Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2020 Methods for correcting and analyzing gene families Akshay Yadav Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Yadav, Akshay, "Methods for correcting and analyzing gene families" (2020). Graduate Theses and Dissertations. 18059. https://lib.dr.iastate.edu/etd/18059 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Methods for correcting and analyzing gene families by Akshay Yadav A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Bioinformatics and Computational Biology Program of Study Committee: Steven Cannon, Co-major Professor David Fernández-Baca, Co-major Professor Karin Dorman Matthew Hufford Oliver Eulenstein The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2020 Copyright © Akshay Yadav, 2020. All rights reserved. ii DEDICATION To my wife, Prajakta, my brother, Digvijay, and to Aai and Baba for their unconditional support and encouragement. iii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ...............................................................................................................v ABSTRACT ................................................................................................................................... vi CHAPTER 1. GENERAL INTRODUCTION ................................................................................1 Homology and Gene Families ................................................................................................... 1 Gene Family Building ............................................................................................................... 2 The Legume Family ................................................................................................................... 4 Protein Domains ........................................................................................................................ 5 References ................................................................................................................................. 7 CHAPTER 2. METHODS FOR ANALYZING, COMPARING AND CORRECTING GENE FAMILIES .....................................................................................................................................11 Abstract .................................................................................................................................... 11 Introduction ............................................................................................................................. 12 Methods ................................................................................................................................... 15 Under-clustering Detection and Correction ....................................................................... 15 Comparison of Family Sets ................................................................................................ 23 Tree-based Over-clustering Detection................................................................................ 23 Results ..................................................................................................................................... 24 Behavior of the Machine Learning Method on “True” YGOB Families ........................... 24 Using the Machine Learning Method to Detect “Pure” but Under-clustered Families ...... 25 Application of the Machine Learning Method to Detect and Correct “Impure” and Under-clustered Families ................................................................................................... 27 Comparing Families Obtained from Existing Methods to Reference Families ................. 29 Application of the Machine Learning Method to Improve Families from Existing Family Building Methods ................................................................................................... 30 Analyzing and Correcting OrthoFinder Legume Families ................................................. 30 Discussion ................................................................................................................................ 36 References ............................................................................................................................... 39 CHAPTER 3. IMPROVING AND ANALYZING CURRENT LEGUME GENE FAMILIES ...45 Abstract .................................................................................................................................... 45 Introduction ............................................................................................................................. 46 Methods ................................................................................................................................... 49 HMM-based Family Merging ............................................................................................ 49 Tree-based Family Scoring and Splitting ........................................................................... 50 Protein-domain-composition-based Family Scoring .......................................................... 52 Results ..................................................................................................................................... 52 Discussion ................................................................................................................................ 56 References ............................................................................................................................... 57 iv CHAPTER 4. CERCIS: A NON-POLYPLOID GENOMIC RELIC WITHIN THE GENERALLY POLYPLOID LEGUME FAMILY ......................................................................61 Abstract .................................................................................................................................... 61 Introduction ............................................................................................................................. 62 Materials and Methods ............................................................................................................ 63 Gene Family Construction, Ks Analysis, and Phylogeny Calculation ............................... 63 Calculation of Ks Values and Modal Ks Peaks ................................................................... 66 Inference of Consensus Branch Lengths from Ks Peaks .................................................... 67 Methods for Mining for Tree Topologies........................................................................... 68 Results ..................................................................................................................................... 68 Ks Peaks from Self-Comparisons of Coding Sequence ...................................................... 68 Genomic Synteny Analysis ................................................................................................ 73 Phylogenomic Analyses ..................................................................................................... 74 Informal Observations About Patterns in Trees ................................................................. 76 Summaries of Sequence Counts for All Gene Families (Legume Phylogeny Working Group et al., 2017) .............................................................................................................. 77 Mining for Tree Topologies Within the Cercidoideae ....................................................... 80 Gene Duplication Patterns Across Diverse Species in the Cercidoideae ........................... 81 Chromosome Counts Across the Legume Phylogeny ........................................................ 84 Genome Sizes in the Cercidoideae ..................................................................................... 89 Discussion ................................................................................................................................ 90 Conclusion ............................................................................................................................... 97 References ............................................................................................................................... 98 CHAPTER 5. FAMILY-SPECIFIC GAINS AND LOSSES OF PROTEIN DOMAINS IN LEGUME AND GRASS PLANT FAMILIES ............................................................................105 Abstract .................................................................................................................................. 105 Introduction ........................................................................................................................... 106 Material and Methods ...........................................................................................................