COMPUTATIONAL IDENTIFICATION, PHYLOGENETIC AND SYNTENY ANALYSIS OF RECEPTOR-LIKE KINASES “RLK” AND RECEPTOR-LIKE PROTEINS “RLP” IN LEGUMES A Dissertation Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Daniel Restrepo Montoya In Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Major Program: Genomics and Bioinformatics October 2018 Fargo, North Dakota North Dakota State University GraDuate School Title COMPUTATIONAL IDENTIFICATION, PHYLOGENETIC AND SYNTENY ANALYSIS OF RECEPTOR-LIKE KINASES “RLK” AND RECEPTOR-LIKE PROTEINS “RLP” IN LEGUMES By Daniel Restrepo Montoya The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of DOCTOR OF PHILOSOPHY SUPERVISORY COMMITTEE: Dr. Juan M. Osorno Co-Chair Dr. Phillip E. McClean Co-Chair Dr. Julia Bowsher Dr. Robert Brueggemann ApproveD: 11/16/2018 Dr. Phillip E. McClean Date Department Chair ABSTRACT Legumes are considered the second most important family of crop plants after the grass family based on economic relevance. In recent years, the field of legume genomics has expanded due to advancements in high-throughput sequencing and genotyping technologies. To date, no published comparative genomic analysis explores receptor-like kinases “RLK” and receptor-like proteins “RLP” among legume genomes. Evaluating these RLK and RLP should provide a source of new information because extensive genetic and phenotypic studies have already discovered the diverse roles of RLK and RLP in cell development, disease resistance, and stress responses among other functions. This study demonstrates that a computational logical approach for classifying the RLK/RLP in legumes/non-legumes is statistically well supported and can be used in other plant species. The analysis of RLK/RLP of 7 legumes and 3 non-legume species evaluated suggests that about 2% are RLK and less than 1% of the proteins are RLP. The results suggest a dynamic evolution of RLK and RLP in the legume family. In fact, between 66% to 85% of RLK and 83% to 88% of RLP belong to orthologous clusters among the species evaluated. The remaining RLK and RLP proteins are classified as singletons. The ratio of the pairwise synteny blocks of RLK/RLP among legumes shows a 1:1 relationship. The exception is G. max, which shows an approximately 2:1 ratio due to its recent whole genome duplication (G. max vs. the other six legumes). The other legumes show evidence of a similar proportion of plasma membrane proteins among the legume pairwise synteny blocks. iii ACKNOWLEDGMENTS I would like to thank Dr. Juan M. Osorno and Dr. Phil McClean for their patience and for teaching me about agriculture, breeding, genetics, genomics, bioinformatics, and much more. Dr. Robert Brueggeman for its invaluable tips, insights, and recommendations about plant pathology. Dr Julia Bowsher for its recommendations and support. The Fulbright scholarship. The Francisco Jose de Caldas – Colciencias scholarship, the North Dakota State University, the ILLiad interlibrary loan service system, and the NDSU dry breeding program. The Google Cloud platform service and the free extended trials. Dr. Mark Miller and Dr. Wayne Pfeiffer and the Cipres-Xsede platform. Dr. Luis F. Niño and Ing. Jonathan Narvaez and the Scientific Cluster at Universidad Nacional de ColomBia. Dr. Henrik Nielsen at DTU. The NCBI staff - Dr. Peter S. Cooper, Dr. Wayne Matten. The OrthoMCL support team. The MCScanX community. Rebecca Kutty and Michael Stein for their editing suggestions, and finally the *NIX, python, and bash communities. iv DEDICATION Simon, Maria, the everlasting gardener, and the regretful fisherman. v TABLE OF CONTENTS ABSTRACT ................................................................................................................................... iii ACKNOWLEDGMENTS ............................................................................................................. iv DEDICATION ................................................................................................................................ v LIST OF TABLES ......................................................................................................................... ix LIST OF FIGURES ........................................................................................................................ x LIST OF APPENDIX TABLES .................................................................................................... xi LIST OF APPENDIX FIGURES .................................................................................................. xii CHAPTER 1. INTRODUCTION ................................................................................................... 1 CHAPTER 2. COMPUTATIONAL IDENTIFICATION OF RLK AND RLP IN LEGUMES .... 5 Abstract ........................................................................................................................... 5 Background ................................................................................................................ 5 Results ........................................................................................................................ 5 Conclusions ................................................................................................................ 6 Background of RLK and RLP ........................................................................................ 7 Methods ........................................................................................................................ 13 Datasets .................................................................................................................... 13 Computational identification of RLK and RLP ....................................................... 14 Independent evaluation of predictive performance .................................................. 17 Results ........................................................................................................................... 18 Performance prediction of RLK and RLP ................................................................ 18 Summary of predicted RLK and RLP ...................................................................... 19 Summary of the presence and prevalence of functional domains ............................ 29 Discussion ..................................................................................................................... 34 Conclusions ................................................................................................................... 39 CHAPTER 3. PHYLOGENETIC ANALYSIS OF RLK AND RLP IN LEGUMES .................. 42 vi Abstract ......................................................................................................................... 42 Background .............................................................................................................. 42 Results ...................................................................................................................... 42 Conclusions .............................................................................................................. 43 Background of RLK and RLP in legumes .................................................................... 43 Methods ........................................................................................................................ 48 Datasets .................................................................................................................... 48 Orthology analysis ................................................................................................... 49 Hierarchical clustering analysis of RLK and RLP ................................................... 49 Results ........................................................................................................................... 50 Orthology and hierarchical clustering analyses of RLK .......................................... 50 Orthology of RLK-nonRD ....................................................................................... 52 Hierarchical clustering analysis of RLK .................................................................. 53 Orthology and hierarchical clustering domain analysis of RLP .............................. 55 Hierarchical clustering analysis of RLP ................................................................... 56 Discussion ..................................................................................................................... 58 Conclusions ................................................................................................................... 60 CHAPTER 4. SYNTENY ANALYSIS OF RLK AND RLP IN LEGUMES .............................. 62 Abstract ......................................................................................................................... 62 Background .............................................................................................................. 62 Results ...................................................................................................................... 62 Conclusions .............................................................................................................. 63 Background of synteny in legumes ..............................................................................