scholarly journals Internal transcribed spacer based identification of Aspergillus fumigatus isolated from poultry feed samples

2017 ◽  
Vol 4 (3) ◽  
pp. 165-171
Author(s):  
Md Muket Mahmud ◽  
Jayedul Hassan ◽  
KHM Nazmul Hussain Nazir
Keyword(s):  
Phylogenetic Analysis ◽  
Aspergillus Fumigatus ◽  
Internal Transcribed Spacer ◽  
Molecular Techniques ◽  
Rrna Genes ◽  
Poultry Feed ◽  
Rrna Gene ◽  
28S Rrna ◽  
Its Regions ◽  
Feed Samples

Among over 180 Aspergilli, Aspergillus fumigatus is the most common etiological agent causing invasive mold infection mostly in immunocompromised human and animal. Besides, the fungus is used for various useful purposes. However, for the utilization of A. fumigatus as a useful candidate, accurate identification is crucial. Here, the research work was aimed at identifying A. fumigatus from poultry feed samples using conventional and molecular techniques. Out of 23 feed samples, 2 (8.7%) were found to be positive for A. fumigatus. The internal transcribed spacer 1 (ITS 1) and ITS 2 regions and the 5.8S ribosomal DNA (rDNA) region of the fungus were amplified by polymerase chain reaction. The ITS regions are located between the 18S and 28S rRNA genes, and rRNA gene for 5.8S RNA separates these two ITS regions. The isolated gene has been sequenced and deposited in the GenBank (accession no. KC142152). The gene was 100% similar to other reference species of A. fumigatus, whereas in phylogenetic analysis, a clear distance was found in the cases of other Aspergilli. Based on the unique nature of the ITS1 and ITS2 regions and phylogenetic analysis of the genes, A. fumigatus was correctly identified. The isolated strain could be a good candidate for further studies especially for utilization in the field of biotechnology.Res. Agric. Livest. Fish.4(3): 165-171, December 2017

Description of a new species of Auriculostoma (Digenea: Allocreadiidae) from Characidium heirmostigmata (Characiformes: Crenuchidae) from Argentina, using morphological and molecular data

2021 ◽  
Vol 95 ◽  
Author(s):  
M.M. Montes ◽  
J. Barneche ◽  
Y. Croci ◽  
D. Balcazar ◽  
A. Almirón ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
National Park ◽  
Molecular Data ◽  
Rrna Gene ◽  
28S Rrna ◽  
The Family ◽  
Parasitological Survey ◽  
Morphological And Molecular Data ◽  
A New Species

Abstract During a parasitological survey of fishes at Iguazu National Park, Argentina, specimens belonging to the allocreadiid genus Auriculostoma were collected from the intestine of Characidium heirmostigmata. The erection of the new species is based on a unique combination of morphological traits as well as on phylogenetic analysis. Auriculostoma guacurarii n. sp. resembles four congeneric species – Auriculostoma diagonale, Auriculostoma platense, Auriculostoma tica and Auriculostoma totonacapanensis – in having smooth and oblique testes, but can be distinguished by a combination of several morphological features, hosts association and geographic distribution. Morphologically, the new species can be distinguished from both A. diagonale and A. platense by the egg size (bigger in the first and smaller in the last); from A. tica by a shorter body length, the genital pore position and the extension of the caeca; and from A. totonacapanensis by the size of the oral and ventral sucker and the post-testicular space. Additionally, one specimen of Auriculostoma cf. stenopteri from the characid Charax stenopterus (Characiformes) from La Plata River, Argentina, was sampled and the partial 28S rRNA gene was sequenced. The phylogenetic analysis revealed that A. guacurarii n. sp. clustered with A. tica and these two as sister taxa to A. cf. stenopteri. The new species described herein is the tenth species in the genus and the first one parasitizing a member of the family Crenuchidae.

scholarly journals Phylogenetic Analysis of 28S rRNA Gene of Indigenous Xiphinema pachydermum

2019 ◽  
Vol 8 (07) ◽  
pp. 1960-1968
Author(s):  
Anju Sharma ◽  
Satish K. Sharma ◽  
Kiran Rana ◽  
Anil Kumar Verma
Keyword(s):  
Phylogenetic Analysis ◽  
Rrna Gene ◽  
28S Rrna ◽  
28S Rrna Gene

scholarly journals The differential expression of ribosomal 18S RNA paralog genes from the chaetognath Spadella cephaloptera

2007 ◽  
Vol 12 (4) ◽  
Author(s):  
Roxane-Marie Barthélémy ◽  
Michel Grino ◽  
Pierre Pontarotti ◽  
Jean-Paul Casanova ◽  
Eric Faure
Keyword(s):  
Physiological Role ◽  
Class Ii ◽  
Class I ◽  
Rrna Genes ◽  
Whole Body ◽  
Rrna Gene ◽  
28S Rrna ◽  
Cellular Functions ◽  
Intraindividual Variation ◽  
Spadella Cephaloptera

