Comparative Analysis of Complete Chloroplast Genomes of 13 Species in Epilobium, Circaea, and Chamaenerion and Insights Into Phylogenetic Relationships of Onagraceae.

Yike Luo,Jin Cheng,Min Yao,Jian He,Lei Xie,Wenhe Li,Jiamin Xiao,Rudan Lyu,Jinyu Li,Linying Pei

doi:10.3389/fgene.2021.730495

Abstract

The evening primrose family, Onagraceae, is a well defined family of the order Myrtales, comprising 22 genera widely distributed from boreal to tropical areas. In this study, we report and characterize the complete chloroplast genome sequences of 13 species in Circaea, Chamaenerion, and Epilobium using a next-generation sequencing method. We also retrieved chloroplast sequences from two other Onagraceae genera to characterize the chloroplast genome of the family. The complete chloroplast genomes of Onagraceae encoded an identical set of 112 genes (with exclusion of duplication), including 78 protein-coding genes, 30 transfer RNAs, and four ribosomal RNAs. The chloroplast genomes are basically conserved in gene arrangement across the family. However, a large segment of inversion was detected in the large single copy region of all the samples of Oenothera subsect. Oenothera. Two kinds of inverted repeat (IR) region expansion were found in Oenothera, Chamaenerion, and Epilobium samples. We also compared chloroplast genomes across the Onagraceae samples in some features, including nucleotide content, codon usage, RNA editing sites, and simple sequence repeats (SSRs). Phylogeny was inferred by the chloroplast genome data using maximum-likelihood (ML) and Bayesian inference methods. The generic relationship of Onagraceae was well resolved by the complete chloroplast genome sequences, showing potential value in inferring phylogeny within the family. Phylogenetic relationship in Oenothera was better resolved than other densely sampled genera, such as Circaea and Epilobium. Chloroplast genomes of Oenothera subsect. Oenothera, which are biparental inheritated, share a syndrome of characteristics that deviate from primitive pattern of the family, including slightly expanded inverted repeat region, intron loss in clpP, and presence of the inversion.

Highlights

Chloroplast is one of the most important organelles in plant cells and play vital metabolic roles in photosynthesis as well as amino acid and lipid synthesis (Daniell et al, 2016)
The chloroplast genome of angiosperms often shows a stable quadripartite ring structure containing one large single copy (LSC) region and one small single copy (SSC) region separated by two copies of an inverted repeat (IR) region
We report the complete chloroplast genomes from three genera (Circaea, Chamaenerion Ség.1, and Epilobium) of Onagraceae, among which those of the Circaea are reported for the first time

Summary

Introduction

Chloroplast is one of the most important organelles in plant cells and play vital metabolic roles in photosynthesis as well as amino acid and lipid synthesis (Daniell et al, 2016). The chloroplast genome of angiosperms often shows a stable quadripartite ring structure containing one large single copy (LSC) region and one small single copy (SSC) region separated by two copies of an inverted repeat (IR) region. It usually shows uniparental inheritance (Ravi et al, 2008), and its sequence, gene number, and gene order have been considered to be very conserved (Wolfe et al, 1987). The use of complete chloroplast genome data for phylogenetic inference has greatly deepened our insight into the evolution of plants at a wide range of taxonomic levels (Park et al, 2017; Wen et al, 2018; Li et al, 2019; Valcárcel and Wen, 2019; Wang L. et al, 2020; Brandrud et al, 2020)

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Conclusion