The implication of plastid transcriptome analysis in petaloid monocotyledons: A case study of Lilium lancifolium (Liliaceae, Liliales)

Hoang Dang Khoa Do,Joo-Hwan Kim

doi:10.1038/s41598-019-43259-7

Abstract

Transcriptome data provide useful information for studying the evolutionary history of angiosperms. Previously, different genomic events (i.e., duplication, deletion, and pseudogenization) were discovered in the plastid genome of Liliales; however, the effects of these events have not addressed because of the lack of transcriptome data. In this study, we completed the plastid genome (cpDNA) and generated transcriptome data of Lilium lancifolium. Consequently, the cpDNA of L. lancifolium is 152,479 bp in length, which consists of one large single copy (81,888 bp), one small single copy (17,607 bp), and two inverted repeat regions (26,544 bp). The comparative genomic analysis of newly sequenced cpDNA and transcriptome data revealed 90 RNA editing sites of which two positions are located in the rRNA coding region of L. lancifolium. A further check on the secondary structure of rRNA showed that RNA editing causes notable structural changes. Most of the RNA editing contents are C-to-U conversions, which result in nonsynonymous substitutions. Among coding regions, ndh genes have the highest number of RNA editing sites. Our study provided the first profiling of plastid transcriptome analyses in Liliales and fundamental information for further studies on post-transcription in this order as well as other petaloid monocotyledonous species.

Highlights

In the genomic era, besides the nuclear, mitochondrial, and plastid genomes, transcriptome data provide useful information for exploring the evolutionary history of angiosperms
In comparison with the previously completed cpDNA of L. lancifolium from China and Korea, of which the length of cpDNA is identical (152,574 bp), the gene contents and orders are similar among the three individuals
The translation initiation factor IF-1 gene was not annotated in previous data, but it was predicted as a pseudogene in this study because of the presence of internal stop codons within the coding region

Summary

Introduction

Besides the nuclear, mitochondrial, and plastid genomes, transcriptome data provide useful information for exploring the evolutionary history of angiosperms. Different transcriptome studies of model plants by applying next-generation sequencing method (NGS) were reported, including Arabidopsis thaliana, rice, sugarcane, and so on[1,2,3,4,5]. These data added a deeper understanding of the gene expression and biological mechanisms that allow plants to survive and adapt to the environment. The effect of RNA editing on the metabolism of plants was reported[12] These studies suggested the necessity of transcriptome data in studying the evolution in angiosperms. We check the effect of RNA editing site on the secondary structure of rRNA

Methods

Results

Conclusion