scholarly journals Systematics of Scleranthus (Caryophyllaceae)

2021 ◽  
Author(s):  
◽  
Robin David Smissen
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Dna Sequence Analysis ◽  
Its Sequences ◽  
Data Sets ◽  
Nuclear Its ◽  
Floral Characters

<p>Scleranthus is a genus of about 12 species of herbaceous flowering plants or small shrubs with a disjunct Eurasian/Australasian distribution. Monophyly of the genus is supported by the close similarity of gynoecial development of all species and consistent with nuclear ITS DNA sequence analysis. Traditionally the genus had been divided into two sections, section Scleranthus and section Mniarum. Section Mniarum is exclusively Australasian while section Scleranthus has been circumscribed to contain exclusively European species or a combination of European and Australasian species. Pollen and floral characters align the species into Australasian and Eurasian groups also supported by nuclear ITS DNA sequence analysis. Section Scleranthus as more broadly defined (i.e., sensu West and Garnock-Jones, 1986) is therefore at least paraphyletic or at worst polypyhyletic. Phylogenetic reconstructions based on morphological characters differ from those based on ITS sequences in supporting different relationships within the Australasian species of Scleranthus. Hybridisation and introgression within the genus are discussed and suggested as the cause of discordance between morphology and DNA sequence based trees. Low sequence divergence among Scleranthus ITS sequences suggests that the European and Australasian clades within the genus diverged within the last l0 million years. Biogeographic implications of these dating and competing hypotheses explaining the disjunct North-South distribution of the genus are discussed. Nuclear ITS and chloroplast ndhF DNA sequences both suggest that Scleranthus belongs to a clade within the family Caryophyllaceae consisting of members of subfamilies Alsinoideae and Caryophylloideae. Phylogenetic relationships between genera belonging to the three subfamilies of Caryophyllaceae (Alsinoideae, Caryophyloideae, and Paronychioideae) are addressed in this thesis through ndhF sequence analysis, which provides no support for the monophyly of traditionally recognised groups. Morphological character data sets are likely to always encompass multiple incongruent data partitions (sensu Bull et al. 1993). It may therefore be appropriate to combine data from DNA sequence and morphology for parsimony analysis even where the two are significantly incongruent.</p>

scholarly journals Systematics of Scleranthus (Caryophyllaceae)

2021 ◽  
Author(s):  
◽  
Robin David Smissen
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Morphological Characters ◽  
Dna Sequence Analysis ◽  
Its Sequences ◽  
Data Sets ◽  
Nuclear Its ◽  
Floral Characters

<p>Scleranthus is a genus of about 12 species of herbaceous flowering plants or small shrubs with a disjunct Eurasian/Australasian distribution. Monophyly of the genus is supported by the close similarity of gynoecial development of all species and consistent with nuclear ITS DNA sequence analysis. Traditionally the genus had been divided into two sections, section Scleranthus and section Mniarum. Section Mniarum is exclusively Australasian while section Scleranthus has been circumscribed to contain exclusively European species or a combination of European and Australasian species. Pollen and floral characters align the species into Australasian and Eurasian groups also supported by nuclear ITS DNA sequence analysis. Section Scleranthus as more broadly defined (i.e., sensu West and Garnock-Jones, 1986) is therefore at least paraphyletic or at worst polypyhyletic. Phylogenetic reconstructions based on morphological characters differ from those based on ITS sequences in supporting different relationships within the Australasian species of Scleranthus. Hybridisation and introgression within the genus are discussed and suggested as the cause of discordance between morphology and DNA sequence based trees. Low sequence divergence among Scleranthus ITS sequences suggests that the European and Australasian clades within the genus diverged within the last l0 million years. Biogeographic implications of these dating and competing hypotheses explaining the disjunct North-South distribution of the genus are discussed. Nuclear ITS and chloroplast ndhF DNA sequences both suggest that Scleranthus belongs to a clade within the family Caryophyllaceae consisting of members of subfamilies Alsinoideae and Caryophylloideae. Phylogenetic relationships between genera belonging to the three subfamilies of Caryophyllaceae (Alsinoideae, Caryophyloideae, and Paronychioideae) are addressed in this thesis through ndhF sequence analysis, which provides no support for the monophyly of traditionally recognised groups. Morphological character data sets are likely to always encompass multiple incongruent data partitions (sensu Bull et al. 1993). It may therefore be appropriate to combine data from DNA sequence and morphology for parsimony analysis even where the two are significantly incongruent.</p>

On Rényi entropies of order statistics

2015 ◽  
Vol 08 (06) ◽  
pp. 1550080 ◽  
Author(s):  
Richa Thapliyal ◽  
H. C. Taneja
Keyword(s):  
Distribution Function ◽  
Sequence Analysis ◽  
Order Statistics ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Biological Systems ◽  
Dna Sequence Analysis ◽  
Entropy Measure ◽  
Entropy Measures ◽  
Cumulative Residual