AbstractChaetognaths constitute a small marine phylum of approximately 120 species. Two classes of both 18S and 28S rRNA gene sequences have been evidenced in this phylum, even though significant intraindividual variation in the sequences of rRNA genes is unusual in animal genomes. These observations led to the hypothesis that this unusual genetic characteristic could play one or more physiological role(s). Using in situ hybridization on the frontal sections of the chaetognath Spadella cephaloptera, we found that the 18S Class I genes are expressed in the whole body, with a strong expression throughout the gut epithelium, whereas the expression of the 18S Class II genes is restricted to the oocytes. Our results could suggest that the paralog products of the 18S Class I genes are probably the “housekeeping” 18S rRNAs, whereas those of class II would only be essential in specific tissues. These results provide support for the idea that each type of 18S paralog is important for specific cellular functions and is under the control of selective factors.

scholarly journals 1358. A Novel Rapidly Growing Mycobacteria (RGM) Species Causing Soft Tissue and Orthopedic Hardware Infection After Trauma

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S492-S492
Author(s):  
David C Nguyen ◽  
Michelle Lisgaris ◽  
Sruthi Vasireddy ◽  
Richard J Wallace ◽  
Federico Perez ◽  
...  
Keyword(s):  
Soft Tissue ◽  
16S Rrna ◽  
Antibiotic Susceptibility ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Mycobacterium Fortuitum ◽  
Rapidly Growing Mycobacteria ◽  
Maldi Tof

Abstract Background The widespread use of molecular techniques has resulted in increasing numbers of newly characterized rapidly growing mycobacteria (RGM). Many RGM cause soft tissue and orthopedic hardware infection, particularly after trauma. RGM species identification remains challenging with few genetic differences between species. Methods We describe a case involving RGM. We report results of matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (Bruker Biotyper), sequencing of rpoB, erm(39), and 16S rRNA genes, and antibiotic susceptibility testing (AST). We review previous reports describing similar RGM infections. Results A 58-year-old male sustained multiple fractures and right thigh compartment syndrome after a motorcycle accident. He underwent fasciotomy and multi-stage surgical fixations. 3 months later, he had wound dehiscence, purulence and multiple fluid collections of his right leg and knee requiring surgical drainage and removal of orthopedic hardware. After 4 days, acid-fast bacilli grew on routine bacterial culture media. MALDI-TOF identified the isolate as Mycobacterium mageritense. In contrast, sequencing of 16S rRNA (100% identity) and erm(39) (> 99% identity) identified the isolate as Mycobacterium houstonense; erm(39) only had 80% similarity with Mycobacterium fortuitum. Sequencing of rpoB showed a 19 bp difference with the M. houstonense type strain, and showed similarity to M. fortuitum (97.64%) than M. houstonense (97.45%). AST demonstrated resistance to clarithromycin only. After initial treatment with imipenem, ciprofloxacin, and doxycycline, definite therapy with ciprofloxacin and doxycycline was successful. In the literature, we found one case each of M. mageritense and M. houstonense infection after trauma. Conclusion This case highlights the importance of RGM other than M. fortuitum as a cause of soft tissue and orthopedic hardware infections, and illustrates the difficulty of identifying them to the species level. Sequencing of erm(39) and 16S rRNA gene identified the isolate as M. houstonense, but the larger difference (>2.5%) in rpoB sequence suggests a novel species. Further characterization is underway. Efforts to determine RGM species and antibiotic susceptibility give important insight into diagnosis and management. Disclosures All authors: No reported disclosures.

Ceriporia albomellea (Phanerochaetaceae, Basidiomycota), a new species from tropical China based on morphological and molecular evidences

Phytotaxa ◽  
2017 ◽  
Vol 298 (1) ◽  
pp. 20 ◽  
Author(s):  
YUAN YUAN ◽  
XIAO-HONG JI ◽  
FANG WU ◽  
JIA-JIA CHEN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Molecular Evidence ◽  
Its Regions ◽  
Tropical China ◽  
A New Species

A new polypore, Ceriporia albomellea, collected from tropical China, is described and illustrated based on morphological characteristics and molecular evidence. It is characterized by thin, resupinate basidiome with a white subiculum, cottony margin, white to cinnamon-buff pores, clavate cystidia and oblong-ellipsoid basidiospores measured as 3.1–3.8 × 1.7–2 µm. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions supported C. albomellea as a distinctive species belonging to Ceriporia.

scholarly journals Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the ‘next-generation’ Tree of Life

