Clinical Microbiology: Open Access

An extension of the Kimura two-parameter model for nucleotide sequences containing gaps

Joint Event on 25^th Asia Pacific Biotechnology Congress & 3^rd International Conference on Medical and Clinical Microbiology

May 01-02, 2019 Kyoto, Japan

Nishimaki Takuma and Keiko Sato

Tokyo University of Science, Japan

Scientific Tracks Abstracts: Clin Microbiol

Abstract:

Introduction & Aim: Accurate estimates of genetic difference are required for research in evolutionary biology. Nucleotides changes are seen during the evolutionary process include substitutions, insertions and deletions. The Kimura two-Parameter (K2P) model, which is probably the most widely used of all models of nucleotide substitution for estimating genetic differences, does not take into account the evolution by insertions and deletions. Therefore, we extended the K2P model by considering gaps (insertions and/or deletions).

Method: We extended the K2P model by assigning rates of insertions and deletions that differ from rates of substitutions and introduced a new measure for estimating genetic difference between two nucleotide sequences in terms of nucleotide changes that have occurred during the evolutionary process. Then, for the nuclear ribosomal DNA Internal Transcribed Spacer 2 (ITS2) region from the genus Physalis, we calculated genetic differences using our difference measure and the K2P difference measure to compare these measures.

Result: Using the ITS2 sequences of Physalis species, we demonstrated that species identification and phylogenetic studies strongly depend on evolutionary models. It is especially noteworthy that the use of different models affects the degree of overlap between intraspecific and interspecific genetic differences. We observed that the percentage of interspecific sequence pairs with values less than the maximum intraspecific genetic difference is 43.2% for the K2P model which is calculated by removing gap sites across all sequences, 22.7% for the K2P model which is calculated by removing gap sites for sequence pairs, and 16.9% for our model which is calculated without removing gap sites.

Conclusion: We believe that appropriately incorporating the evolutionary information of sites containing insertions and deletions into genetic difference measures for not only the K2P model but also other evolutionary models will be helpful to detect meaningful difference in an evolutionary process and facilitate accurate species identification and classification.

Biography :

Nishimaki Takuma is currently pursuing his PhD in the Department of Information Sciences at Tokyo University of Science. His research interests are molecular phylogenetic and evolutionary biology.

E-mail: xtnphone@gmail.com