Comparison of the complete plastomes and the phylogenetic analysis of Paulownia species

Pingping Li,Bin Zhang,Gongli Lou,Hongwei Wang,Xiaoran Cai,Yueqin Cheng

doi:10.1038/s41598-020-59204-y

Abstract

Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. The complete chloroplast genomes of six Paulownia species were assembled by next-generation sequencing data. By adding two known Paulownia chloroplast genomes to these six assembled genomes, we performed the comparative analysis and phylogenetic tree reconstruction of Paulownia. The results indicated that the chloroplast genomes of Paulownia species ranged in size from 154,107 to 154,694 bp. These chloroplast genomes contained 117 unique functional genes, including 80 protein-coding genes, four rRNA genes, and 33 tRNA genes. Twelve hotspot regions, five protein-coding genes and seven noncoding regions, were identified in the chloroplast genomes that showed high levels of sequence variation. Additionally, positive selection was observed in three genes, rps2, rbcL and ndhG. The maximum likelihood (ML) and Bayesian (BI) analysis strongly supported the monophyletic origin of Paulownia species, which clustered into two major clades: One clade included P. coreana, P. tomentosa and P. kawakamii, while the other clade comprised the 5 other species including P. fargesii and P. australis. This study provides useful genetic information for phylogenetic reconstruction, taxonomic discrepancies, and studying species evolution and phylogeography in Paulownia.

Highlights

Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources
Paulownia is a general term for plants from the genus Paulownia, which includes a total of eight species, P. coreana, P. tomentosa, P. kawakamii, P. fargesii, P. australis, P. fortunei, P. elongata and P. catalpifolia[1,2]
The chloroplast genome lengths of six Paulownia species ranged in size from 154,107 bp for P. kawakamii to 154,694 bp for P. catalpifolia (Fig. 1 and Table 1)

Summary

Introduction

Paulownia species are important ecological, economic and ornamental species, but their phylogenetic relationship remains unclear, which seriously affects the development and utilization of these important resources. The evolution rate or genetic diversity of different regions of the chloroplast genome varies greatly, and the successful development of common primers in those high-variability regions make these loci widely used in the study of phylogenetic relationships among species; among these loci, matK and rbcL are most commonly used[16,17]. This study applied high-throughput sequencing technology to assemble chloroplast genomes of six Paulownia species to explore the following topics: The genetic diversity of the chloroplast genomes of Paulownia; the hypervariable regions of the chloroplast genomes of Paulownia; the loci in the chloroplast genome involved in adaptive selection during the evolution of Paulownia; and the phylogenetic relationships of the eight Paulownia species

Methods

Results

Conclusion