In this paper we consider a generalize dynamic entropy measure and prove that this measure characterizes the distribution function uniquely. Also we propose cumulative residual Rényi entropy of order statistics and prove that it also determines the distribution function uniquely. Applications of entropy concepts to DNA sequence analysis, the ultimate support for the biological systems, have been widely explored by researchers. The entropy measures discussed here can be applied for analysis of ordered DNA sequences.

scholarly journals DNA Sequence Analysis of dtxR Gene (Partial) of Corynebacterium diphtheriae Causing Diphtheria in Jawa and Kalimantan Islands, Indonesia

2017 ◽  
Vol 9 (2) ◽  
pp. 91
Author(s):  
Sunarno Sunarno ◽  
Yuanita Mulyastuti ◽  
Nelly Puspandari ◽  
Kambang Sariadji
Keyword(s):  
Sequence Analysis ◽  
Multiplex Pcr ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Sequence Data ◽  
Clinical Specimen ◽  
Corynebacterium Diphtheriae ◽  
Dna Sequence Analysis ◽  
Local Alignment ◽  
Pcr Products

BACKGROUND: dtxR gene is a global regulator that can be used as a marker for detection of Corynebacterium diphtheriae (C. diphtheriae) and it is also a representative tool for mapping purpose (molecular typing) of this bacteria. The aim of this study was to analyze the DNA sequences of partial dtxR gene of C. diphtheriae causing diphtheria in some region of Indonesia. DNA sequence analysis was used to verify the accuracy of the in-house multiplex polymerase chain reaction (PCR) method that used for detection of C. diphtheriae in the clinical specimen as well as a preliminary study to determine the strain diversity of C. diphtheriae circulating in Indonesia.METHODS:Ten PCR products targeting the dtxR gene that have been detected as positive C. diphtheriae previously by in-house multiplex PCR used as samples in this study. The DNA sequencing carried out by Sanger method and the sequence data was analyzed by Bioedit software offline and basic local alignment sequence typing (BLAST) online.RESULTS: All of DNA sequence analyzed in this study were similar or identical to the dtxR gene sequence data of C. diphtheriae registered in GenBank. Within the 162 nucleotides (base 150-311) of dtxR gene that analyzed, at least 2 clonals were found among 10 samples. Substitutions of 2 nucleotides (base 225 and 273) was detected, both were silent mutation.CONCLUSION:Ten partial DNA sequences of dtxR genes in this study verify the accuracy of in-house multiplex PCR which used to identify the bacteria causing diphtheria in the clinical specimen. The DNA sequences also represent the existing diversity of the bacteria causing diphtheria circulating in Indonesia.KEYWORDS: dtxR, C. diphtheriae, diphtheria, Indonesia

scholarly journals SEQUENCE ANALYSIS OF 18s DNA OF Melosira sp., Dunaliella sp., Isochrysis sp. AND Porphyridium sp.

2015 ◽  
Vol 2 (1) ◽  
pp. 592
Author(s):  
Lucia Kusumawati ◽  
Ruben Wahyudi ◽  
Reinhard Pinontoan ◽  
Maria Gorreti Lily Panggabean
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Rdna Sequences ◽  
Pcr Products ◽  
18S Rdna Sequences ◽  
Pcr Method ◽  
High Level

<p>Phytoplankton has high level of biodiversity. In previous years phytoplankton was identified by their morphological characters. However, their morphology might change in different environments. These difficulties can be overcome by comparing their 18S rDNA sequences. This research is aimed to verify the identity of Melosira sp., Dunaliella sp., Isochrysis sp. and Porphyridium sp. Here, PCR method was used to amplify 18s DNA sequences. Three primer pairs were used, i.e. 18S-F and 18S-R; 501F and 1700R; 18S-2F and 18S-2R. PCR products were sequenced. MEGA5 was used to make phylogenetic tree. Genus verification for Isochrysis sp., Dunaliella sp. and Melosira sp. were conducted successfully using Blast and phylogenetic tree. 18s DNA sequence of Porphyridium sp. shows an interesting result and needs further verification.</p><p><br /><strong>Keywords</strong>: Phytoplankton, Melosira sp., Dunaliella sp., Isochrysis sp., Porphyridium sp.</p>

scholarly journals DNA Sequence Similarity between California Isolates of Cryptosporidium parvum

1998 ◽  
Vol 64 (4) ◽  
pp. 1584-1586 ◽  
Author(s):  
Maria das Graças C. Pereira ◽  
Edward R. Atwill ◽  
Melissa R. Crawford ◽  
Rance B. Lefebvre
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Cryptosporidium Parvum ◽  
Dna Sequences ◽  
Sequence Similarity ◽  
Complete Sequence ◽  
Dna Sequence Analysis ◽  
Nucleic Acid Amplification ◽  
Reference Sequence ◽  
Sequence Identity

