Comparison Of DNA Sequences Research Articles

Corticimorbus sinomyrti gen. et sp. nov. (Cryphonectriaceae) pathogenic to native Rhodomyrtus tomentosa (Myrtaceae) in South China

The Cryphonectriaceae includes many important tree pathogens, especially of the Myrtales. Disease surveys on Myrtales in South China revealed a stem canker disease on native Rhodomyrtus tomentosa (Myrtaceae, Myrtales) trees in the proximity of Eucalyptus plantations in GuangXi Province and in a natural forestry area in the Hong Kong Region. Fruiting structures with typical characteristics of the Cryphonectriaceae were observed on the canker surfaces. The fungus was identified based on DNA sequence comparisons and morphological features, and its pathogenicity was tested on R. tomentosa under field conditions. DNA sequence comparisons for the partial large subunit, partial internal transcribed spacer nuclear ribosomal DNA, and two regions of the β‐tubulin gene showed that the fungus represents a previously undescribed genus and species in the Cryphonectriaceae. Based on morphology, the fungus is most similar to species in the genus Chrysoporthe, but can be distinguished from this and the other genera of Cryphonectriaceae. The fungus provided with the name Corticimorbus sinomyrti gen. et sp. nov., is described. Field inoculations showed that it is highly pathogenic to R. tomentosa trees, with the ability to kill inoculated branches within 4 weeks. Pathogenicity tests also showed that C. sinomyrti is pathogenic to a tested Eucalyptus clone. Pathogenicity on both native R. tomentosa and non‐native Eucalyptus suggests that this fungus should be monitored carefully to limit its possible spread to commercially grown Eucalyptus in South China.

Guarianthe, a generic name for the “Cattleya” skinneri complex

<div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p><span>Molecular systematics, the comparison of DNA sequences, has brought a continuing revolution to plant taxonomy. In most cases, the results are intu- itively reasonable, even when they demand changing long-known names. </span></p></div></div></div>

Rapport et recommandations sur la mise en œuvre en France des techniques de séquençage de nouvelle génération

SUMMARY Next generation sequencing (NGS) technologies, which allow high speed automated DNA sequencing, DNA sequence analysis and comparisons using big data algorithms are being used more and more in medical diagnosis, to provide prognosis information and for choosing a treatment that best fits the patient. The French “Academie nationale de medecine ” (ANM) and “ Academie des technologies “ (NATF) jointly stress the scientific and medical importance of these technologies and call for bringing together strengths of the national computer science industry and the medical community in a public-private consortium in order to build a Demonstrator and Center network filling up the growing gap between France and the most advanced countries in this field with great potential. They underline also common pitfalls which need to be addressed in technic, legal, economic, education and ethics issues, in order to make this complex project a success.

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga).

Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga The group has a range of divergence dates (0.5-6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga We inferred non-monophyletic relationships of Piranga lutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone.

Botryosphaeria sinensia sp nov., a new species from China

A new Botryosphaeria species (B. sinensia) is described and illustrated from China. It is characterized by erumpent, botryose clustered ascostromata, ostiolate ascomata, bitunicate, 8-spored and clavate asci, filiform, rarely branched pseudoparaphyses, hyaline, 1-celled, fusiform ascospores, and a Fusicoccum asexual morph. The hyaline old and discharged conidia with 1–2 septa, broader spermatia formed in the culture and smaller ascostroma readily distinguished it from B. dothidea and other species in Botryosphaeria. The intergenic spacer (ITS) and translation elongation factor 1-alpha (EF1) DNA sequence analysis results also support its separation from other Botryosphaeria species. Its relationships with other species of Botryosphaeria are also discussed based on morphology and DNA sequence comparisons.

