scholarly journals Genetic diversity analysis of an isolate of microsporidia infesting Athetis lepigone

2019 ◽  
Author(s):  
Haijian Zhang ◽  
Jian Song ◽  
Yunhe Yang ◽  
Jingjie An ◽  
Hongxia Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Sequencing Analysis ◽  
Multiple Sequence ◽  
Intergenic Spacers ◽  
Link Type ◽  
Close Relationship ◽  
Small Subunit Ribosomal Dna

AbstractIn this study, PCR amplification, cloning and sequencing analysis were adopted to explore genetic diversity of microsporidia (LEP9557) infecting Athetis lepigone. The small subunit ribosomal DNA (SSU rDNA), internal transcribed spacer (ITS) and intergenic spacers (IGS) of ribosomal RNA (rRNA) were cloned from the strain and sequenced. By means of multiple sequence alignment, we found that the three gene regions had different levels of polymorphism. There was greater polymorphism in ITS (74 variable sites) and IGS (55.59%) regions than in the SSU rDNA (17 variable sites). Phylogenetic analysis was performed using Kimura 2-parameter with neighbor joining and the results showed that LEP9557 had a close relationship with Nosema bombycis. Sequences of each clone were submitted to Genbank (Accession number: MF150254-MF150258). All of the results indicated the presence of genetic diversity in LEP9557, which established the foundation for identifying the phylogeny and relationships with other microsporidian strains, and had significant biological meaning for maintaining the survival and population continuity of the strain.

scholarly journals Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

1998 ◽  
Vol 64 (12) ◽  
pp. 5064-5066 ◽  
Author(s):  
Clifford F. Brunk ◽  
Nicole Eis
Keyword(s):  
Internal Standard ◽  
Pcr Amplification ◽  
Quantitative Measure ◽  
Pcr Primers ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

scholarly journals Are microbes fundamentally different than macroorganisms? Convergence and a possible case for neutral phenotypic evolution in testate amoeba (Amoebozoa: Arcellinida)

2015 ◽  
Vol 2 (12) ◽  
pp. 150414 ◽  
Author(s):  
Angela M. Oliverio ◽  
Daniel J. G. Lahr ◽  
Jessica Grant ◽  
Laura A. Katz
Keyword(s):  
Testate Amoebae ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Coi Gene ◽  
Testate Amoeba ◽  
Phenotypic Evolution ◽  
Gene Sequences ◽  
Small Subunit Ribosomal Dna ◽  
Mitochondrial Cytochrome Oxidase ◽  
Phenotypic Convergence

This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for ‘core Nebela ’ species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses corroborate the prior ssu-rDNA findings of morphological convergence in test (shell) morphologies, as COI and ssu-rDNA phylogenies are concordant. Further, the monophyly of morphospecies is rejected using approximately unbiased tests. Given that testate amoebae are used as bioindicators in both palaeoecological and contemporary studies of threatened ecosystems such as bogs and fens, understanding the discordance between morphology and genetics in the hyalosphenids is essential for interpretation of indicator species. Further, while convergence is normally considered the result of natural selection, it is possible that neutrality underlies phenotypic evolution in these microorganisms.

scholarly journals First record of Nocturama (Batrachospermales, Rhodophyta) in South America, with the description of a new species N. novamundensis

Phytotaxa ◽  
2016 ◽  
Vol 278 (3) ◽  
pp. 273
Author(s):  
ORLANDO NECCHI JR ◽  
TIMOTHY J. ENTWISLE ◽  
CIRO C.Z. BRANCO ◽  
MONICA O. PAIANO
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Large Subunit ◽  
First Record ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Evidence ◽  
Southern Brazil ◽  
Small Subunit Ribosomal Dna ◽  
A New Species

Specimens from southeastern and southern Brazil previously identified as Sheathia arcuata (= Batrachospermum arcuatum) are shown to be members of the recently described genus Nocturama, previously known only from Australia and New Zealand. Morphological and molecular evidence support recognizing the Brazilian specimens as a new species, described here as Nocturama novamundensis, sp. nov. Comparison of DNA sequences of the plastid-encoded ribulose-1,5-bisphosphatecarboxylase–oxygenase large subunit (rbcL) and the nuclear small subunit ribosomal DNA (SSU rDNA) markers showed Nocturama as a well supported clade. The sequence divergences between the new and the type species were high (95-98bp, 7.4–7.6%) for rbcL and 19bp, 1.1% for SSU), and those within each species were extremely low (0-1 bp, 0-0.1%). The new species can be distinguished from N. antipodites in having curved primary fascicles composed of non-‘audouinelloid’ cells (compared to straight primary fascicles with audouinelloid—cylindrical—cells) and in being always dioecious (only rarely is N. antipodites dioecious).

