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

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.

Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea

“…In general, previous studies showed that Ka/Ks values are usually less than one [ 68 ], because synonymous nucleotide substitutions occur more frequently than nonsynonymous substitutions. Additionally, most genes of the chloroplast genome evolved under purifying selection due to functional limitation during chloroplast genome evolution [ 69 , 70 , 71 , 72 ]. Furthermore, both the positive selection of the rbcL gene and the NADH dehydrogenase subunit genes were previously reported in several studies, which is related to temperature, drought, carbon dioxide concentration, and photosynthetic rate [ 71 , 72 , 73 , 74 ].…”

“…Additionally, most genes of the chloroplast genome evolved under purifying selection due to functional limitation during chloroplast genome evolution [ 69 , 70 , 71 , 72 ]. Furthermore, both the positive selection of the rbcL gene and the NADH dehydrogenase subunit genes were previously reported in several studies, which is related to temperature, drought, carbon dioxide concentration, and photosynthetic rate [ 71 , 72 , 73 , 74 ]. Positive selection is considered to be indicative of an adaptation to environmental change, ecological niche, or coevolutionary processes [ 73 , 75 ], and we can, thus, speculate that the selection patterns detected for the Rosaceae endemic taxa on Ulleung Island may be associated with adaptation to an oceanic climate in the insular setting.…”

Plastome Characterization and Phylogenomic Analysis Yield New Insights into the Evolutionary Relationships among the Species of the Subgenus Bryocles (Hosta; Asparagaceae) in East Asia

“…Most plastome genes evolved under purifying selection due to functional constraints throughout the chloroplast genome evolution [ 48 , 49 , 50 , 51 ]. In 12 plastomes of the genus Hosta , we found that all but five genes (70 out of 75 genes) were under strong purifying selection with an average Ka/Ks ratio of <1.…”

Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea

“…Most genes of the plastome evolve under purifying selection due to functional limitations during the course of evolution [ 65 , 66 , 67 , 68 ]. In the five Fagus plastomes studied, nearly 7.8% of protein-coding genes, including two photosynthesis-related genes encoding NADH-dehydrogenase subunits ( ndhD and ndhJ ), two genes encoding DNA-dependent RNA polymerase ( rpoB and rpoC2 ), one self-replication-related gene encoding the ribosomal small subunit ( rps16 ), and two unknown genes ( ycf1 and ycf2 ), were under positive selection pressure.…”