Sequence comparison of the ribosomal DNA internal transcribed spacers (ITSs) and 5.8S ribosomal gene and their secondary structures in 17 Pteriomorphian bivalves

10.5580/36c ◽  
2009 ◽  
Vol 5 (1) ◽  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Comparison ◽  
Secondary Structures ◽  
Ribosomal Gene ◽  
Internal Transcribed Spacers

Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

2021 ◽  
pp. 1-8
Author(s):  
Zainab M. Almutairi
Keyword(s):  
Pearl Millet ◽  
Phylogenetic Trees ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Internal Transcribed Spacers ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region ◽  
Local Cultivars ◽  
Pearl Millet Cultivars

Abstract Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

The Xenopus laevis ribosomal gene terminator contains sequences that both enhance and repress ribosomal transcription

1989 ◽  
Vol 9 (9) ◽  
pp. 3777-3784
Author(s):  
S Firek ◽  
C Read ◽  
D R Smith ◽  
T Moss
Keyword(s):  
Xenopus Laevis ◽  
Point Mutation ◽  
Ribosomal Dna ◽  
Ribosomal Gene ◽  
Promoter Element ◽  
Base Pairs ◽  
Transcription Terminator ◽  
Upstream Promoter

A DNA segment approximately 200 base pairs upstream of the Xenopus laevis ribosomal promoter acts both as an upstream promoter element that augments transcription and as a transcription terminator. It is, however, unclear to what extent these two activities are related. A segment of the X. laevis ribosomal DNA, containing the terminator and the upstream promoter element, was subjected to point mutation, and the effects of the resulting mutations were investigated by oocyte microinjection. Analysis of 26 point mutants revealed not only sequences that augment 40S transcription but also those that repress it. The sequences that augmented transcription lay within the T3 homology box and also near the site of 3'-end formation. These sequences also played a role in termination. The sequences that repressed transcription lay within the G+C-rich DNA flanking the T3 box. It can be concluded that termination is probably essential but may not be sufficient for the activity of the upstream promoter element.

scholarly journals Fusarium incarnatum-equiseti complex from China

2019 ◽  
Vol 43 (1) ◽  
pp. 70-89 ◽  
Author(s):  
M.M. Wang ◽  
Q. Chen ◽  
Y.Z. Diao ◽  
W.J. Duan ◽  
L. Cai
Keyword(s):  
Rna Polymerase ◽  
Elongation Factor ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Ribosomal Gene ◽  
Internal Transcribed Spacers ◽  
Translation Elongation ◽  
Cultural Methods ◽  
Wide Range

The Fusarium incarnatum-equiseti species complex (FIESC) is shown to encompass 33 phylogenetic species, across a wide range of habitats/hosts around the world. Here, 77 pathogenic and endophytic FIESC strains collected from China were studied to investigate the phylogenetic relationships within FIESC, based on a polyphasic approach combining morphological characters, multi-locus phylogeny and distribution patterns. The importance of standardised cultural methods to the identification and classification of taxa in the FIESC is highlighted. Morphological features of macroconidia, including the shape, size and septum number, were considered as diagnostic characters within the FIESC. A multi-locus dataset encompassing the 5.8S nuclear ribosomal gene with the two flanking internal transcribed spacers (ITS), translation elongation factor (EF-1α), calmodulin (CAM), partial RNA polymerase largest subunit (RPB1) and partial RNA polymerase second largest subunit (RPB2), was generated to distinguish species within the FIESC. Nine novel species were identified and described. The RPB2 locus is demonstrated to be a primary barcode with high success rate in amplification, and to have the best species delimitation compared to the other four tested loci.

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 64-68 ◽  
Author(s):  
G.H. Liu ◽  
W. Zhou ◽  
A.J. Nisbet ◽  
M.J. Xu ◽  
D.H. Zhou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Variation ◽  
Animal Health ◽  
Trichuris Trichiura ◽  
Its Rdna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Rdna Sequences

AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222–1267 bp and 1339–1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600–627 bp and 655–661 bp, 154 bp, and 468–486 bp and 530–538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2–1.7% within T. trichiura, and 0–1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0–1.3% within T. trichiura and 0.2–1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7–65.3% for ITS-1 and 59.3–61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

Sign in / Sign up

Export Citation Format

Share Document