredients mixed in optimal ratios by weight: vermicompost (70-80%), vermiculite (10-15%), coco peat (10-15%), and Rhizobium (0-1%). The medium exhibits better physical and chemical characteristics than existing conventional media. The vermiculite to coco peat ratio is reduced, while the vermicompost ratio is increased, with the goals of lowering toxicity, increasing plant and water holding capacity, avoiding drying of the media, and conserving water. The medium provides balanced nutrition and proper ventilation for seed germination and the growth of seedlings. Rhizobium is also used to treat the plastic bags and seeds. The results clearly show that the current synergistic soil-less environment is best for complete plant growth. Securing genetic advantages via sexual recombination, induced random mutations, and transgenic techniques have been essential for the development of improved agricultural varieties. The recent availability of targeted genome-editing technology provides a new path for integrating beneficial genetic modifications into the most significant agricultural species on the planet. Clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR/Cas9) has evolved into a potent genome-editing tool for imparting genetic modifications to crop species. In addition, the integration of analytical methods like population genomics, phylogenomics, and metagenomics addresses conservation problems, while whole genome sequencing has opened up a new dimension for explaining the genome architecture and its interactions with other species. The in silico genomic and proteomic investigation was also conducted to forecast future investigations for the growth of French beans on a synergistic soil-less medium with the purpose of studying how a blend of vermicompost, vermiculite, cocopeat, and Rhizobium secrete metal ions, and other chemical compounds into the soil-less medium and affect the development of our target plant as well as several other plants. This interaction was studied using functional and conserved region analysis, phylogenetic analysis, and docking tools.

Molecular characterization and phylogenetic analysis of kaurene synthase protein in Stevia rebaudiana MS007

Stevia rebaudiana is a plant under the Asteraceae family and has been reported as a healthier alternative to sugar. Steviol glycosides (SGs) is the group of secondary metabolites responsible for the sweet taste. Among nine SGs synthesised by S. rebaudiana, stevioside and rebaudioside A are the sweetest. The biosynthetic pathway of SGs partly involves conversion of geranylgeranyl diphosphate (GGDP) into steviol, catalysed by ent- kaurene synthase (KS), ent-copalyl diphosphate synthase (CPPS), and kaurene oxidase (KO). This study focuses on in silico molecular characterization and phylogenetic analysis of KS from Malaysia’s S. rebaudiana MS007 variety (Stevia MS007). The transcriptomic dataset of S. rebaudiana accession MS007 was used in initial experiment toward analysing the KS. Through the blastx homology search using transcriptomic dataset query Cluster-31069.42907, the Stevia rebaudiana kaurene synthase (SrKS) sequence was identified with the highest similarity percentage identity (99.62%). The protein domain prediction using InterPro yields IPR005630 (terpene synthase metal-binding domain) at positions 490 to 755 and IPR001906 (terpene synthase-N-terminal-domain) at positions 258 to 477. Multiple sequence alignment was conducted using MUSCLE and MEGA-X as phylogenetic tree analysis tool for constructing the phylogenetic analysis tree. Based on the bootstrap value from the phylogenetic analysis, Cluster-31069.42907 represents relationships between the ancestors. Since both Helianthus annuus and S. rebaudiana are Asteraceae species, the bootstrap value for both species was 100%. In conclusion, this research contributes to a better understanding of Stevia MS007 KS via in silico analysis.

Investigation of the Molecular Evolution of Treg Suppression Mechanisms Indicates a Convergent Origin.

Regulatory T cell (Treg) suppression of conventional T cells is a central mechanism that ensures immune system homeostasis. The exact time point of Treg emergence is still disputed. Furthermore, the time of Treg-mediated suppression mechanisms’ emergence has not been identified. It is not yet known whether Treg suppression mechanisms diverged from a single pathway or converged from several sources. We investigated the evolutionary history of Treg suppression pathways using various phylogenetic analysis tools. To ensure the conservation of function for investigated proteins, we augmented our study using nonhomology-based methods to predict protein functions among various investigated species and mined the literature for experimental evidence of functional convergence. Our results indicate that a minority of Treg suppressor mechanisms could be homologs of ancient conserved pathways. For example, CD73, an enzymatic pathway known to play an essential role in invertebrates, is highly conserved between invertebrates and vertebrates, with no evidence of positive selection (w = 0.48, p-value < 0.00001). Our findings indicate that Tregs utilize homologs of proteins that diverged in early vertebrates. However, our findings do not exclude the possibility of a more evolutionary pattern following the duplication degeneration−complementation (DDC) model. Ancestral sequence reconstruction showed that Treg suppression mechanism proteins do not belong to one family; rather, their emergence seems to follow a convergent evolutionary pattern.

