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

Abstract

Compared to traditional DNA markers, genome-scale datasets can provide mass information to effectively address historically difficult phylogenies. <i>Primula</i> 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 <i>Primula</i> 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 (<i>Primula handeliana</i>, <i>Primula woodwardii</i>, <i>Primula knuthiana</i>, and <i>Androsace laxa</i>) by Illumina paired-end sequencing. A total of 10 <i>Primula</i> species (including 7 published plastid genomes) were analyzed to investigate the plastid genome sequence divergence and their inferences for the phylogeny of <i>Primula</i>. The 10 <i>Primula</i> 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 <i>Primula</i> plastid genomes. Phylogenetic analysis strongly supported that <i>Primula</i> was monophyletic and more closely related to <i>Androsace</i> in the Primulaceae family. The phylogenetic relationships among the 10 <i>Primula</i> species showed that the placement of <i>P. knuthiana-P. veris</i> clade was uncertain in the phylogenetic tree. This study indicated that plastid genome data were highly effective to investigate the phylogeny.