Evolutionary analysis of a billion years of auxin biology

Abstract

Auxin is a key phytohormone for growth and development across many plant species. With the advances in next-generation sequencing, and ever-growing genomes and transcriptomes in the last decade, helped us infer the detailed origin and evolution of auxin biology in this thesis. We have developed a simple yet effective methodology to reconstruct the origin and evolution of various genes families across all plant lineages, including the algal ancestors. We first tested this protocol to study the evolution of auxin biosynthesis gene families Tryptophan aminotransferase of Arabidopsis (TAA) and YUCCA (YUC). Further, we exploited the evolution of Gretchen Hagen 3 (GH3) protein family involved in the auxin homeostasis that conjugate amino acids to hormones. Moreover, we also showed that this method could be applied to proteins with unknown or novel domains, by studying the evolution and annotation of SOSEKI (SOK) proteins. Auxin elicit both genomic and non-genomic responses, through nuclear auxin pathway (NAP) and Auxin binding protein 1 (ABP1), respectively. Hence, we also studied the origin and evolution of ABP1 as well as Auxin Response Factor (ARF), Auxin/Indole-3-acetic acid (Aux/IAA) and Transport inhibitor response 1/Auxin-signaling F-box (TIR1/AFB) gene families of NAP. A key step in the nuclear auxin pathway, is the interaction between ARF and Aux/IAA proteins through C-terminal Phox and Bem1 (PB1) domain. As PB1 domain is also identified in protozoans, fungi as well as in animals, we studied if the PB1 domain is originated in Last Eukaryote Common Ancestor (LECA). The results in this thesis collectively show the step-wise origins of auxin biology in green algae and subsequent functionality in land plants. We also highlighted questions that still remain and synchronize these findings with the on-going efforts to understand ‘non-canonical’ routes of auxin action in plants.