Molecular Identification of Yeast Strains with High Fermentation Capacity Isolated from Kırkağaç Melon Varieties

The yield of fermentation process, bioethanol, is one of the important product obtained from renewable energy sources. Yeasts are commonly used in ethanol production due to their high ethanol tolerance, high ethanol productivity, and their ability to ferment different kinds of simple sugars. Saccharomyces cerevisiae yeast species is the most commonly used in industrial ethanol production. Therefore, isolation and identification of new yeast strains with high fermentation capacity is very important for the bioethanol industry. The aim of this study was isolation of novel and industrially applicable yeast species that can be used in bioethanol production. Yeast strains were isolated from the Dalaman, Altınbaş and Kıvırcık sarı dilim melon varieties that are unique to Kırkağaç district of Manisa province. The fermentation ability of yeast strains was evaluated and the selected yeast strains were identified by PCR-RFLP analysis of 26S and ITS1-5.8S-ITS2 rDNA gene regions. Sequence analysis of the 26S rDNA-D1/D2 gene region was used for molecular identification of yeast strains. The phylogenetic analysis of identified yeast strains was carried out using the MEGA XI phylogenetic analysis tool. It was determined that 14 of the 53 yeast strains isolated were able to ferment glucose and sucrose, and four of them were able to ferment lactose. The yeast strains having the fermentation capacity were identified as Pichia kluyverii, Lachancea thermotolerans, Pichia kudriavzevii, Saccharomyces cf. cerevisiae/paradoxus and Saccharomyces cerevisiae. These yeast strains have the potential to be used in the bioethanol industry after other physiological and biochemical tests are complete

ITS1 Barcode and Phytochemical Analysis by Gas Chromatography–Mass Spectrometry of Corynaea crassa Hook. f (Balanophoraceae) from Ecuador and Peru

The use of medicinal plants is the basis of traditional healthcare. Recently, the use of herbal medicine has been increasing among consumers due to availability, economy, and less side effect. For instance, the hemiparasite plant Corynaea crassa has medicinal properties and could be found in some regions of America, from Costa Rica to Bolivia. Phytochemical and genetic characterization of medicinal plants is needed for proper identification of metabolites responsible for medicinal properties and for genotyping, respectively. Moreover, characterization of medicinal plants through the use of DNA barcodes is an important tool for phylogenetic analysis and identification of species; furthermore, complemented with phytochemical analysis, both are useful for identification of plant species and quality control of medicinal products. The objective of this study was to analyze the species of C. crassa collected in Ecuador and Peru from the phylogenetic and phytochemical point of view. Polymerase chain reaction (PCR) was performed for amplification of the internal transcribed spacer 1 (ITS1) region after DNA extraction of samples of C. crassa. Blast analysis was performed in the GenBank database with the ITS1 sequences obtained from two accessions of C. crassa from Ecuador (GenBank accession numbers OM471920 and OM471919 for isolates CIBE-17 and CIBE-18, respectively) and three from Peru (GenBank accession numbers OM471921, OM471922, and OM471923 for isolates CIBE-13, CIBE-14, and CIBE-15, respectively). The accessions available in the GenBank were used for phylogenetic analysis. For the phytochemical analysis, hydroalcoholic extracts were obtained by maceration using 80% ethanol as solvent, followed by a derivatization process and analysis by gas chromatography-mass spectrometry. Based on the phylogenetic analysis of the C. crassa samples, the ITS1 sequence could be used to differentiate C. crassa of different locations. The samples of C. crassa from Ecuador and Peru are more similar between them than with other clades including Helosis spp. The phytochemical study revealed differences in the presence and relative abundance of some metabolites; mainly eugenol, 1,4-lactone arabinonic acid, dimethoxyrabelomycin and azelaic acid, which are reported for the first time for the species under study and the genus Corynaea. These results are the first findings on the combined analysis using genetic and phytochemical analysis for C. crassa, which could be used as a useful tool for quality control of the C. crassa species in medicinal products.

Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus

Sugarcane bacilliform virus (SCBV) is a plant pararetrovirus causing leaf fleck disease in sugarcane across the globe. Since it occurs throughout the sugarcane growing areas and germplasm in India, we have assessed the genetic divergences among its 104 isolates from various germplasm and Saccharum hybrid varieties. With the evidence gathered from phylogenetic analysis and sequence demarcation tool, five novel subgroups, viz., SCBV-U, SCBV-V, SCBV-W, SCBV-X and SCBV-Y, were proposed. Interestingly, SCBV-W isolate CBJ 46 showed highest variation in its nucleotide and protein sequence. Compared with the existing genomic database of SCBV and the findings from the present study, SCBV isolates from India exhibited greater diversity than that isolated from other regions. SCBV-U, SCBV-W and SCBV-X, potent recombinants with other eight recombinants discovered in this study indicated the plausible heterogeneity and genetic exchange occurred within SCBV species over time that might have led to the evolution of new variants. Neutrality tests indicated the existence of low-frequency polymorphism and selection pressure of < 1 pointed out at purifying selection of SCBV population. The current study regarding the genetic variation within SCBV species will aid in devising robust diagnostic tools for the detection of virus in quarantine laboratories and improving the knowledge of evolutionary changes in SCBV species.

