Partial sequences of mitochondrial 12S and 16S rRNA genes from 19 Asian frog species of the tribe Paini (Ranidae, Dicroglossinae) allowed a first molecular study of the phylogenetic relationships of this tribe. This analysis confirmed that this tribe is a monophyletic group, but suggested relationships did not agree with previous generic classification of this clade based on morphology. Two maj...

A new species of indotyphlid caecilian amphibian, Gegeneophis tejaswini sp. nov., is described based on eight specimens from lowlands of the most northerly district of the state of Kerala in the southern part of the Western Ghats region, India. This species is distinguished from all other Gegeneophis in annulation characters and genetics (> 6% different from most similar nominal species for ...

PCR-RFLP with nine restriction enzymes was applied to the 16S and 23S rRNA genes of 42 rhizobial and agrobacterial strains to determine the phylogenetic position of Rhizobium galegae and increase the understanding of the evolution of ribosomal operons. The strains were selected based on previous phylogenetic studies. PCR primers were designed so that they amplified a 2.3 kb fragment of the 23S ...

Mitochondrial 12S rRNA sequence data were used to examine the taxonomic status of the endemic brown, Auckland Island, and Campbell Island teal. Based on phylogenetic reconstructions using the 12S rRNA data we have found that the Great Barrier Island brown teal, and the Auckland and Campbell Island teals form a discrete clade, to the exclusion of the Fiordland brown teal. All of the Fiordland br...

Fish eDNA metabarcoding is a nonintrusive, time- and cost-effective way to detect biodiversity, with potential applications in ecosystem-based management fisheries assessment. Nevertheless, fish-specific resources are currently not well-developed, many fish species yet sequenced reference databases. We developed Mitohelper, Python-based command line tool annotate align mitochondrial sequences a...

To successfully implement environmental DNA-based (eDNA) diversity monitoring, the completeness and accuracy of reference databases used for taxonomic assignment eDNA sequences are among challenges to be tackled. Here, we have developed a workflow that evaluates current status GenBank marine fishes. For given combination species barcodes, gap analysis is performed potentially erroneous identifi...

16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation within closely related taxa or within a genome. Here we use the information from sequenced bacterial genomes to explore the variability of 16S r...

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identificat...

A premature female Dirofilaria species, subsequently identified as Dirofilaria repens by its morphological features and mitochondrial 12S ribosomal RNA (12S rRNA) gene sequence, was removed from a subcutaneous nodule of the right temporal region of the head in a Japanese woman 2 years after she noticed swelling of her left calf following an insect sting during a tour to Europe; headache symptom...

BACKGROUND The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification. The aims of this study were to determine the utility, and compare the performance of several clustering and classification algorithms to identify the species of 364 seq...