scholarly journals Molecular signature of nrDNA-ITS marker in Isodon rugosus (Lamiaceae)

Botanica ◽  
2021 ◽  
pp. 53-61
Author(s):  
Devendra Kumar Srivastava ◽  
Pekhna Bansal ◽  
Pradeep Kumar Singh ◽  
Manjit Inder Singh Saggoo
Keyword(s):  
Large Subunit ◽  
18S Rrna Gene ◽  
Complete Sequence ◽  
Its Sequences ◽  
Molecular Signature ◽  
Partial Sequence ◽  
Rrna Gene ◽  
Nrdna Its ◽  
Molecular Features ◽  
Isodon Rugosus

Molecular features of nrDNA-ITS sequences in medicinal plant Isodon rugosus were assessed with universal ITS-1 and ITS-2 primers. ITS sequences of 46 Isodon species were defined for their respective ITS-1, 5.8S and ITS-2 regions through in-silico datamining and analysis. Only in 32 species, sequence of all the three defined regions was complete, while in the rest of 14 species was partial. Isodon rugosus revealed five genic regions, namely, 18S rRNA gene (partial sequence, > 1…..38), ITS-1 (complete sequence, > 39…..236), 5.8S rRNA gene (complete sequence, > 237…..400), ITS-2 (complete sequence, > 401…..607) and large subunit 26S rRNA gene (partial sequence, > 608…..672). The sequence regions were recorded with variable sites (VS), singleton (ST) and species-specific parsimonious-informative (PI) sites. The information was also collected in a phylogenetic tree obtained using the maximum likelihood (ML) method.

Nature of the genome of the saprophytic spirochete Spirochaeta aurantia and its ribosomal RNA operons

2004 ◽  
Vol 50 (11) ◽  
pp. 967-971 ◽  
Author(s):  
Richard McLaughlin ◽  
David M Secko ◽  
Catherine J Paul ◽  
Andrew M Kropinski
Keyword(s):  
Ribosomal Rna ◽  
Gel Electrophoresis ◽  
Large Subunit ◽  
Complete Sequence ◽  
Pulsed Field Gel Electrophoresis ◽  
23S Rrna ◽  
Rrna Gene ◽  
Pulsed Field ◽  
23S Rrna Gene ◽  
Intergenic Regions

Using restriction endonucleases DraI, AseI, and I-CeuI in conjunction with pulsed-field gel electrophoresis, we have shown that Spirochaeta aurantia M1 possesses a circular 3.98-Mb genome. This is the second largest spirochete chromosome yet analyzed. The observation that the latter enzyme cuts in 3 places suggests the presence of 3 copies of the large subunit (23S) rRNA gene (rrl), which was confirmed by Southern hybridizations. The complete sequence of 2 of the ribosomal RNA operons was determined, revealing that their structure resembled that of the typical member of the bacterial superkingdom: rrs (16S; 1561 bp), tRNA, rrl (23S; 2972 bp), and rrf (5S; 110 bp). The S. aurantia rrs–rrl intergenic regions, as with Treponema denticola, contain genes specifying a 73-nt tRNAAla (anticodon TGC) and a 77-nt tRNAIle (anticodon GAT).Key words: spirochete, pulsed-field gel electrophoresis, ribosomal RNA, operon, Spirochaeta aurantia.

Genetic differentiation within the Paralia longispina (Bacillariophyta) species complex

Botany ◽  
2012 ◽  
Vol 90 (3) ◽  
pp. 205-222 ◽  
Author(s):  
Michael L. MacGillivary ◽  
Irena Kaczmarska
Keyword(s):  
Large Subunit ◽  
Morphological Diversity ◽  
Its Region ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Tropical Species ◽  
Rrna Gene ◽  
Rbcl Gene ◽  
Extant Species ◽  
Practical Implications

We report on undiscovered genetic and morphological diversity within a diatom taxon known as Paralia longispina and propose three new, extant species of Paralia — Paralia allisonii sp. nov., Paralia crawfordii sp. nov., and Paralia ehrmanii sp. nov. — obtained from subtropical and tropical coasts of the Atlantic and Pacific oceans. Comprehensive examination and hierarchical clustering of frustule characters separated these three species from each other and from P. longispina. Each species possessed one or two unique morphological diagnostic characters. The internal transcribed spacer (ITS) region and a fragment of the small subunit (18S rRNA gene) of nuclear encoded rRNA and a portion of the 5′ end of the large subunit of the ribulose bisophosphate carboxylase (rbcL) gene of the chloroplast genome were related to the morphological groupings of monoclonal isolates of P. allisonii and P. crawfordii. The ITS2 secondary structure of the cultured clones of these two species had four helices. They differed by five hemicompensatory base changes (HCBCs) and substantial changes to the distal end of helix I, the region between helix II and helix III, and nearly all of helix IV. Our results better our understanding of the distribution of subtropical and tropical species of Paralia and have practical implications for the conservation of native microbial florae and for the possibility of ship ballast in human-mediated dispersal of these diatoms.

scholarly journals Partial Sequence Analysis of the 5S to 18S rRNA Gene Region of the Maize Mitochondrial Genome

