Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae)

• Published in: Molecular phylogenetics and evolution Vol. 127; pp. 978 - 987
• Main Authors: Ye, Wen-Qing, Yap, Zhao-Yan, Li, Pan, Comes, Hans Peter, Qiu, Ying-Xiong
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.10.2018
• Subjects: Adaptive evolution; Genome structure; Phylogeny; Plastome; Podophylloideae; Adaptive evolution; Plastome; Genome structure; Podophylloideae; Phylogeny
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2018.07.001

[Display omitted] •15 new plastome sequences are presented, including all species of Podophylloideae and Achlys triphylla.•Phylogenomic analyses provide improved phylogenetic resolution of Podophylloideae.•matK is the fastest evolving gene under positive selection in Podophylloideae.•We identify variable regions in Podophylloideae and Ranunculales plastomes. Species of Podophylloideae (Berberidaceae, Ranunculales) are of great pharmacogenetic importance and represent the classic biogeographic disjunction between eastern Asia (EA; 10 ssp.) and eastern North America (ENA; 2 ssp.). However, previous molecular studies of this group suffered from low phylogenetic resolution and/or insufficient marker variability. This study is the first to report whole-plastome sequence data for all 12 species of Podophylloideae (14 individuals) and a close relative, Achlys triphylla. These 15 plastomes proved highly similar in overall size (156,240–157,370 bp), structure, gene order and content, also when compared to other Ranunculales, but also revealed some structural variations caused by the expansion or contraction of the inverted repeats (IRs) into or out of adjacent single-copy regions. Our phylogenomic analysis, based on 63 plastome-derived protein-coding genes (CDS), supported the monophyly of Podophylloideae and its two major genera (EA: Dysosma, EA/ENA: Diphylleia), with Podophyllum peltatum L. (ENA) being more closely related to Diphylleia than to the group’s earliest diverging species, Sinopodophyllum hexandrum (EA). Furthermore, within this subfamily/dataset, matK was identified as the fastest evolving gene, which proved to be under positive selection especially in more recently derived, lower-elevation lineages of Dysosma, possibly reflecting an adaptive response to novel environmental (i.e. subtropical compared to higher-elevation/alpine) conditions. Finally, several highly variable noncoding regions were identified in the plastomes of Podophylloideae and Ranunculales. These highly variable loci should be the best choices for future phylogenetic, phylogeographic, and population-level genetic studies. Overall, our results demonstrate the power of plastid phylogenomics to improve phylogenetic resolution, and contribute to a better understanding of plastid gene evolution in Podophylloideae.