scholarly journals Sequence analysis of 18SrDNA gene from sagoplast degrading fungi

2021 ◽  
Vol 26 (2) ◽  
pp. 72-78
Author(s):  
Tri Gunaedi ◽  
Arsyam Mawardi
Keyword(s):  
Acetic Acid ◽  
Data Analysis ◽  
Sequence Analysis ◽  
Gene Sequence ◽  
Sequence Data ◽  
Fungal Morphology ◽  
Gene Sequences ◽  
Fungal Isolates ◽  
Orange Color ◽  
Yellowish Orange

The bioplastic can be made from sago flour and known as sagoplast. It was widely known that for making bioplastic, the addition of acetic acid and glycerol are needed. Products that are air-dried are easy to grow fungi within a few weeks. This makes the basis for researchers to undestand more about the character and identity of the sagoplast degrading fungi. Characterization and identification were carried out by observed morphology and analyzing the 18SrDNA gene sequence of fungal isolates that had grown on the sagoplast. Fungal isolates morphology showed yellowish-orange color with white thread-like mycelia and a blackish brown mace with white thread-shaped mycelia. These characters of fungal morphology that similar with Aspergillus. The gene sequences of the fungal isolates were aligned with reference gene sequences of the fungi obtained from the Gen Bank of the National Center for Biotechnology Information (NCBI). Sequence data analysis was performed by using the Clustal X program to determine the kinship and taxonomy of the fungal isolates that able to degrade sagoplast. The result showed that two fungal isolates, DFSP.J1 and DFSP.J4, were found and demonstrated their ability for degrading sagoplast. Isolate DFSP.J1 is related to Aspergillus flavus strain PSU2 LC127086.1, while isolate DFSP.J4 is related to Aspergillus niger IFO4033 D63697.1.

scholarly journals Sequence analysis of 18SrDNA gene from sagoplast degrading fungi

2021 ◽  
Vol 26 (2) ◽  
pp. 72-78
Author(s):  
Tri Gunaedi ◽  
Arsyam Mawardi
Keyword(s):  
Acetic Acid ◽  
Data Analysis ◽  
Sequence Analysis ◽  
Gene Sequence ◽  
Sequence Data ◽  
Fungal Morphology ◽  
Gene Sequences ◽  
Fungal Isolates ◽  
Orange Color ◽  
Yellowish Orange

The bioplastic can be made from sago flour and known as sagoplast. It was widely known that for making bioplastic, the addition of acetic acid and glycerol are needed. Products that are air-dried are easy to grow fungi within a few weeks. This makes the basis for researchers to undestand more about the character and identity of the sagoplast degrading fungi. Characterization and identification were carried out by observed morphology and analyzing the 18SrDNA gene sequence of fungal isolates that had grown on the sagoplast. Fungal isolates morphology showed yellowish-orange color with white thread-like mycelia and a blackish brown mace with white thread-shaped mycelia. These characters of fungal morphology that similar with Aspergillus. The gene sequences of the fungal isolates were aligned with reference gene sequences of the fungi obtained from the Gen Bank of the National Center for Biotechnology Information (NCBI). Sequence data analysis was performed by using the Clustal X program to determine the kinship and taxonomy of the fungal isolates that able to degrade sagoplast. The result showed that two fungal isolates, DFSP.J1 and DFSP.J4, were found and demonstrated their ability for degrading sagoplast. Isolate DFSP.J1 is related to Aspergillus flavus strain PSU2 LC127086.1, while isolate DFSP.J4 is related to Aspergillus niger IFO4033 D63697.1.

scholarly journals Inferring the Evolutionary History of Vibrios by Means of Multilocus Sequence Analysis

2007 ◽  
Vol 189 (21) ◽  
pp. 7932-7936 ◽  
Author(s):  
Tomoo Sawabe ◽  
Kumiko Kita-Tsukamoto ◽  
Fabiano L. Thompson
Keyword(s):  
Sequence Analysis ◽  
Evolutionary History ◽  
Gene Sequence ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Amino Acid Identity ◽  
Multilocus Sequence Analysis ◽  
Protein Coding ◽  
History Of

ABSTRACT We performed the first broad study aiming at the reconstruction of the evolutionary history of vibrios by means of multilocus sequence analysis of nine genes. Overall, 14 distinct clades were recognized using the SplitsTree decomposition method. Some of these clades may correspond to families, e.g., the clades Salinivibrio and Photobacteria, while other clades, e.g., Splendidus and Harveyi, correspond to genera. The common ancestor of all vibrios was estimated to have been present 600 million years ago. We can define species of vibrios as groups of strains that share >95% gene sequence similarity and >99.4% amino acid identity based on the eight protein-coding housekeeping genes. The gene sequence data were used to refine the standard online electronic taxonomic scheme for vibrios (http://www.taxvibrio.lncc.br ).

Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes

Microbiology ◽  
2005 ◽  
Vol 151 (7) ◽  
pp. 2141-2150 ◽  
Author(s):  
Sabri M. Naser ◽  
Fabiano L. Thompson ◽  
Bart Hoste ◽  
Dirk Gevers ◽  
Peter Dawyndt ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rapid Identification ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Enterococcal Species ◽  
Species Groups

The aim of this study was to evaluate the use of RNA polymerase α subunit (rpoA) and phenylalanyl-tRNA synthase (pheS) gene sequences as species identification tools for enterococci. Ninety-six representative strains comprising all currently recognized Enterococcus species were examined. rpoA gene sequences generated a robust classification into species groups similar to the one based on 16S rRNA gene sequence analysis. On the other hand, the pheS gene is a fast-evolving clock even better suited for species delineation than the rpoA gene, but not for recognition of species groups within Enterococcus as determined by both rpoA and 16S rRNA genes. All enterococcal species were clearly differentiated on the basis of their rpoA and pheS sequences. Evaluation of intraspecies variation showed that both rpoA and pheS genes have a high degree of homogeneity among strains of the same species. Strains of the same enterococcal species have at least 99 % rpoA and 97 % pheS gene sequence similarity, whereas, different enterococcal species have at maximum 97 % rpoA and 86 % pheS gene sequence similarity. It was concluded that both genes can be used as reliable tools for identification of clinical and environmental species of Enterococcus and are efficient screening methods for the detection of novel species. The sequence data obtained in this study were compared to the available atpA and 16S rRNA gene sequences. The MLSA approach to Enterococcus taxonomy provides portable, highly reproducible data with lower costs for rapid identification of all enterococcal species.

scholarly journals Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote

2020 ◽  
Vol 70 (7) ◽  
pp. 4416-4417 ◽  
Author(s):  
Iain C. Sutcliffe ◽  
Lenie Dijkshoorn ◽  
William B. Whitman ◽  
on behalf of the ICSP Executive Board
Keyword(s):  
Gene Sequence ◽  
Online Discussion ◽  
Sequence Data ◽  
International Committee ◽  
International Code ◽  
Gene Sequences ◽  
Scientific Discussion ◽  
Code Of Nomenclature ◽  
Gene Sequence Data ◽  
International Code Of Nomenclature

The International Committee on Systematics of Prokaryotes has held an electronic discussion on proposals to amend the International Code of Nomenclature of Prokaryotes in order to allow the use of gene sequence data as type. The scientific discussion is reported. Subsequently members of the International Committee on Systematics of Prokaryotes voted on these proposals, which were rejected.

scholarly journals Description of ‘Candidatus Helicobacter heilmannii’ based on DNA sequence analysis of 16S rRNA and urease genes

2004 ◽  
Vol 54 (6) ◽  
pp. 2203-2211 ◽  
Author(s):  
Jani L. O'Rourke ◽  
Jay V. Solnick ◽  
Brett A. Neilan ◽  
Karin Seidel ◽  
Robert Hayter ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Gene Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Gastric Disease ◽  
Rrna Gene ◽  
Helicobacter Heilmannii ◽  
Gene Sequence Analysis

While Helicobacter pylori is accepted as the major bacterial agent of gastric disease in humans, some patients and many animals are infected with a larger, tightly helical-shaped bacterium previously referred to as ‘Helicobacter heilmannii’ or ‘Gastrospirillum hominis’. Taxonomic classification of these bacteria has been hampered by the inability to cultivate them in vitro and by the inadequate discriminatory power of 16S rRNA gene sequence analysis. This study describes the detection and phylogenetic analysis of 26 different gastrospirillum isolates from humans and animals, which incorporates sequence data based on the 16S rRNA and urease genes. Fifteen gastrospirilla detected in humans, primates and pigs clustered with ‘Candidatus Helicobacter suis’, thus expanding the host range for this organism. By comparison, based on 16S rRNA data, the remaining 11 gastrospirilla could not be differentiated from Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis. However, urease gene sequence analysis allowed for the discrimination of this latter group into four discrete clusters, three of which contained the above recognized species. The fourth cluster contained isolates from human and feline hosts, and should provisionally be considered a unique bacterial species, for which the name ‘Candidatus Helicobacter heilmannii’ is proposed.