Birds, nutrients, and climate change: mtDNA haplotype diversity of Arctic Daphnia on Svalbard revisited

Ecosystems in the high Arctic are in transition due to climate change and species shifts. On the Svalbard archipelago, the average annual temperature has increased by more than 2 °C over the past 30 years, and there has been a striking increase in breeding populations of geese. Birds serve as a dominant source of nutrients (via faeces) and may also serve as vectors of dispersal of many small aquatic organisms. We compared samples of species and haplotype composition of the dominant freshwater crustacean Daphnia spp., from 1992, and those resampled in 2014 to see if these major impacts on Arctic freshwater ecosystems may also have affected this key grazer over the past three decades. The study covers tundra ponds that vary in levels of nutrients, abundance, and diversity of birds. Comparison of genetic mitochondrial DNA sequences revealed little change in haplotype and nucleotide diversity between 1992 and 2014, but higher species and haplotype diversity were found in nutrient-rich ponds that hosted large migratory bird populations. This could either reflect that high nutrient levels allow for the maintenance of higher levels of genetic diversity (i.e. haplotypes, lineages), that birds serve as vectors for the dispersal of clones, or likely a combination of both mechanisms.

First report of Phoma leaf spot disease on cherry palm caused by Phoma herbarum in Thailand

A leaf spot disease caused by Phoma herbarum was observed in a plantation of cherry palm (Pseudophoenix sargentii) in Chiang Mai Province, Thailand. The fungus was isolated from lesions on leaves and pathogenicity tests showed that Ph. herbarum could infect P. sargentii, producing the same symptoms after inoculation as those observed naturally in the field. The fungus was identified based on morphological characteristics and confirmed using comparisons of DNA sequences of internal transcribed spacer (ITS)1, 2 and 5.8S rDNA. This is the first report of this disease on cherry palm.

New Geometric Representations and Domination Problems on Tolerance and Multitolerance Graphs

Tolerance graphs model interval relations in such a way that intervals can tolerate a certain amount of overlap without being in conflict. In one of the most natural generalizations of tolerance graphs with direct applications in the comparison of DNA sequences from different organisms, namely multitolerance graphs, two tolerances are allowed for each interval: one on the left side and the other on the right side. Several efficient algorithms for optimization problems that are NP-hard in general graphs have been designed for tolerance and multitolerance graphs. In spite of this progress, the complexity status of some fundamental algorithmic problems on tolerance and multitolerance graphs, such as the dominating set problem, remained unresolved until now---three decades after the introduction of tolerance graphs. In this paper we introduce two new geometric representations for tolerance and multitolerance graphs, given by points and line segments in the plane. Apart from being important on their own, these...

The efficacy of sex-chromosomal markers in studies ofCercopithecushybridization: Discovery of a captive hybrid and applications in wild populations

We demonstrate the utility of previously described molecular methods for identifying hybrid Cercopithecus monkeys. Using phylogenetic analyses and DNA sequence comparisons at X-chromosomal and Y-chromosomal loci, we have identified a hybrid animal in the Cheyenne Mountain Zoo (USA)--an identification that was not known a priori but was later confirmed by review of zoo records. The molecular techniques employed here are of great use to studies of the genus Cercopithecus because, unlike most mammals, these monkeys frequently form polyspecific associations, and recent deforestation is likely to have driven otherwise low-level hybridization to higher frequencies which may reduce the fitness of threatened populations. Y-chromosomal markers are especially informative because they provide working hypotheses for (1) the primary mechanism of hybridization (i.e., species A males × species B females) and, by extension; (2) the major direction of gene flow.

