Establishing strategies of genome assembly for unprecedented species

Abstract

Advancement of sequencing technologies provide more possibility to build unprecedented genomes. Building genome sequence is one of the most effective ways to identify the specific genomic features and evolutional history of unprecedented species. However, even though genome project can be conducted in more reasonable price than before, genome project still need quite amount of research funds. Therefore, many researchers who study non-model or novel organisms have difficulty in researches in genomic level. To solve this difficulty, this study mainly focused on not only building genome sequences of unprecedented species and but also practical use of genome assembly technique for resolving the limitations of previous methods. Custom pipelines were built with various programs which have its unique characteristics for each purpose of study. In chapter 1, the general background of NGS and de novo assembly was summarized. Characteristics of current sequencing technologies were presented, and the assembly algorithms and representative programs were listed. In chapter 2, microbial genome project had been conducted. I built the complete genome of microbe using Pacbio RS II system. Using comparative genomic analysis, I identified potential genetic background of specific phenotype such as host immune system enhancement. In chapter 3, abalone genome project had been conducted with various type of sequencing data. This is the first Haliotidae genome project and I identified specific evolutionary signature recorded in the abalone genome via comparative genomics analysis. And not only for abalone genome but also genomes and transcriptomes in abalone viscera were analyzed to identify the unknown origin of tumor suppression effect. In chapter 4, I constructed effective complete mitochondrial genome assembly pipeline for unprecedented species. This pipeline includes various experimental process from different types of studies. Constructed pipeline was validated using real sequencing data and mitochondrial genome sequence of Menathais tuberosa was successfully constructed. Chapter 5 is about the microsatellite marker development pipeline for unprecedented species based on whole genome assembly. Constructed pipeline was tested for Antheraea yamamai genome and it successfully built microsatellite markers which showed possibility to be used for population genetics study. Last chapter is about unaligned read assembly. Unaligned read assembly is one of the ways to solve the limitations of reference based re-sequencing study. Developed pipeline was applied to Hanwoo population data and it identified structural variation which might be related with its phenotypes. Based on these studies, I expect my analysis and constructed pipelines can provide more understanding for unprecedented species and contribute to ameliorate limitations of current researches in this field.