DISSERTATION RESEARCH: Evaluating Methods to Study the Phylogenetic Distribution of Genome Sizes in Carabid Beetles, including Next-Generation Sequencing of Old Museum Specimens

Oregon State University, Corvallis OR

Investigators

Abstract

The goal of this project is to measure and investigate genome sizes in ground beetles, a diverse and economically important group of insects, using a combination of new and traditional techniques. Genome size is a measurement of the amount of DNA found inside the nucleus of a single cell. A puzzling question about genome size is why it varies so much in different organisms. The largest animal genome is over 3,000 times bigger than the smallest. Understanding the cause of these differences can provide important insights into the evolutionary processes and history that shaped organisms, since differences in genome size may be caused by organisms gaining or loosing genes or other parts of the genome. Genome size is also important to consider when planning DNA sequencing projects, as larger genomes require more resources than small ones. An important barrier to understanding the patterns that cause genome size variation is how few measurements there are. Currently, genome size estimates exist for only 0.4% of animal species. This number is so small due to how difficult it is to get a reliable estimate. Traditional methods rely on specially prepared cells from living organisms. However, live specimens can be difficult or impossible to obtain for species that are rare, endangered, or extinct. Fortunately, there are new methods to estimate genome size using DNA sequencing that do not require living tissue. This project will examine the reliability of DNA sequence-based genome size estimates on both live beetles and old, preserved specimens from museum collections. No previous experiments have specifically compared these methods or tested their reliability in old specimens. This project will also contribute additional data points for the broader study of genome sizes across the tree of life, and will further the use of museum collections in the study of the world's diversity. Next generation sequencing (NGS) has given researchers a new set of tools for estimating genome size. This project will investigate the viability of NGS coverage-based methods for determining genome size in carabid beetles by performing flow cytometry and shallow Illumina sequencing on ten species of carabid beetle. It will also determine if genome size estimation by coverage analysis can be reliably employed on preserved material from museum collections by repeating shallow Illumina sequencing on old museum specimens of the same ten species. A total of 36 genomic libraries will be prepared and sequenced across four Illumina lanes. Coverage-based analyses will be performed on all resulting sequences, and the resulting genome size estimates will then be compared with those obtained by flow cytometry using a one-way ANOVA test to determine if coverage-based estimation is a viable alternative for both fresh and museum specimens. If shallow genome sequencing is successful in estimating genomes sizes, it will allow for the study of material from the world's natural history museums without the cost of extensive fieldwork to collect fresh material. This could potentially transform the study of genome size by increasing the number of species it is possible to analyze by orders of magnitude.