Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)

Genome ◽  
2003 ◽  
Vol 46 (4) ◽  
pp. 595-604 ◽  
Author(s):  
Ana Insua ◽  
María J López-Piñón ◽  
Ruth Freire ◽  
Josefina Méndez
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Evolutionary Relationship ◽  
Gc Content ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
Internal Transcribed Spacer Region ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Aequipecten Opercularis

The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209–276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270–294 bp) and GC content ranged between 47 and 50% (ITS1, 43–49%; 5.8S rRNA gene, 56–57%; ITS2, 44–49%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, including Chlamys farreri whose ITS sequence appears in databases, significant variation was observed in both ITS1 and ITS2. Phylogenetic analysis using ITS1, ITS2, or both spacer sequences always yielded trees with similar topology. Aequipecten opercularis and P. maximus grouped in one clade and the other three scallops (C. farreri, M. varia, and H. distortus) in another, where M. varia and H. distortus are the more closely related species. These results provide new insights into the evolutionary relationships of scallop species and corroborate the close evolutionary relationship between the tribes Aequipectinini and Pectinini previously deduced from 18S rDNA sequences.Key words: scallops, Pectinidae, ribosomal DNA, internal transcribed spacers, phylogeny.

scholarly journals The internal transcribed spacers and 5.8S rRNA gene show extensive diversity among isolates of the species complex

2004 ◽  
Vol 4 (4-5) ◽  
pp. 377-388 ◽  
Author(s):  
M KATSU ◽  
S KIDD ◽  
A ANDO ◽  
M MORETTIBRANCHINI ◽  
Y MIKAMI ◽  
...  
Keyword(s):  
Species Complex ◽  
Internal Transcribed Spacers ◽  
Rrna Gene ◽  
5.8S Rrna Gene ◽  
5.8S Rrna

scholarly journals Internal Transcribed Spacer Regions of rRNA Genes of Pneumocystis carinii from Monkeys

2001 ◽  
Vol 8 (3) ◽  
pp. 503-508 ◽  
Author(s):  
John Y. C. Hsueh ◽  
Rudolf P. Bohm ◽  
Peter J. Didier ◽  
Xing Tang ◽  
Mark E. Lasbury ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Pneumocystis Carinii ◽  
Distinct Species ◽  
Its2 Sequence ◽  
Rrna Genes ◽  
Its2 Region ◽  
Rrna Gene ◽  
5.8S Rrna Gene ◽  
Sequence Variations ◽  
5.8S Rrna

ABSTRACT Analysis of sequence variations among isolates ofPneumocystis carinii f. sp. macacae from 14 Indian rhesus monkeys (Macaca mulatta) at the internal transcribed spacer (ITS) regions of the nuclear rRNA gene was undertaken. Like those from P. carinii f. sp.hominis, the ITS sequences from various P. carinii f. sp. macacae isolates were not identical. Two major types of sequences were found. One type of sequence was shared by 13 isolates. These 13 sequences were homologous but not identical. Variations were found at 13 of the 180 positions in the ITS1 region and 28 of the 221 positions in the ITS2 region. These sequence variations were not random but exhibited definite patterns when the sequences were aligned. According to this sequence variation, ITS1 sequences were classified into three types and ITS2 sequences were classified into five types. The remaining specimen had ITS1 and ITS2 sequences substantially different from the others. Although some specimens had the same ITS1 or ITS2 sequence, all 14 samples exhibited a unique whole ITS sequence (ITS1 plus ITS2). The 5.8S rRNA gene sequences were also analyzed, and only two types of sequences that differ by only one base were found. Unlike P. carinii f. sp. hominis infections in humans, none of the monkey lung specimens examined in this study were found to be infected by more than one type of P. carinii f. sp. macacae. These results offer insights into the genetic differences between P. carinii organisms which infect distinct species.

