MicroRNA and mRNA analysis of two species of New Zealand Pachycladon : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, Manawatu, New Zealand

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs important in post-transcriptional regulation. In this study, potential miRNAs from two New Zealand Pachycladon species, P. cheesemanii and P. fastigiatum, are identified and compared. Sixteen miRNAs were differentially expressed between the species, most of which have roles in flower and leaf development. Potential targets for 15 miRNAs were located in expressed sequence tag (EST) libraries for P. cheesemanii and/or P. fastigiatum, including a new potential relationship in P. cheesemanii between miR825 and MYB29 (AT5G07690), a transcription factor involved in the synthesis of methionine-derived glucosinolates. From the results of the differential expression analysis and target identification, 27 miRNAs from 21 miRNA families were chosen for pre-miRNA sequencing. Sequences of 15 P. cheesemanii miRNA hairpins and 13 P. fastigiatum miRNA hairpins were validated experimentally. Additionally, mRNA-Seq data obtained at the same time as the miRNAs were analysed. A gene ontology analysis indicated enriched terms for defence responses and miRNAs in P. fastigiatum. This study is the first investigation of the miRNAs present in Pachycladon and how their differential expression contributes to the adaptive divergence between the species.