scholarly journals Molecular Analysis of Medicinally-Used Chinese and Japanese Curcuma Based on 18S rRNA Gene and trnK Gene Sequences.

2001 ◽  
Vol 24 (12) ◽  
pp. 1389-1394 ◽  
Author(s):  
Hui CAO ◽  
Yohei SASAKI ◽  
Hirotoshi FUSHIMI ◽  
Katsuko KOMATSU
Keyword(s):  
Molecular Analysis ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Trnk Gene

scholarly journals Molecular identification and characterization of Sarcocystis spp. in horsemeat and beef marketed in Japan

Parasite ◽  
2018 ◽  
Vol 25 ◽  
pp. 27 ◽  
Author(s):  
Rie Murata ◽  
Jun Suzuki ◽  
Ayako Hyuga ◽  
Takayuki Shinkai ◽  
Kenji Sadamasu
Keyword(s):  
Intraspecific Variation ◽  
Molecular Analysis ◽  
18S Rrna ◽  
Direct Sequencing ◽  
Food Poisoning ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Identification And Characterization

Human Sarcocystis infections are known to be caused by the ingestion of raw or undercooked beef or pork containing mature sarcocysts of Sarcocystis hominis or S. suihominis, respectively. In addition, several cases of parasitic food poisoning in Japan have recently been reported after consumption of raw horsemeat containing sarcocysts of S. fayeri. In this study, the presence of sarcocysts in 28 horsemeat and 121 beef samples collected in Tokyo was investigated. Sarcocysts of S. fayeri were found in 16 horsemeat samples. Sarcocysts of S. hominis were not detected in beef samples, while sarcocysts of S. cruzi were detected in 60 beef samples. In addition, S. hirsuta and S. bovini were isolated only from New Zealand beef samples. Bradyzoites in sarcocysts collected from 62/73 sarcocyst-positive refrigerated horsemeat and beef samples were determined to be viable. Molecular analysis of S. fayeri 18S rRNA gene sequences revealed that intraspecific variation among eight individual bradyzoites from a single sarcocyst was as high as 9.8%. In contrast, mitochondrial cytochrome c oxidase subunit 1 (mtDNA cox1) gene sequences from the six fragments of a single sarcocyst were 100% identical. Sarcocysts of S. bovini isolated from beef also exhibited intraspecific variation in 18S rRNA gene sequences and had to be cloned before sequencing, while mtDNA cox1 gene sequences were obtained by direct sequencing. Therefore, we conclude that molecular analysis of the mtDNA cox1 gene is the most useful for identification of Sarcocystis species. This study provides the first published partial sequence of the S. fayeri mtDNA cox1 gene.

18S rRNA Gene Sequences and Supraordinal Classification of the Erysiphales

Mycologia ◽  
1994 ◽  
Vol 86 (2) ◽  
pp. 212 ◽  
Author(s):  
Gregory S. Saenz ◽  
John W. Taylor ◽  
Andrea Gargas
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences

scholarly journals Revealing the Composition of the Eukaryotic Microbiome of Oyster Spat by CRISPR-Cas Selective Amplicon Sequencing (CCSAS)

2021 ◽  
Author(s):  
Kevin Xu Zhong ◽  
Anna Cho ◽  
Christophe M. Deeg ◽  
Amy M. Chan ◽  
Curtis A. Suttle
Keyword(s):  
18S Rrna ◽  
Amplicon Sequencing ◽  
18S Rrna Gene ◽  
Model Organisms ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Oyster Spat ◽  
Guide Rna ◽  
16S Rna ◽  
Eukaryotic Microbes

Abstract BackgroundThe microbiome affects the health of plants and animals, including humans, and has many biological, ecological and evolutionary consequences. Microbiome studies typically rely on sequencing ribosomal 16S RNA gene fragments, which serve as taxonomic markers for prokaryotic communities; however, for eukaryotic microbes this approach is compromised, because 18S rRNA gene sequences from microbial eukaryotes are swamped by contaminating host rRNA gene sequences. ResultsTo overcome this problem, we developed CRISPR-Cas Selective Amplicon Sequencing (CCSAS), a high-resolution and efficient approach for characterizing eukaryotic microbiomes. CCSAS uses taxon-specific single-guide RNA (sgRNA) to direct Cas9 to cut 18S rRNA gene sequences of the host, while leaving protistan and fungal sequences intact. We validated the specificity of the sgRNA on ten model organisms and an artificially constructed (mock) community of nine protistan and fungal pathogens. The results showed that >96.5% of host rRNA gene amplicons were cleaved, while 18S rRNA gene sequences from protists and fungi were unaffected. When used to assess the eukaryotic microbiome of oyster spat from a hatchery, CCSAS revealed a diverse community of eukaryotic microbes, typically with much less contamination from oyster 18S rRNA gene sequences than other methods using non-metazoan or blocking primers. However, each method revealed taxonomic groups that were not detected using the other methods, showing that a single approach is unlikely to uncover the entire eukaryotic microbiome in complex communities. To facilitate the application of CCSAS, we designed taxon-specific sgRNA for ~16,000 metazoan and plant taxa, making CCSAS widely available for characterizing eukaryotic microbiomes that have largely been neglected. ConclusionCCSAS provides a high-through-put and cost-effective approach for resolving the eukaryotic microbiome of metazoa and plants with minimal contamination from host 18S rRNA gene sequences. Keywords: Eukaryotic microbiome, 18S rRNA gene, Microeukaryote, CRISPR-Cas, Taxon-specific single-guide RNA, gRNA-target-site, CasOligo, CCSAS

scholarly journals A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences

2017 ◽  
Vol 36 ◽  
pp. 33-39 ◽  
Author(s):  
Pablo Yarza ◽  
Pelin Yilmaz ◽  
Katrin Panzer ◽  
Frank Oliver Glöckner ◽  
Marlis Reich
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phylogenetic Framework
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