Comparative Plastid Genomes of Primula Species: Sequence Divergence and Phylogenetic Relationships

Ting Ren,Tao Zhou,Yanci Yang,Zhan-Lin Liu

doi:10.3390/ijms19041050

Abstract

Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. Primula is the largest genus in the family Primulaceae, with members distributed mainly throughout temperate and arctic areas of the Northern Hemisphere. The phylogenetic relationships among Primula taxa still maintain unresolved, mainly due to intra- and interspecific morphological variation, which was caused by frequent hybridization and introgression. In this study, we sequenced and assembled four complete plastid genomes (Primula handeliana, Primula woodwardii, Primula knuthiana, and Androsace laxa) by Illumina paired-end sequencing. A total of 10 Primula species (including 7 published plastid genomes) were analyzed to investigate the plastid genome sequence divergence and their inferences for the phylogeny of Primula. The 10 Primula plastid genomes were similar in terms of their gene content and order, GC content, and codon usage, but slightly different in the number of the repeat. Moderate sequence divergence was observed among Primula plastid genomes. Phylogenetic analysis strongly supported that Primula was monophyletic and more closely related to Androsace in the Primulaceae family. The phylogenetic relationships among the 10 Primula species showed that the placement of P. knuthiana–P. veris clade was uncertain in the phylogenetic tree. This study indicated that plastid genome data were highly effective to investigate the phylogeny.

Highlights

Primula is the largest genus in the family Primulaceae with approximately 500 species [1,2], where they are especially rich in the temperate and arctic areas of the Northern Hemisphere, with only a few outliers found in the Southern Hemisphere
The sizes of the plastid genomes of the 10 Primula species ranged from 150,856 bp to 153,757 bp, where they had a typical quadripartite structure, including a large single copy (LSC) region (82,048–84,479 bp) and a small single copy (SSC) region (17,568–17,896 bp) separated by a pair of inverted repeat (IR) regions (25,182–25,855 bp) (Table 1)
The accD gene was a pseudogene in P. sinensis, whereas it was missing in P. persimilis and P. kwangtungensis

Summary

Introduction

Primula is the largest genus in the family Primulaceae with approximately 500 species [1,2], where they are especially rich in the temperate and arctic areas of the Northern Hemisphere, with only a few outliers found in the Southern Hemisphere. Numerous molecular phylogenetic works of the genus Primula have been conducted by using plastid and/or nuclear gene fragments [12,13,14]. These studies have greatly advanced our understanding of the evolutionary history of Primula species. The phylogenetic relationships within the genus Primula are still uncertain, mainly due to intra- and interspecific morphological variation, which was caused by frequent hybridization and introgression [1,2,14]. Further research has been hindered by the insufficient information of the traditional DNA markers, such as one or few chloroplast gene fragments, and by the complex evolutionary relationships in Primula.

Methods

Results

Conclusion