ABSTRACT We evaluated whether nucleic acid amplification with primers specific for Cryptosporidium parvum followed by automated DNA sequence analysis of the PCR amplicons could differentiate between California isolates of C. parvum obtained from livestock, humans, and feral pigs. Almost complete sequence identity existed among the livestock isolates and between the livestock and human isolates. DNA sequences from feral pig isolates differed from those from livestock and humans by 1.0 to 1.2%. The reference sequence obtained by Laxer et al. (M. A. Laxer, B. K. Timblin, and R. J. Patel, Am. J. Trop. Med. Hyg. 45:688–694, 1991.) differed from California isolates of C. parvum by 1.8 to 3.2%. These data suggest that DNA sequence analysis of the amplicon of Laxer et al. does not allow for differentiation between various strains of C. parvum or that our collection of isolates obtained from various hosts from across California was limited to one strain ofC. parvum.

Phylogenetic relationships in Leptographium based on morphological and molecular characters

2001 ◽  
Vol 79 (6) ◽  
pp. 719-732 ◽  
Author(s):  
K Jacobs ◽  
M J Wingfield ◽  
B D Wingfield
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Bark Beetles ◽  
Morphological Characters ◽  
Dna Sequence Analysis ◽  
Phylogenetic Studies ◽  
Blue Stain ◽  
Woody Substrates ◽  
Molecular Characters

Species of Leptographium Lagerberg & Melin are characterized by mononematous conidiophores with dark stipes and conidiogenous apparatuses with complex series of branches. These fungi generally inhabit woody substrates, are associated with bark beetles (Coleoptera: Scolytidae) and cause blue-stain in conifers. Few phylogenetic studies have been conducted on Leptographium species, and those that have been undertaken have been focused on a small number of species. The objective of this study was to investigate the phylogenetic relationships among species in Leptographium based on partial DNA operon sequences and to ascertain whether morphological characters are congruent with DNA-based phylogeny. Morphological characters were analyzed and compared with results from DNA sequence analysis. Results indicate that there are three groups within Leptographium based on DNA sequence analysis. There was, however, no congruence between these groups and those emerging from morphological characters. Data from this study strongly support the connection between Leptographium and Ophiostoma Sydow & Sydow. They also provide us with an objective means to confirm the identity of many Leptographium species that are difficult to distinguish based on morphological characters.Key words: Leptographium, phylogeny, morphology, Ophiostoma, rRNA.

Expressed sequence tags for the chicken genome from a normalized 10-day-old white leghorn whole-embryo cDNA library. 3. DNA sequence analysis of genetic variation in commercial chicken populations

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 261-267 ◽  
Author(s):  
E J Smith ◽  
L Shi ◽  
G Smith
Keyword(s):  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Expressed Sequence Tags ◽  
Chicken Genome ◽  
Dna Sequence Analysis ◽  
Genetic Maps ◽  
Commercial Chicken ◽  
Genomic Regions ◽  
Expressed Sequence

Single nucleotide polymorphisms (SNPs) have emerged as a major class of DNA markers with the advantage of permitting the development of high-density genetic maps adequate for quantitative trait loci (QTL) identification by linkage-disequilibrium analysis. Here we describe results of a relatively high-depth survey of chicken broiler and layer populations for SNPs in targeted genomic regions of chicken expressed sequence tag (EST) sites. The sequences scanned, representing the composite sequence of 12 amplified fragments for a total of 6489 bp, were randomly distributed, occurring on six different chromosomes or linkage groups in the chicken genome. Although one of the genomic DNA sequences did not match the reference cDNA sequence, another contained an intron that separated two putative exons. The number of SNPs observed within each of the 12 EST-targeted genomic regions ranged from 0 to 10 for a total of 44 and a frequency of 0.7%. About 70% of the polymorphisms were shared between layer and broiler populations. The average heterozygosity within the populations ranged from 0.15 to 0.48, with the layer populations showing the higher heterozygosity. SNPs and oligonucleotides described will provide a resource for genetic analysis in commercial chicken populations. The data appear to indicate that the relative frequency of SNPs in the targeted regions scanned is higher than the frequency reported for any of the other regions scanned to date in other eukaryotic genomes. Additionally, the results suggest that the use of DNA pools may offer an efficient approach to SNP detection in chickens, as has been shown in other vertebrates.Key words: DNA sequence analysis, SNPs, expressed sequence tags, chicken.

scholarly journals A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

2003 ◽  
Vol 1 (1) ◽  
pp. 3-9
Author(s):  
Fei Chen ◽  
Yuan-Ting Zhang
Keyword(s):  
Wavelet Transform ◽  
Sequence Analysis ◽  
Energy Distribution ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Structural Information ◽  
Dna Structure ◽  
Structural Features ◽  
Dna Sequence Analysis ◽  
Adaptive Wavelet

DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT) – the bionic wavelet transform (BWT) – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

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