Sporolithon amadoi sp. nov. (Sporolithales, Rhodophyta), a new rhodolith-forming non-geniculate coralline alga from offshore the northwestern Gulf of Mexico and Brazil

Phytotaxa ◽  
2019 ◽  
Vol 423 (2) ◽  
pp. 49-67 ◽  
Author(s):  
JOSEPH L. RICHARDS ◽  
RICARDO G. BAHIA ◽  
MICHEL B. JESIONEK ◽  
SUZANNE FREDERICQ
Keyword(s):  
Sequence Analysis ◽  
Gulf Of Mexico ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Lsu Rdna ◽  
Coralline Alga ◽  
Anatomical Features ◽  
Spore Release ◽  
Cell Layers ◽  
Thallus Surface

DNA sequence analysis of plastid-encoded psbA and rbcL loci, and nuclear-encoded LSU rDNA of rhodolith-forming specimens of Sporolithales from Brazil and the northwestern Gulf of Mexico reveal that they belong to an unnamed species of Sporolithon (Sporolithaceae). Sporolithon amadoi sp. nov. is morpho-anatomically characterized by a vegetative thallus reaching more than 20 cell layers, a tetrasporophyte with tetrasporangial sori slightly raised above the thallus surface that become overgrown and buried after spore release, and by cruciately divided tetrasporangia with pores surrounded by 9–13 rosette cells. Since these morpho-anatomical features are shared with some other Sporolithon species, identification of this species can only be confirmed by DNA sequences.

scholarly journals Range extension of Mesophyllum erubescens (Foslie) Me. Lemoine (Hapalidiales, Rhodophyta): first report from mesophotic rhodolith beds in the northwestern Gulf of Mexico offshore Louisiana and Texas, including the Flower Garden Banks National Marine Sanctuary

Check List ◽  
2020 ◽  
Vol 16 (3) ◽  
pp. 513-519
Author(s):  
Joseph L. Richards ◽  
Ronald P. Kittle III ◽  
Jaida R. Abshire ◽  
Dijel Fuselier ◽  
William E. Schmidt ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Gulf Of Mexico ◽  
Dna Sequence ◽  
Dna Sequence Analysis ◽  
Range Extension ◽  
Lsu Rdna ◽  
First Report ◽  
Anatomical Characters ◽  
Texas Border ◽  
First Time

DNA sequence analysis of plastid-encoded psbA and UPA, mitochondrion-encoded COI, and nuclear-encoded LSU rDNA of rhodolith-forming crustose coralline algal specimens from the northwestern Gulf of Mexico reveals that Mesophyllum erubescens (Foslie) Me. Lemoine is present in mesophotic rhodolith beds offshore Louisiana and Texas at 39–57 m depth. Morpho-anatomical characters viewed with SEM support the identification of these specimens. Mesophyllum erubescens is reported for the first time offshore Louisiana at Ewing Bank, the Louisiana–Texas border at Bright Bank, and Texas in the Flower Garden Banks National Marine Sanctuary.

scholarly journals Estimation of Similarity between DNA Sequences and Its Graphical Representation

2020 ◽  
Vol 9 (1) ◽  
pp. 43-51
Keyword(s):  
Sequence Analysis ◽  
Molecular Biology ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Graphical Representation ◽  
Similarity Analysis ◽  
Biological Sequence ◽  
Field Of Study ◽  
Biological Sequence Analysis ◽  
Wide Range

Bioinformatics, which is now a well known field of study, originated in the context of biological sequence analysis. Recently graphical representation takes place for the research on DNA sequence. Research in biological sequence is mainly based on the function and its structure. Bioinformatics finds wide range of applications specifically in the domain of molecular biology which focuses on the analysis of molecules viz. DNA, RNA, Protein etc. In this review, we mainly deal with the similarity analysis between sequences and graphical representation of DNA sequence.

scholarly journals NanoDJ: A Dockerized Jupyter Notebook for Interactive Oxford Nanopore MinION Sequence Manipulation and Genome Assembly

2019 ◽  
Author(s):  
Héctor Rodríguez-Pérez ◽  
Tamara Hernández-Beeftink ◽  
José M. Lorenzo-Salazar ◽  
José L. Roda-García ◽  
Carlos J. Pérez-González ◽  
...  
Keyword(s):  
Quality Control ◽  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Genome Assembly ◽  
Interactive Visualization ◽  
Hybrid Assembly ◽  
Genomic Technologies ◽  
Oxford Nanopore ◽  
Oxford Nanopore Technologies