1983 ◽  
Vol 71 (1) ◽  
pp. 190-193 ◽  
Author(s):  
Shiaoman Chao ◽  
Ronald R. Sederoff ◽  
Charles S. Levings
Keyword(s):  
Sequence Analysis ◽  
Mitochondrial Genome ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gene Region ◽  
Partial Sequence ◽  
Rrna Gene

scholarly journals Comparison of potential diatom ‘barcode’ genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1369-1380 ◽  
Author(s):  
Liliang Guo ◽  
Zhenghong Sui ◽  
Shu Zhang ◽  
Yuanyuan Ren ◽  
Yuan Liu
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Mitochondrial Gene ◽  
Large Subunit ◽  
18S Rrna Gene ◽  
Marine Ecology ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Potential Marker

Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome c-oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (rbcL)] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (p-distance of 1.569, 85.84 % parsimony-informative sites) and COI (6.084, 82.14 %), followed by the 18S rRNA gene (0.139, 57.69 %), rbcL (0.120, 42.01 %) and UPA (0.050, 14.97 %), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and rbcL performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of Cyclotella, Skeletonema and Stephanodiscus gathered in separate clades, and were paraphyletic with those of Thalassiosira. Finally, UPA was too conserved to serve as a diatom barcode.

scholarly journals Prisutnost pijavice Pontobdella muricata (Hirudinea: Piscicolidae) na hrskavičnjačama u Tirenskom moru (Srednje Sredozemlje)

2017 ◽  
Vol 58 (2) ◽  
pp. 225-234
Author(s):  
Teresa Bottari ◽  
Adriana Profeta ◽  
Daniela Giordano ◽  
Francesco Smedile ◽  
Gina La Spada ◽  
...  
Keyword(s):  
Mitochondrial Gene ◽  
Morphological Characteristics ◽  
18S Rrna Gene ◽  
Complete Sequence ◽  
12S Rrna ◽  
Rrna Gene ◽  
Tyrrhenian Sea ◽  
12S Rrna Gene ◽  
Gene Coi ◽  
Mitochondrial 12S Rrna

This paper provides the first report of the leech, Pontobdella muricata (Linnaeus, 1758), in the Tyrrhenian Sea. The leech was found on the brown ray, Raja miraletus (Linnaeus 1758), and on the spotted ray, Raja montagui (Fowler, 1910), caught by trawling during autumn 2014.Complete sequence of 18S rRNA gene, COI mitochondrial gene and partial sequences of the mitochondrial 12S rRNA gene corroborate the determination based on morphological characteristics.

scholarly journals Morphometeric criteria and partial sequence of the 18S rRNA gene of Ceratomyxa sultani n. sp. from the gallbladder of Upeneus margarethae in the Arabian Gulf, with a note on its seasonal prevalence

2018 ◽  
Vol 25 (3) ◽  
pp. 597-603
Author(s):  
Abdel-Azeem S. Abdel-Baki ◽  
Hussain A. Al-Qahtani ◽  
Esam Almalki ◽  
Saleh Al-Quraishy ◽  
Ali Al Ghamdi ◽  
...  
Keyword(s):  
18S Rrna ◽  
Arabian Gulf ◽  
18S Rrna Gene ◽  
Partial Sequence ◽  
Rrna Gene ◽  
Seasonal Prevalence

scholarly journals Sarocladium and Lecanicillium Associated with Maize Seeds and Their Potential to Form Selected Secondary Metabolites

Biomolecules ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 98
Author(s):  
Lidia Błaszczyk ◽  
Agnieszka Waśkiewicz ◽  
Karolina Gromadzka ◽  
Katarzyna Mikołajczak ◽  
Jerzy Chełkowski
Keyword(s):  
Large Subunit ◽  
Solid Substrate ◽  
Rrna Gene ◽  
Decenoic Acid ◽  
Bioactive Substances ◽  
Lecanicillium Lecanii ◽  
Maize Seeds ◽  
Internally Transcribed Spacer ◽  
First Time

The occurrence and diversity of Lecanicillium and Sarocladium in maize seeds and their role in this cereal are poorly understood. Therefore, the present study aimed to investigate Sarocladium and Lecanicillium communities found in endosphere of maize seeds collected from fields in Poland and their potential to form selected bioactive substances. The sequencing of the internally transcribed spacer regions 1 (ITS 1) and 2 (ITS2) and the large-subunit (LSU, 28S) of the rRNA gene cluster resulted in the identification of 17 Sarocladium zeae strains, three Sarocladium strictum and five Lecanicillium lecanii isolates. The assay on solid substrate showed that S. zeae and S. strictum can synthesize bassianolide, vertilecanin A, vertilecanin A methyl ester, 2-decenedioic acid and 10-hydroxy-8-decenoic acid. This is also the first study revealing the ability of these two species to produce beauvericin and enniatin B1, respectively. Moreover, for the first time in the present investigation, pyrrocidine A and/or B have been annotated as metabolites of S. strictum and L. lecanii. The production of toxic, insecticidal and antibacterial compounds in cultures of S. strictum, S. zeae and L. lecanii suggests the requirement to revise the approach to study the biological role of fungi inhabiting maize seeds.

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