Comparative study between molecular and genetic evolutionary analysis tools using African SARS-CoV-2 variants

Phylogenetic analysis is one of the most reliable and important analyses in bioinformatics. Currently, many phylogenetic analysis tools can be used for the visualization and interpretation of biological data. However, a lot of technical expertise is required in order to use these tools. It is challenging for biologists to have to deal with this issue.This study therefore compared three multipurpose phylogenetic analysis tools and informed on their features so as to help the user choose the appropriate tool for their research and resources, especially those who want to do research in bioinformatics in Africa.Phylogenetic analysis was done on whole genome sequences obtained from NCBI repositories using MEGA, SeaView and Geneious separately. Subsequently, a detailed comparison table based on features for each tool was generated. What makes our study unique is that we used the African SARS-CoV-2 genomes which have rarely been used for studies describing the evolution of coronaviruses.After the benchmarking, we recommend tools based on the user's resources and objectives. MEGA and SeaView would be the best option for a researcher with no technical bioinformatics knowledge and looking for a free tool. Geneious is as easy to use as MEGA and SeaView, and it additionally gives more options and information. On the other hand, it requires a lot of time and it is not free to use.We have highlighted the relevant molecular and genetic evolutionary analysis tool based on the user's resources.

Evolutionary origin and functional specialization of Dormancy-Associated MADS box (DAM) proteins in perennial crops

BackgroundBud dormancy is a phenological adaptation of temperate perennials that ensures survival under winter temperature conditions by ceasing growth and increasing cold hardiness. SHORT VEGETATIVE PHASE (SVP)-like factors, and particularly a subset of them named DORMANCY-ASSOCIATED MADS-BOX (DAM), are master regulators of bud dormancy in perennials, prominently Rosaceae crops widely adapted to varying environmental conditions.ResultsSVP-like proteins from recently sequenced Rosaceae genomes were identified and characterized using sequence, phylogenetic and synteny analysis tools. SVP-like proteins clustered in three clades (SVP1–3), with known DAM proteins located within SVP2 clade, which also included Arabidopsis AGAMOUS-LIKE 24 (AthAGL24). A more detailed study on these protein sequences led to the identification of a 15-amino acid long motif specific to DAM proteins, which affected protein heteromerization properties by yeast two-hybrid system in peach PpeDAM6, and the unexpected finding of predicted DAM-like genes in loquat, an evergreen species lacking winter dormancy. DAM gene expression in loquat trees was studied by quantitative PCR, associating with inflorescence development and growth in varieties with contrasting flowering behaviour.ConclusionsPhylogenetic, synteny analyses and heterologous overexpression in the model plant Arabidopsis thaliana supported three major conclusions: 1) DAM proteins might have emerged from the SVP2 clade in the Amygdaloideae subfamily of Rosaceae; 2) a short DAM-specific motif affects protein heteromerization, with a likely effect on DAM transcriptional targets and other functional features, providing a sequence signature for the DAM group of dormancy factors; 3) in agreement with other recent studies, DAM associates with inflorescence development and growth, independently of the dormancy habit.

DNA BARCODING OF SOME ZYGOPHYLLACEAE SPECIES IN THE EGYPTIAN FLORA

DNA barcoding is gaining a high popularity and due to its simplicity and high accuracy as compared to the complexity associated with morphological identification of taxa. Therefore, we tested the potential of the rbcL, matK and ITS f markers for the identification of wild plants belonging to diverse Zygophyllaceae species from different sites of Egypt. Maximum likelihood tree analysis was performed to evaluate the resolution power of each marker to discriminate species. The analyses of nucleotide sequences of rbcL, matK and ITS revealed that the topology of the rbcL tree was the best resolved which enabled identification of the majority of the species, perfectly. Therefore, we can suggest use of the rbcL region as an additional tool for phylogenetic analysis in Zygophyllaceae species. We recommend this study for any further studies on Zygophyllaceae family and contribution to taxonomical researches by adding a new dimension to the Egyptian flora.

Reconstruction of the origin of the first major SARS-CoV-2 outbreak in Germany

The first major COVID-19 outbreak in Germany occurred in Heinsberg in February 2020 with 388 officially reported cases. Unexpectedly, the first outbreak happened in a small town with little to no travelers. We used phylogenetic analyses to investigate the origin and spread of the virus in this outbreak. We sequenced 90 (23%) SARS-CoV-2 genomes from the 388 reported cases including the samples from the first documented cases. Phylogenetic analyses of these sequences revealed mainly two circulating strains with 74 samples assigned to lineage B.3 and 6 samples assigned to lineage B.1. Lineage B.3 was introduced first and probably caused the initial spread. Using phylogenetic analysis tools, we were able to identify closely related strains in France and hypothesized the possible introduction from France.