Phylogeny of Sisymbrium (Brassicaceae) based on ITS sequences of nuclear ribosomal DNA

2002 ◽  
Vol 80 (9) ◽  
pp. 1002-1017 ◽  
Author(s):  
Suzanne I Warwick ◽  
Ihsan A Al-Shehbaz ◽  
Robert A Price ◽  
Connie Sauder
Keyword(s):  
Ribosomal Dna ◽  
New World ◽  
Sequence Data ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Old World ◽  
5.8S Rrna Gene

The genus Sisymbrium as currently circumscribed includes about 94 species disjunctly distributed in the Old (41 spp.) and the New World (53 spp.). Sisymbrium has been variously delimited, with several segregate genera proposed (subtribe Sisymbriinae) primarily for the new World taxa, including Schoenocrambe, Coelophragmus, and Mostacillastrum. Using sequence data from the internal transcribed spacers of nuclear ribosomal DNA and the 5.8S rRNA gene (collectively, ITS region), we examined the evolutionary relationships of Old and New World Sisymbrium species with its segregate genera and the validity of O.E. Schulz's classical sectional treatment of Sisymbrium. Sequence data were obtained from 33 Sisymbrium species, representing all 14 sections and two Sisymbrium species formerly assigned to segregate genera Coelophragmus and Mostacillastrum (subtribe Sisymbriinae), and two putative Sisymbrium species currently assigned to Neotorularia. Sequence data were also obtained from 26 taxa from segregate or related genera includingSchoenocrambe, Werdermannia (subtribe Sisymbriinae), eight genera in the Thelypodieae, Sibara (tribe Arabideae) and Pringlea (tribe Pringleeae), four members of the tribe Brassiceae, and three other Neotorularia species. Results from maximum parsimony analysis showed a polyphyletic origin for Sisymbrium and did not correspond well to Schulz's sectional classification. Sisymbrium species were split into three major clades: Old World Sisymbrium (including Neotorularia aculeolata, Neotorularia afghanica, and the type species of Schoenocrambe, Schoenocrambe linifolia, the sole New World member of this Old World clade); New World Sisymbrium (along with the remaining New World taxa) and designated as the New World Thelypodieae alliance; and the tribe Brassiceae ( including Sisymbrium supinum and Sisymbrium thellungii).Key words: Sisymbrium, Schoenocrambe, ITS, Thelypodieae, taxonomy, Brassicaceae.

scholarly journals Genotyping ofPneumocystis jiroveciiby Use of a New Simplified Nomenclature System Based on the Internal Transcribed Spacer Regions and 5.8S rRNA Gene of the rRNA Operon

2019 ◽  
Vol 57 (6) ◽  
Author(s):  
Ting Xue ◽  
Zhuang Ma ◽  
Fan Liu ◽  
Wei-Qin Du ◽  
Li He ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Rrna Operon ◽  
Rrna Gene ◽  
Length Variation ◽  
Nomenclature System ◽  
Content Type ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Its1 And Its2 ◽  
New System

ABSTRACTGenotyping based on internal transcribed spacer 1 (ITS1) and ITS2 of the rRNA operon has played an important role in understanding the transmission and epidemiology ofPneumocystis jirovecii, one of the major opportunistic pathogens in individuals with AIDS and other immunocompromised individuals. The widespread use of this typing system has resulted in several problems, including inconsistent genotype nomenclatures, difficult data transferability, and complicated interpretation of the length variation in multiple homopolymeric tracts. The aim of this study was to establish a new, simplified genotype nomenclature system forP. jiroveciibased on the ITS1 and ITS2 sequences. We first analyzed the complete ITS1, 5.8S rRNA gene, and ITS2 sequences (termed ITS1-5.8S-ITS2) in 27 recentP. jiroveciiisolates from China and identified 18 unique genotypes. Subsequently, we performed a comprehensive classification of more than 400 ITS1- and ITS2-related sequences from GenBank and an in-depth evaluation of the length variation of multiple homopolymeric tracts within ITS1-5.8S-ITS2. Integration of the results from these analyses led to a new, simplified genotype nomenclature system including 62 unique ITS1-5.8S-ITS2 genotypes, simply designated types 1 through 62. This new system offers several advantages over traditional ITS1- and ITS2-based typing systems, including a simpler analysis and interpretation process, a higher discriminative power, and no limitation in assigning potential new genotypes. This new system is expected to facilitate the standardization ofP. jiroveciigenotyping and easy data exchanges across different laboratories.

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