The challenge of genetic selection for heat tolerance: the dairy cattle example

Exposure of livestock to high heat loads negatively affects animal’s productivity. Genetic selection for heat tolerance using quantitative approaches has been developed by making use of the milk recording information merged with the meteorological information in the test date. The main conclusions of the studies following this approach have been that there is genetic variability in the response to heat stress (HS), that a genotype by environment interaction between thermal comfort and HS conditions exists and that there is a genetic antagonism between HS tolerance and high milk production. This approach has the advantage of adding no extra costs to the existing milk recording schemes, but it has some disadvantages. Current milk recording information does not seem to fully capture the productive response to high heat loads. Moreover, the antagonism between heat tolerance and high milk production may offset the benefits of selection for this trait if heat-tolerant animals are less productive. The use of new tools from phenomics, genomics and transcriptomics can help in achieving an accurate selection of heat-tolerant animals without damaging progress in milk production. New phenotypes for this selection are measure of body temperature and respiration rates together with measures of indicators of heat tolerance in milk, through the use of mid IR spectroscopy. The use of commercial DNA chips to perform genome wide association studies or comparison of whole genome DNA sequence of animals of heat adapted and temperate climate breeds could also provide useful genomic information. Finally, RNA sequencing together with the recent discovery of the possibility to use the milk transcriptome instead of tissue biopsies could help to discover differentially expressed genes under HS and thermoneutrality. The existence of powerful tools to achieve better phenotypes to identify tolerantv. susceptible animals and to gain insights about the genetic mechanisms underlying HS response to be able to disentangle the genetic puzzle of heat tolerance may make possible the selection of heat-tolerant and still productive animals.

結石内部に真菌塊がみられた頰粘膜小唾液腺唾石症の1例

We describe a case of sialolithiasis of the buccal mucosa with a fungal mass in a calculus of the minor salivary gland. An 87-year-old man was referred to our hospital because of a small nodule in the right buccal mucosa. On examination, an elastic, hard, painless, movable nodule, measuring 3 × 3 mm and located under the right buccal mucosa, was detected. The overlying mucosal surface was intact. Radiographic examination revealed no abnormalities in the right buccal region. We resected the nodule with the patient under local anesthesia. Histological examination of the resected specimen revealed lightly eosinophilic material with lamellar calcification and colonies of yeast-like fungus in a duct of the minor salivary gland. Comparative 26S ribosomal DNA sequence analysis of paraffin sections identified the fungus as Candida parapsilosis. This case suggests a potential role of mycosis in the etiopathogenesis of sialolithiasis.

Use of FFT in Protein Sequence Comparison under Their Binary Representations

The paper considers Voss type representation of amino acids and uses FFT on the represented binary sequences to get the spectrum in the frequency domain. Based on the analysis of this spectrum by using the method of inter coefficient difference (ICD), it compares protein sequences of ND5 and ND6 category. Results obtained agree with the standard ones. The purpose of the paper is to extend the ICD method of comparison of DNA sequences to comparison of protein sequences. The topic of discussion is to develop a novel method of comparing protein sequences. The main achievements of the work are that the method applied is completely new of its kind, so far as protein sequence comparison is concerned and moreover the results of comparison agree with the previous results obtained by other methods for the same category of protein sequences.

Distinct phylogeographic structure recognized within Desmazierella acicola

Desmazierella acicola (anamorph Verticicladium trifidum, Chorioactidaceae) represents a frequent colonizer of pine needles in litter. Considering the global diversity and distribution of pine species, we expected different phylogenetic lineages to exist in different geographical and climatic areas inhabited by these hosts. We compared DNA sequence data with phenotypic characteristics (morphology of the anamorph and growth at three different temperatures) of 43 strains isolated mostly from pine and also spruce needle litter sampled in various geographical areas. Analyses of ITS rDNA recovered eight geographically structured lineages. Fragments of genes for the translation elongation factor 1-α, and the second largest subunit of RNA polymerase II reproduced similar lineages, although not all of them were monophyletic. The similarity in ITS sequences among the clade with samples from Continental-Atlantic Europe and four other clades was lower than 95%. Several lineages exhibit also a tendency toward host specificity to a particular pine species. Growth tests at different temperatures indicated a different tolerance to specific climatic conditions in different geographic areas. However, the surveyed phenotypic characteristics also showed high variation within lineages, most evident in the morphology of the anamorph. Until a morphological study of the teleomorph is carried out, all of these lineages should be treated as distinct populations within a single species.