2019 ◽  
Vol 93 (3) ◽  
pp. 260-276 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
D.I. Hernández-Mena
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
28S Rdna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Next Generation ◽  
Phylogenetic Classification ◽  
Rdna Sequences

AbstractDigenea Carus, 1863 represent a highly diverse group of parasitic platyhelminths that infect all major vertebrate groups as definitive hosts. Morphology is the cornerstone of digenean systematics, but molecular markers have been instrumental in searching for a stable classification system of the subclass and in establishing more accurate species limits. The first comprehensive molecular phylogenetic tree of Digenea published in 2003 used two nuclear rRNA genes (ssrDNA = 18S rDNA and lsrDNA = 28S rDNA) and was based on 163 taxa representing 77 nominal families, resulting in a widely accepted phylogenetic classification. The genetic library for the 28S rRNA gene has increased steadily over the last 15 years because this marker possesses a strong phylogenetic signal to resolve sister-group relationships among species and to infer phylogenetic relationships at higher levels of the taxonomic hierarchy. Here, we have updated the database of 18S and 28S rRNA genes until December 2017, we have added newly generated 28S rDNA sequences and we have reassessed phylogenetic relationships to test the current higher-level classification of digeneans (at the subordinal and subfamilial levels). The new dataset consisted of 1077 digenean taxa allocated to 106 nominal families for 28S and 419 taxa in 98 families for 18S. Overall, the results were consistent with previous higher-level classification schemes, and most superfamilies and suborders were recovered as monophyletic assemblages. With the advancement of next-generation sequencing (NGS) technologies, new phylogenetic hypotheses from complete mitochondrial genomes have been proposed, although their power to resolve deep levels of trees remains controversial. Since data from NGS methods are replacing other widely used markers for phylogenetic analyses, it is timely to reassess the phylogenetic relationships of digeneans with conventional nuclear rRNA genes, and to use the new analysis to test the performance of genomic information gathered from NGS, e.g. mitogenomes, to infer higher-level relationships of this group of parasitic platyhelminths.

The effect of transposon Pokey insertions on sequence variation in the 28S rRNA gene of Daphnia pulex

Genome ◽  
2008 ◽  
Vol 51 (12) ◽  
pp. 988-1000 ◽  
Author(s):  
Shiona K. Glass ◽  
Anna Moszczynska ◽  
Teresa J. Crease
Keyword(s):  
Sequence Variation ◽  
Insertion Site ◽  
Daphnia Pulex ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Intraindividual Variation ◽  
Rdna Array ◽  
The Impact ◽  
Host Genes

The goal of this study was to determine the impact of breeding system and the presence of the transposon Pokey on intraindividual variation in 28S rRNA genes. We PCR-amplified, cloned, and sequenced 1000 nucleotides downstream of the Pokey insertion site in genes with and without insertions from 10 obligately and 10 cyclically parthenogenetic isolates of Daphnia pulex. Variation among genes with Pokey insertions was higher than variation among genes without insertions in both cyclic and obligate isolates. Although the differences were not quite significant (p = 0.06 in both cases), the results suggest that Pokey insertions are likely to inhibit the homogenization of their host genes to some extent. We also observed that the complement of 28S rRNA alleles differed between genes with and without inserts in some isolates, suggesting that a particular inserted gene can persist for substantial periods of time and even spread within the rDNA array, despite the fact that insertions are deleterious. This apparently contradictory pattern can be explained if homogenization of rRNA genes occurs primarily by gene conversion, but copies with Pokey inserts can occasionally increase in frequency within arrays owing to unequal crossing over events that do not originate in the inserted genes themselves.

The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.)

Genome ◽  
1996 ◽  
Vol 39 (1) ◽  
pp. 140-149 ◽  
Author(s):  
Bernard R. Baum ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analysis ◽  
5S Rdna ◽  
Hordeum Spontaneum ◽  
Wild Relatives ◽  
5S Rrna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Rdna Sequences ◽  
Cultivated Barley

5S rRNA genes from several accessions of Hordeum spontaneum and Hordeum bulbosum, wild relatives of cultivated barley, Hordeum vulgare, have been amplified by the polymerase chain reaction, cloned, and sequenced. Evaluation of aligned sequences along with principal coordinate analysis demonstrates that the two classes of 5S rDNA sequences found in cultivated barley, and subclasses (groups) of these sequences, can also be found in its closest wild relatives. The two classes of units, formerly categorized as containing short or long 5S rDNA repeats, are distinguishable by the presence or absence of a TAG repeating unit. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for further phylogenetic analysis in the genus Hordeum and possibly in the Triticeae. Key words : 5S rDNA, barley, sequence diversity, phylogenetic analysis.

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