Ciliate DNA barcoding

Abstract

DNA barcoding is a taxonomic method that uses a short genetic marker in an organisms DNA to identify it as belonging to a particular species. A desirable gene region for DNA barcoding should be standardized, present in most of the taxa of interest and sequencable without species-specific PCR primers, short enough to be easily sequenced with current technology, and provide a large variation between species yet a relatively small amount of variation within a species. For animals and many other eukaryotes, the mitochondrial CO1 gene have been suggested, and verified as most suitable gene region for DNA barcoding. However this CO1 has been used rarely as DNA barcoding gene for many microbial eukaryotes such as ciliates because the universal primers for CO1 are seldom universal for these organisms. Ribosomal RNA gene often used in phylogenetic and molecular taxonomic studies because of its ubiquitous and well conserved nature in eukaryotes. In particular, the highly conservative nature of SSU rRNA gene facilitates its utility in the study of culture-independent microbial eukaryote communities using universal PCR primers. To verify which regions of rRNA gene are suitable as a diagnostic marker for species discrimination, SSU~the partial large subunit (LSU) including D1 and D2 (SSU~D2) region were sequenced from the species belonging to family Euplotidae and Loxophyllum and sequences divergencea of interest and sequencable without species-specific PCR primers, short enough to be easily sequenced with current technology, and provide a large variation between species yet a relatively small amount of variation within a species. For animals and many other eukaryotes, the mitochondrial CO1 gene have been suggested, and verified as most suitable gene region for DNA barcoding. However this CO1 has been used rarely as DNA barcoding gene for many microbial eukaryotes such as ciliates because the universal primers for CO1 are seldom universal