Statistical and Alignment Based Methods for Comparison of Non-Coding DNA Sequences

Statistical and Alignment Based Methods for Comparison of Non-Coding DNA Sequences

Multigene phylogenies and morphological characterization of five new Ophiostoma spp. associated with spruce-infesting bark beetles in China

Ophiostoma spp. (Ophiostomatales, Ascomycota) are well-known fungi associated with bark beetles (Coleoptera: Scolytinae). Some of these are serious tree pathogens, while the majority is blue-stain agents of timber. In recent years, various bark beetle species have been attacking spruce forests in Qinghai province, China, causing significant damage. A preliminary survey was done to explore the diversity of the ophiostomatoid fungal associates of these beetles. The aims of the present study were to identify and characterize new Ophiostoma spp. associated with spruce-infesting bark beetles in Qinghai Province, and to resolve phylogenetic relationships of Ophiostoma spp. related to the Chinese isolates, using multigene phylogenetic analyses. Results obtained from four gene regions (ribosomal internal transcribed spacer regions, β-tubulin, calmodulin, translation elongation factor-1α) revealed five new Ophiostoma spp. from Qinghai. These included O. nitidus sp. nov., O. micans sp. nov., and O. qinghaiense sp. nov. in a newly defined O. piceae complex. The other two new species, O. poligraphi sp. nov. and O. shangrilae sp. nov., grouped in the O. brunneo-ciliatum complex. Based on DNA sequence and morphological comparisons, we also show that O. arduennense and O. torulosum are synonyms of O. distortum, while O. setosum is a synonym of O. cupulatum.

Novel DNA Sequence Comparison Method Based on Markov Chain and Information Entropy

Novel DNA Sequence Comparison Method Based on Markov Chain and Information Entropy

Comparison of Flow Injection MS, NMR, and DNA Sequencing: Methods for Identification and Authentication of Black Cohosh (Actaea racemosa).

Flow injection mass spectrometry and proton nuclear magnetic resonance spectrometry, two metabolic fingerprinting methods, and DNA sequencing were used to identify and authenticate Actaea species. Initially, samples of Actaea racemosa from a single source were distinguished from other Actaea species based on principal component analysis and soft independent modeling of class analogies of flow injection mass spectrometry and proton nuclear magnetic resonance spectrometry metabolic fingerprints. The chemometric results for flow injection mass spectrometry and proton nuclear magnetic resonance spectrometry agreed well and showed similar agreement throughout the study. DNA sequencing using DNA sequence data from two independent gene regions confirmed the metabolic fingerprinting results. Differences were observed between A. racemosa samples from four different sources, although the variance within species was still significantly less than the variance between species. A model based on the combined A. racemosa samples from the four sources consistently permitted distinction between species. Additionally, the combined A. racemosa samples were distinguishable from commercial root samples and from commercial supplements in tablet, capsule, or liquid form. DNA sequencing verified the lack of authenticity of the commercial roots but was unsuccessful in characterizing many of the supplements due to the lack of available DNA.

Next Generation Sequencing Identifies a Distinct Transcriptional Profile, Including Isoform Dysregulation That Segue with Genomic Alterations in Waldenstrom's Macoglobulinemia

