The complete chloroplast genome sequence of Malus sieboldii (Rosaceae) and its phylogenetic analysis.

Malus sieboldii belongs to the genus Malus (Rosaceae) and is commonly considered a good rootstock for apple trees. The chloroplast (cp) genome of M. sieboldii was assembled using Illumina HiSeq sequencing. The whole cp genome is 160,168 bp in size, with a typical quadripartite structure consisting of a pair of inverted repeats (IR 52,716 bp), a large single-copy region (LSC 88,267 bp), and a small single-copy region (SSC 19,185 bp). The plastid genome contains 129 genes, 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Bayesian phylogenetic analysis showed that M. sieboldii is most closely related to M. hupehensis. The cp genome will provide more information about the taxonomy and cp evolution of the genus Malus.

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

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.