Description of the pseudocryptic species Conticribra weissflogiopsis sp. nov. (Thalassiosirales, Bacillariophyta) isolated from brackish waters in Korea, based on its cingulum structure and molecular analysis

Phytotaxa ◽  
2014 ◽  
Vol 191 (1) ◽  
pp. 115 ◽  
Author(s):  
JOON SANG PARK ◽  
JIN HWAN LEE
Keyword(s):  
Morphological Evolution ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Diatom Species ◽  
Brackish Waters ◽  
Valve Structure ◽  
Small Subunit Ribosomal Dna ◽  
Pseudocryptic Species

We describe the new fultoportulate diatom species, Conticribra weissflogiopsis, isolated from brackish waters in Korea, based on morphological characters and molecular data. The new species is characterized by having areolae venation with internal (semi-) continuous cribra, a flat valve face, a single marginal rimoportula replacing a marginal fultoportula, a subcentral ring of the valve face fultoportulae, and a dextral pattern of cingulum structure. The overall valve structure of C. weissflogiopsis resembles that of C. weissflogii; however, the cingulum structure differs between the two species—C. weissflogiopsis has a dextral offset of band opening in the cingulum, whereas C. weissflogii has a sinistral offset. Phylogenetic analysis of the nuclear small subunit ribosomal DNA (SSU rDNA) revealed that C. weissflogiopsis is located in the Conticribra clade. Further, the pairwise genetic distance based on the SSU rDNA and the internal transcribed spacer 2 (ITS2) indicated that C. weissflogiopsis is a distinct Conticribra species. On the basis of the morphology and molecular phylogeny, we expand the hypothesis regarding the morphological evolution of Conticribra species.

scholarly journals Evidence for Interspecies Gene Transfer in the Evolution of 2,4-Dichlorophenoxyacetic Acid Degraders

1998 ◽  
Vol 64 (10) ◽  
pp. 4089-4092 ◽  
Author(s):  
Catherine McGowan ◽  
Roberta Fulthorpe ◽  
Alice Wright ◽  
J. M. Tiedje
Keyword(s):  
Gene Transfer ◽  
Burkholderia Cepacia ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Dichlorophenoxyacetic Acid ◽  
Rdna Genes ◽  
Degrading Bacteria ◽  
Pcr Products ◽  
2,4 Dichlorophenoxyacetic Acid ◽  
Small Subunit Ribosomal Dna

ABSTRACT Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the classProteobacteria. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway, tfdA, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of Proteobacteria. None of the α-Proteobacteria yieldedtfdA PCR products. A comparison of the dendrogram of thetfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains withtfdA sequences highly similar to the tfdAsequence of strain JMP134 (tfdA class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to aBurkholderia cepacia recipient.

Molecular and Phylogenetic Analysis of Pyridoxal Phosphate- Dependent Acyltransferase of Exiguobacterium acetylicum

2009 ◽  
Vol 64 (11-12) ◽  
pp. 891-898 ◽  
Author(s):  
Narayanan Rajendran ◽  
Colby Smith ◽  
Williard Mazhawidza
Keyword(s):  
Amino Acid ◽  
Pyridoxal Phosphate ◽  
Extreme Environments ◽  
Pcr Amplification ◽  
Evolutionary Development ◽  
Sequencing Analysis ◽  
Amino Acid Residues ◽  
Exiguobacterium Acetylicum ◽  
Close Relationship ◽  
Relationship Of

The pyridoxal-5’-phosphate (PLP)-dependent family of enzymes is a very diverse group of proteins that metabolize small molecules like amino acids and sugars, and synthesize cofactors for other metabolic pathways through transamination, decarboxylation, racemization, and substitution reactions. In this study we employed degenerated primer-based PCR amplification, using genomic DNA isolated from the soil bacterium Exiguobacterium acetylicum strain SN as template. We revealed the presence of a PLP-dependent family of enzymes, such as PLP-dependent acyltransferase, and similarity to 8-amino-7-oxononoate synthase. Sequencing analysis and multiple alignment of the thymidine-adenine-cloned PCR amplicon revealed PLP-dependent family enzymes with specific confering codes and consensus amino acid residues specific to this group of functional proteins. Amino acid residues common to the majority of PLP-dependent enzymes were also revealed by the Lasergene MegAlign software. A phylogenetic tree was constructed. Its analysis revealed a close relationship of E. acetylicum to other bacteria isolated from extreme environments suggesting similarities in anabolic adaptability and evolutionary development.

Molecular identification of cryptic species of Ceratomyxa Thélohan, 1892 (Myxosporea: Bivalvulida) including the description of eight novel species from apogonid fishes (Perciformes: Apogonidae) from Australian waters

2013 ◽  
Vol 58 (3) ◽  
Author(s):  
Holly Heiniger ◽  
Robert Adlard
Keyword(s):  
Cryptic Species ◽  
Genetic Markers ◽  
Novel Species ◽  
Molecular Data ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Phylogenetic Relatedness ◽  
Biological Characters ◽  
Multiple Species ◽  
Small Subunit Ribosomal Dna

AbstractCeratomyxa parasites from the gall bladders of 23 species of cardinalfishes (family Apogonidae) from Australian waters were examined for their taxonomic identity and phylogenetic relatedness. We identified 15 of the 23 apogonid fish species infected with species of Ceratomyxa. Although the majority of apogonid species harboured only a single Ceratomyxa species, four were found with multiple species of Ceratomyxa. This study describes eight novel species using a combination of morphological, small subunit ribosomal DNA (SSU rDNA) and biological characters. Six Ceratomyxa species are reported from single apogonid species, while two are reported from multiple host species. Molecular data were critical in identifying several morphologically cryptic species. However, our results suggest that SSU rDNA was not capable of distinguishing all the species present in the current study system and alternative genetic markers should be investigated in the future.

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