Background: Whole genome sequencing has identified highly prevalent somatic mutations including MYD88, CXCR4 and ARID1A, as well as gene losses in Waldenström's Macroglobulinemia (WM) (NEJM 367(9):826-33; Blood 123(11):1637-46). At least three genomic defined subpopulations of WM have been identified based on MYD88 and CXCR4 mutation status (Blood 123(18):2791-6).The regulatory impact for these genomic alterations remain to be clarified.Methods: Next generation transcriptome profiling was performed using Illumina HiSeq. RNA was isolated from CD19-selected bone marrow cells from 57 WM patients, as well as memory (CD19+CD27+) and non-memory (CD19+CD27-) B-cells from 9 healthy donors. Differential gene expression analysis was performed based on MYD88, CXCR4 and ARID1A mutation status, as well as common cytogenetic abnormalities encountered in WM including amplifications in chromosomes 3q, 4, 6p, and deletions in 6q. Reads were aligned to KnownGene HG19/GRCh37 reference using STAR. Read counts per gene were obtained using featureCounts from Rsubread, and analyzed using voom from the edgeR/limma Bioconductor packages in R. Differential isoform expression was assessed using the Cufflinks software suite. Functional enrichment analysis was conducted using Ingenuity Pathway Analysis.Results: Transcriptional profilingof WM cells showed a stronger correlation with healthy donor memory B-cells, their putative cell of origin. Differential gene expression analysis between WM patients and healthy donors generated a distinct transcriptional profile for WM that included dysregulation of PIM1, RGS7, IL11RA and EPHB4, as well as differential isoform usage in TP53, PRDM1 and XBP1. MYD88mutatedCXCR4wild-type(WT) WM patients consistently over-expressed genes unique to this cohort including, IL17RB, GPER, WNT5A, WNK2, CABELS1, and PRDM5. MYD88mutated patients who harbored nonsense (NS) or frame-shift (FS) mutations in CXCR4 showed functional enrichment of genes that indicated inhibition of Toll-like receptor inflammatory pathways. CXCR4 mutated patients showed strong up-regulation of CXCR7 and TSPAN33, and exhibited isoform level dysregulation of MEF2B, FOXO3, KDM2A and PRKAG2. Unsupervised clustering differentiated MYD88mutatedCXCR4WT from MYD88mutatedCXCR4NS/FS patients, while samples from MYD88WTCXCR4WT clustered with CXCR4NS/FS group. Clusters based on clonality and disease burden were also observed (Figure 1). CXCR4NS/FS transcripts were preferentially expressed over CXCR4WT transcripts despite the subclonal presence of CXCR4mutations. These findings were further validated by comparative DNA versus cDNA Sanger sequencing indicating allelic dysregulation within CXCR4NS/FS subclones. Controlling for MYD88 and CXCR4 mutation status, the presence of ARID1A mutations and cytogenetic abnormalities generated distinct transcriptional profiles. Random forest regression analysis identified subsets of genes strongly associated with bone marrow disease involvement, serum IgM and hemoglobin levels. Notably, increased bone marrow disease burden was associated with increased CXCL13, and decreased TP53 and RBL1 expression. Likewise, higher levels of serum IgM corresponded with increased IL27RA expression.Conclusion: Using next generation sequencing, we have identified a distinct transcriptional profile, including isoform dysregulation that segue with highly prevalent genomic mutations in WM. The findings provide valuable insights into the molecular pathogenesis and clinical presentation of WM. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Knoxdaviesia proteae is not the only Knoxdaviesia-symbiont of Protea repens.

Two polyphyletic genera of ophiostomatoid fungi are symbionts of Proteaceae in southern Africa. One of these, Knoxdaviesia, includes two closely related species, K. proteae and K. capensis, that have overlapping geographical distributions, but are not known to share Protea host species. Knoxdaviesia capensis appears to be a generalist that occupies numerous hosts, but has never been found in P. repens, the only known host of K. proteae. In this study, extensive collections were made from P. repens and isolates were identified using DNA sequence comparisons. This led to the surprising discovery of K. capensis from P. repens for the first time. The fungus was encountered at a low frequency, suggesting that P. repens is not its preferred host, which may explain why it has not previously been found on this plant. The basis for the specialisation of K. proteae and K. capensis on different Protea species remains unknown.

A New Heuristic Approach for DNA Sequences Alignment

The problem of comparing DNA sequences is one of the most significant tasks in the field of computational biology. It helps locating the similarities and differences between pairs of DNA sequences. This task can be achieved by finding the longest common substrings between DNA sequences and consequently aligning them. The complexity of this task is due to the high computational power and huge space consuming. Comparing DNA sequences leads to infer the cause of a certain disease beside many significant biological applications. This paper introduces a new Heuristic Approach for DNA Sequences Alignment between two DNA sequences. The new approach is based on three processing phases: the first phase finds the multiple common substrings in the two sequences, the second one sorts the obtained common substrings descending according to their lengths, and the last phase generates the optimal two aligned sequences. The modules of the new approach have been implemented and tested in C# language under Windows platform. The obtained results manifest a reduction in both time of processing and memory requirements.