Research Collection Doctoral Thesis Gene copy number variation among and within plant species Author(s): Liu, Xuanyu Publication Date: 2014 Permanent Link: https://doi.org/10.3929/ethz-a-010432389 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 22293 Gene copy number variation among and within plant species A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) Presented by Xuanyu Liu M.S. in Cell Biology, Chinese Academy of Sciences Born on April 10th, 1985 Citizen of China Accepted on the recommendation of Prof. Dr. Alex Widmer, examiner Prof. Dr. Ute Krämer, co-examiner Dr. Weihong Qi, co-examiner Dr. Alessia Guggisberg, co-examiner 2014 TABLE OF CONTENTS SUMMARY .................................................................................................................................................................................. I ZUSAMMENFASSUNG ........................................................................................................................................................... II ACKNOWLEDGMENTS .......................................................................................................................................................... IV GENERAL INTRODUCTION .................................................................................................................................................... 1 THE CONCEPT OF A GENE FAMILY ............................................................................................................................ 1 GENE GAINS AND LOSSES ............................................................................................................................................ 1 COPY NUMBER VARIANTS ........................................................................................................................................... 4 STUDY SYSTEMS ............................................................................................................................................................. 5 MAIN GOALS AND METHODS ...................................................................................................................................... 6 REFERENCES .................................................................................................................................................................... 8 CHAPTER ONE: Evolutionary analysis of gene family size variation in Arabidopsis and its relatives .................................. 10 ABSTRACT ...................................................................................................................................................................... 10 INTRODUCTION ............................................................................................................................................................. 11 RESULTS .......................................................................................................................................................................... 13 DISCUSSION .................................................................................................................................................................... 17 EXPERIMENTAL PROCEDURES ................................................................................................................................. 21 SUPPORTING INFORMATION ................................................................................................................................... 25 REFERENCES .................................................................................................................................................................. 27 CHAPTER TWO: Genome-wide comparative analysis of the GRAS gene family in Populus, Arabidopsis and rice ............. 30 ABSTRACT ...................................................................................................................................................................... 30 INTRODUCTION ............................................................................................................................................................. 31 RESULTS .......................................................................................................................................................................... 32 DISCUSSION .................................................................................................................................................................... 43 EXPERIMENTAL PROCEDURES ................................................................................................................................. 46 SUPPORTING INFORMATION ................................................................................................................................... 50 REFERENCES .................................................................................................................................................................. 51 CHAPTER THREE: Copy number variants and their putative involvement in edaphic adaptation of Arabidopsis lyrata ...... 54 ABSTRACT ...................................................................................................................................................................... 54 INTRODUCTION ............................................................................................................................................................. 55 RESULTS .......................................................................................................................................................................... 56 DISCUSSION .................................................................................................................................................................... 61 EXPERIMENTAL PROCEDURES ................................................................................................................................. 62 SUPPORTING INFORMATION ................................................................................................................................... 68 REFERENCES .................................................................................................................................................................. 69 GENERAL DISCUSSION ......................................................................................................................................................... 72 REFERENCES .................................................................................................................................................................. 74 Summary SUMMARY For more than a century, biologists have sought to understand the origins, adaptive mechanisms and evolutionary processes underlying genomic variation within and among species. So far, our knowledge about these aspects, however, has been mainly limited to one type of genomic variation, i.e. single nucleotide polymorphisms (SNPs). There is growing evidence that another class of genomic variation, gene copy number variation (GCNV, a.k.a. gene family size variation), is pervasive and contributes to environmental adaptation and organismal diversification. While substantial progress has been made in animal studies, our understanding about GCNV in plants is still limited. In this thesis, I investigated several questions surrounding GCNV, both within and among plant species. Firstly, I performed an evolutionary analysis of gene family size variation among five Brassicaceae species that diverged relatively recently using a likelihood approach. The average rate of gene gain-and-loss (λ) was estimated to be 0.0022 gains and losses per gene per million years, which corroborates the view that gene gain-and-loss evolves at similar average rate across different eukaryotic lineages. Branch-specific rate estimation further supported my hypothesis that plant mating system may influence the rate of gene gain-and-loss. Gene families that were inferred to have been evolving rapidly in size were found to be mainly involved in plant-pathogen/herbivore interactions and pollen-pistil interactions, and exhibited a high incidence of positive selection acting at the nucleotide level. Finally, I showed that gene gains via tandem duplication predominantly contributed to the adaptive evolution of gene family size. Secondly, I pursued my investigations on GCNV among plant species, but over a much longer evolutionary time-scale in an individual gene family. The expansion and diversification of the GRAS gene family in Populus was investigated through comparative analyses with Arabidopsis and rice. I detected 106, 34 and 60 putative GRAS genes in Populus, Arabidopsis and rice, respectively, which could be grouped into 13 subfamilies. The joint action of tandem and segmental duplications could explain the rapid expansion of the GRAS family in Populus, while site-specific shifts in evolutionary rates might constitute the main driver in functional diversification. The observation that GRAS genes evolved mainly under purifying selection after duplication however revealed strong functional constraints. Expression divergence analyses between paralogous pairs of GRAS genes finally suggested that their retention likely resulted