Phylogenetic Analysis and Extracellular Enzyme Profiles of Yeast Strains Isolated from Raspberry Fruits

Raspberry fruit contains phenolic compounds, flavones, flavonoids, vitamins, and antioxidant substances that are important properties for health and pharmacological sciences. Edible berries provide also a suitable habitat for the growth of various microorganisms. In this study, yeast biota associated with raspberry fruits was determined by molecular identification techniques. Raspberry fruits were collected from Çanakkale, Gelibolu (Gallipoli). Yeast strains were isolated and then identified by using the analysis of ITS1-5.8S-ITS2 rDNA gene sequences. The phylo-genetic analysis of all yeast strains was carried out by using the MEGA–X phylogenetic analysis tool. The extracel-lular enzyme profiles of identified yeast species were determined by the API-ZYM kit system. The distribution of yeast species on the raspberry fruits was determined as Hanseniaspora uvarum, Metschnikowia viticola, Aureo-basidium pullulans, and Metschnikowia pulcherrima. It was observed that yeast strains belong to Metschnikowia genus were dominant on raspberry fruits. All yeast strains in Metschnikowia genus showed different enzyme pro-files against seven extracellular enzymes. These enzymes may be the discriminatory enzymes for the yeast strains in the Metschnikowia genus. When the phylogenetic relationships among all yeast strains were investigated, all strains were divided into two main clades. While the first clade consists of only Metschnikowia genus, second clade includes H. uvarum and A. pullulans yeast species. Our results indicated that restriction patterns and also extracel-lular enzyme profiles could be utilized for differentiation of yeast strains within the genus. M. pulcherrima, H. uvarum, and A. pullulans can be used for industrial applications for future researches.

Cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets

BackgroundThe quantity of genomic data is expanding at an increasing rate. Tools for phylogenetic analysis which scale to the quantity of available data are required. To address this need, we present cognac, a user-friendly software package to rapidly generate concatenated gene alignments for phylogenetic analysis.ResultsWe illustrate that cognac is able to rapidly identify phylogenetic marker genes using a data driven approach and efficiently generate concatenated gene alignments for very large genomic datasets. To benchmark our tool, we generated core gene alignments for eight unique genera of bacteria, including a dataset of over 11,000 genomes from the genus Escherichia producing an alignment with 1353 genes, which was constructed in less than 17 h.ConclusionsWe demonstrate that cognac presents an efficient method for generating concatenated gene alignments for phylogenetic analysis. We have released cognac as an R package (https://github.com/rdcrawford/cognac) with customizable parameters for adaptation to diverse applications.

Molecular Phylogenetic Analysis Of Morkaraman Sheeps In Bingol Region

In the present study, we report mitochondrial DNA (mtDNA) 16S rRNA gene sequence analysis of the Morkaraman ewe, (Ovis aries) was investigated. In domestic sheep, the 16S rRNA gene is ca 1574 bp in length. Partial fragment of 536 bp 16S rRNA gene of mtDNA was amplified by using designed primers from published data of Sheep sequences derived from National Center for Biotechnology Information (NCBI) web server (ncbi.nlm.nih.gov/NC_001941.1). Homology of the sequences obtained from the present work were performed by using BLAST program at NCBI. Obtained 16S rRNA gene sequences were submited to the GenBank database with accession numbers, KU686952.1, KU686953.1, KU686954.1, KU686955.1, KU686956.1, KU686957.1, KU686958.1, KU686959.1, KU686960.1, KU686961.1 and KU686962.1, respectively. According to nucleotide differences of mtDNA 16S rRNA gene region 10 polymorphic regions and 8 haplotypes were detected in Turkish domestic sheep Morkaraman (n=11). The nucleotide composition averages of all the sequences was 32.1% Adenine (A), 24.2% Thymine (T), 22.2% Cytosine (C) and 21.5% Guanine (G); G+C was 43.7%. DNA polymorphism based on 16S rRNA gene sequences, haplotype diversity (Hd) and nucleotide diversity (π) were found to be 0,9273±0,00442, and 0,00427±0,00125, respectively. Based on gene sequences information, in sheeps, mtDNA haplotypes, the phylogenetic relationship among mtDNA polymorphism, haplotypes and relationship between native sheep breeds and foreign sheep breeds were determined and discussed. Thus, sequence analysis of mitochondrial 16S rRNA gene can be used as a tool for phylogenetic analysis of Morkaraman sheep.