The complete chloroplast genome of Rhododendron ambiguum and comparative genomics of related species

By

Ma, Wenbao
Ou, Yafei
Dayananda, Buddhi
Ji, Huijuan
Yu, Tao

Type

Article

Date of Publication

2024

Original Publication

Comparative cytogenetics : international journal of plant & animal cytogenetics, karyosystematics and molecular systematics

Volume

18

Pages

143--159

Subjects

chloroplast genome , Molecular evolution , phylogenetic analysis , Rhododendron , Rhododendron ambiguum

Contributed by

Pensoft Publishers

Language

English

Published by

St. Petersburg, Russia [Published] with technical support of Zoological Institute RAS [2007]-

Identifiers

DOI: https://doi.org/10.3897/compcytogen.18.119929

 

Abstract

Rhododendron Linnaeus, 1753, the largest genus of woody plants in the Northern Hemisphere, includes some of the most significant species in horticulture. Rhododendron ambiguum Hemsl, 1911, a member of subsection Triflora Sleumer 1947, exemplifies typical alpine Rhododendron species. The analysis of the complete chloroplast genome of R. ambiguum offers new insights into the evolution of Rhododendron species and enhances the resolution of phylogenetic relationships. This genome is composed of 207,478 base pairs, including a pair of inverted repeats (IRs) of 47,249 bp each, separated by a large single-copy (LSC) region of 110,367 bp and a small single-copy (SSC) region of 2,613 bp. It contains 110 genes: 77 protein-coding genes, 29 tRNAs, four unique rRNAs (4.5S, 5S, 16S, and 23S), with 16 genes duplicated in the IRs. Comparative analyses reveal substantial diversity in the Rhododendron chloroplast genome structures, identifying a fourth variant pattern. Specifically, four highly divergent regions (trnI-rpoB, ndhE-psaC, rpl32-ndhF, rrn16S-trnI) were noted in the intergenic spacers. Additionally, 76 simple sequence repeats were identified. Positive selection signals were detected in four genes (cemA, rps4, rpl16, and rpl14), evidenced by high Ka/Ks ratios. Phylogenetic reconstruction based on two datasets (shared protein-coding genes and complete chloroplast genomes) suggests that R. ambiguum is closely related to R. concinnum Hemsley, 1889. However, the phylogenetic positions of subsection Triflora Pojarkova, 1952 species remain unresolved, indicating that the use of complete chloroplast genomes for phylogenetic research in Rhododendron requires careful consideration. Overall, our findings provide valuable genetic information that will enhance understanding of the evolution, molecular biology, and genetic improvement of Rhododendron spieces.