AbstractBackgroundThe Oxford Nanopore Technologies (ONT) MinION portable sequencer makes it possible to use cutting-edge genomic technologies in the field and the academic classroom.ResultsWe present NanoDJ, a Jupyter notebook integration of tools for simplified manipulation and assembly of DNA sequences produced by ONT devices. It integrates basecalling, read trimming and quality control, simulation and plotting routines with a variety of widely used aligners and assemblers, including procedures for hybrid assembly.ConclusionsWith the use of Jupyter-facilitated access to self-explanatory contents of applications and the interactive visualization of results, as well as by its distribution into a Docker software container, NanoDJ is aimed to simplify and make more reproducible ONT DNA sequence analysis. The NanoDJ package code, documentation and installation instructions are freely available at https://github.com/genomicsITER/NanoDJ.

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 Neogoniolithon (Corallinales, Rhodophyta) on the Atlantic coast of Mexico, including N. siankanensis sp. nov. 

Phytotaxa ◽  
2014 ◽  
Vol 190 (1) ◽  
pp. 64 ◽  
Author(s):  
Luz Elena Mateo-Cid ◽  
A. Catalina Mendoza González ◽  
Paul W. Gabrielson
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
East Coast ◽  
Atlantic Coast ◽  
Type Specimens ◽  
Western Atlantic ◽  
Cell Layers ◽  
Reproductive Material ◽  
Species Descriptions ◽  
Reproductive Characters

This is the first revision of Neogoniolithon species on the east coast of Mexico based on both DNA sequences (psbA) and morpho-anatomical characters. Nine species names are provisionally applied based on morpho-anatomical comparisons with type specimens or with species descriptions: N. accretum, N. acropetum, N. erosum, N. mamillare, N. propinquum, N. rhizophorae, N. solubile, N. spectabile and N. strictum. For none of these species was type or topotype material sequenced, but all have their type localities in the subtropical or tropical western Atlantic Ocean. Neogoniolithon siankanensis is described on the basis of a distinctive branched thallus, apical tetrasporangial conceptacles and DNA sequence. Another four species are present, each characterized by DNA sequence, but insufficient reproductive material was available to adequately describe these species. A suite of vegetative and reproductive characters can adequately segregate the currently named Mexican east coast Neogoniolithon species, including 1) branched versus unbranched thalli, 2) monomerous versus dimerous construction, 3) disposition of trichocytes, 4) interior dimensions of mature tetrasporangial conceptacles, 5) number of cell layers comprising tetrasporangial conceptacle roof and 6) shape of cells that line tetrasporangial pore canal. Morpho-anatomical descriptions and distributions are provided for all named species.

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 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 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 CNN Model With Hilbert Curve Representation of DNA Sequence For Enhancer Prediction

2019 ◽  
Author(s):  
Monowar Md. Anjum ◽  
Ibrahim Asadullah Tahmid ◽  
M. Sohel Rahman
Keyword(s):  
Deep Learning ◽  
Sequence Analysis ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Computational Prediction ◽  
Vital Role ◽  
Hilbert Curve ◽  
Cis Acting ◽  
Predictor Model ◽  
Feature Dependency

AbstractMotivationEnhancers are distal cis-acting regulating regions that play a vital role in gene transcription. However, due to the inherent nature of enhancers being linearly distant from the affected gene in an irregular manner while being spatially close at the same time, systematically predicting enhancers has been a challenging task. Although several computational predictor models through both epigenetic marker analysis and sequence-based analysis have been proposed, they lack generalization capacity across different enhancer datasets and have feature dependency. On the other hand, the recent proliferation of deep learning methods has opened previously unknown avenues of approach for sequence analysis tasks which eliminates feature dependency and achieves greater generalization. Therefore, harnessing the power of deep learning based sequence analysis techniques to develop a more generalized model than the ones developed before to predict enhancer region in a DNA sequence is a topic of interest in bioinformatics.ResultsIn this study, we develop the predictor model CHilEnPred that has been trained with the visual representation of the DNA sequences with Hilbert Curve. We report our computational prediction result on FANTOM5 dataset where CHilEnPred achieves an accuracy of 94.97% and AUC of 0.987 on test data.AvailabilityOur CHilEnPred model can be freely accessed at https://github.com/iatahmid/[email protected]

Sign in / Sign up

Export Citation Format

Share Document