Transcriptome Responses of Spirodela polyrhiza

Abstract

In order to analyze the transcriptome of any species, RNA-seq has become the gold standard and evolved into a variety of library preparations and sequencing platforms to study more than mRNA abundance. This chapter reviews the transcriptional studies of Spirodela polyrhiza, the best-characterized member of the Lemnaceae family in a genomic sense. To date, there have been three studies of its transcriptome. The first two analyzed ribosomal RNA depleted total RNA of fronds and fronds developing into turions after exposure to abscisic acid. The first study analyzed 154 down-regulated genes involved in growth and 208 upregulated genes involved in starch, anthocyanin production, and seed development. The second study found 66 sites where chloroplast mRNAs were edited to create a functional protein, supporting the hypothesis that mRNA editing was evolved once, and the conservation of editing sites was phylogenetically correlated. The third study, also performed in the 7498 ecotypes, was sequencing of the uncapped polyadenylated transcripts. While the main aim was to observe miRNA induced cleavage, differences in the post-transcriptional regulation or abundance of degraded transcripts across the eight sequencing conditions can be observed. Taken together, these studies cover mRNA expression, post-transcriptional editing, and finally degradation.