Terpene Synthases in Rice Pan-Genome and Their Responses to Chilo suppressalis Larvae Infesting

Abstract

Terpene synthase (TPS) catalyzes the synthesis of terpenes and plays an important role in plant defense. This study identified 45 <i>OsTPS</i> genes (32 core genes and 13 variable genes) based on the high-quality rice gene-based pan-genome. This indicates limitations in <i>OsTPS</i> gene studies based on a single reference genome. In the present study, through collinearity between multiple rice genomes, one <i>OsTPS</i> gene absent in the reference (Nipponbare) genome was found and two <i>TPS</i> genes in the reference genome were found to have atypical structures, which would have been ignored in single genome analysis. <i>OsTPS</i> genes were divided into five groups and TPS-b was lost according to the phylogenetic tree. <i>OsTPSs</i> in TPS-c and TPS-g were all core genes indicating these two groups were stable during domestication. In addition, through the analysis of transcriptome data, some structural variations were found to affect the expression of <i>OsTPS</i> genes. Through the Ka/Ks calculation of <i>OsTPS</i> genes, we found that different <i>OsTPS</i> genes were under different selection pressure during domestication; for example, <i>OsTPS22</i> and <i>OsTPS29</i> experienced stronger positive selection than the other <i>OsTPS</i> genes. After <i>Chilo suppressalis</i> larvae infesting, 25 differentially expressed <i>OsTPS</i> genes were identified, which are involved in the diterpene phytoalexins precursors biosynthesis and ent-kaurene biosynthesis pathways. Overall, the present study conducted a bioinformatics analysis of <i>OsTPS</i> genes using a high-quality rice pan-genome, which provided a basis for further study of <i>OsTPS</i> genes.