Identification of acetic acid bacteria isolated in Thailand and assigned to the genus Acetobacter by groEL gene sequence analysis

2014 ◽  
Vol 65 (3) ◽  
pp. 1557-1564 ◽  
Author(s):  
Nittaya Pitiwittayakul ◽  
Pattaraporn Yukphan ◽  
Wilawan Sintuprapa ◽  
Yuzo Yamada ◽  
Gunjana Theeragool
Keyword(s):  
Acetic Acid ◽  
Sequence Analysis ◽  
Gene Sequence ◽  
Acetic Acid Bacteria ◽  
Groel Gene ◽  
Gene Sequence Analysis

scholarly journals Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA–DNA hybridization in the Bacillus subtilis group

2007 ◽  
Vol 57 (8) ◽  
pp. 1846-1850 ◽  
Author(s):  
Li-Ting Wang ◽  
Fwu-Ling Lee ◽  
Chun-Ju Tai ◽  
Hiroaki Kasai
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

The Bacillus subtilis group comprises eight closely related species that are indistinguishable from one another by 16S rRNA gene sequence analysis. Therefore, the gyrB gene, which encodes the subunit B protein of DNA gyrase, was selected as an alternative phylogenetic marker. To determine whether gyrB gene sequence analysis could be used for phylogenetic analysis and species identification of members of the B. subtilis group, the congruence of gyrB grouping with both 16S rRNA gene sequencing and DNA–DNA hybridization data was evaluated. Ranges of gyrB nucleotide and translated amino acid sequence similarities among the eight type strains were 75.4–95.0 % and 88.5–99.2 %, respectively, whereas 16S rRNA gene sequence similarities were 98.1–99.8 %. Results showed that gyrB gene sequences provide higher resolution than 16S rRNA gene sequences. The classification achieved by gyrB sequence analysis was in agreement with results obtained with DNA–DNA hybridization. It is concluded that the gyrB gene may be an efficient alternative target for identification and taxonomic analysis of members of the B. subtilis group.

Sequence Analysis of Game Data

2021 ◽  
pp. 265-306
Author(s):  
Magy Seif El-Nasr ◽  
Truong Huy Nguyen Dinh ◽  
Alessandro Canossa ◽  
Anders Drachen
Keyword(s):  
Data Analysis ◽  
Sequence Analysis ◽  
Sequential Analysis ◽  
Sequence Data ◽  
University Of California ◽  
Santa Cruz ◽  
Data Sequence ◽  
Practical Guide ◽  
Shed Light

This chapter is devoted to sequence game data analysis. It will first define what sequence data is and how it is represented, and then delve more deeply into how to develop models from such data. Sequence analysis has a lot of utility and is important as it conserves the sequence of player actions and can shed light on how players solved different problems within the different game levels. Further, sequence analysis can also be a great way to develop a more robust and accurate player model. The chapter will discuss such advantages in light of showcasing the use of sequential analysis for DOTA 2. Further, the chapter will also be a practical guide on how to develop models from sequence data using practical step-by-step labs. Please note that this chapter was written with Erica Kleinman (a PhD student at University of California at Santa Cruz).

scholarly journals Optimization of Multilocus Sequence Analysis for Identification of Species in the Genus Vibrio

2014 ◽  
Vol 80 (17) ◽  
pp. 5359-5365 ◽  
Author(s):  
Michael W. Gabriel ◽  
George Y. Matsui ◽  
Robert Friedman ◽  
Charles R. Lovell
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Multilocus Sequence Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Accurate Identification ◽  
Content Type

ABSTRACTMultilocus sequence analysis (MLSA) is an important method for identification of taxa that are not well differentiated by 16S rRNA gene sequences alone. In this procedure, concatenated sequences of selected genes are constructed and then analyzed. The effects that the number and the order of genes used in MLSA have on reconstruction of phylogenetic relationships were examined. TherecA,rpoA,gapA, 16S rRNA gene,gyrB, andftsZsequences from 56 species of the genusVibriowere used to construct molecular phylogenies, and these were evaluated individually and using various gene combinations. Phylogenies from two-gene sequences employingrecAandrpoAin both possible gene orders were different. The addition of thegapAgene sequence, producing all six possible concatenated sequences, reduced the differences in phylogenies to degrees of statistical (bootstrap) support for some nodes. The overall statistical support for the phylogenetic tree, assayed on the basis of a reliability score (calculated from the number of nodes having bootstrap values of ≥80 divided by the total number of nodes) increased with increasing numbers of genes used, up to a maximum of four. No further improvement was observed from addition of the fifth gene sequence (ftsZ), and addition of the sixth gene (gyrB) resulted in lower proportions of strongly supported nodes. Reductions in the numbers of strongly supported nodes were also observed when maximum parsimony was employed for tree construction. Use of a small number of gene sequences in MLSA resulted in accurate identification ofVibriospecies.

Sign in / Sign up

Export Citation Format

Share Document