The Complete Plastid Genome of Rhododendron pulchrum and Comparative Genetic Analysis of Ericaceae Species

Jianshuang Shen,Xiaoling Huang,Xueqin Li,Xiangtao Zhu,Songheng Jin

doi:10.3390/f11020158

Jianshuang Shen, Xiaoling Huang + Show 3 more

Open Access

https://doi.org/10.3390/f11020158

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Abstract

Background and Objectives: Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Materials and Methods: In this study, the complete cp genome of R. pulchrum was sequenced with NGS Illumina HiSeq2500, analyzed, and compared to eight species in the Ericaceae family. Results: Our study reveals that the cp genome of R. pulchrum is 136,249 bp in length, with an overall GC content of 35.98% and no inverted repeat regions. The R. pulchrum chloroplast genome encodes 73 genes, including 42 protein-coding genes, 29 tRNA genes, and two rRNA genes. The synonymous (Ks) and nonsynonymous (Ka) substitution rates were estimated and the Ka/Ks ratio of R. pulchrum plastid genes were categorized; the results indicated that most of the genes have undergone purifying selection. A total of 382 forward and 259 inverted long repeats, as well as 221 simple-sequence repeat loci (SSR) were detected in the R. pulchrum cp genome. Comparison between different Ericaceae cp genomes revealed significant differences in genome size, structure, and GC content. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton. This study provides a theoretical basis for species identification and future biological research of Rhododendron resources.

Highlights

Rhododendron species belong to family Ericaceae and have been widely used as valuable horticultural and medicinal plants in China, Western Europe, the US, and Japan due to their beautiful vegetative forms and bright-colored flowers [1,2]
The overall GC content of the R. pulchrum cp genome is 35.98% (Table 1) and we identified 73 functional genes, including two rRNA genes, 29 tRNA genes, and 42 protein-coding genes (Table 2)
We found signs of purifying selection in rpl32, which is the only gene annotated in this transformation, in four heterotrophic species (Allotropa virgata, species (Allotropa virgata, Hemitomes congestum, Monotropsis odorata, and Pityopus californicus); whereas the rpl32 gene was absent from two heterotrophic species, Monotropa hypopitys and Monotropa uniflora

Summary

Introduction

Rhododendron species belong to family Ericaceae and have been widely used as valuable horticultural and medicinal plants in China, Western Europe, the US, and Japan due to their beautiful vegetative forms and bright-colored flowers [1,2]. Chloroplast genome has been widely employed for studying the transition from autotrophy to heterotrophy due to its conserved size, gene content, linear gene order, and structure. Rhododendron pulchrum Sweet (R. pulchrum) belongs to the genus Rhododendron (Ericaceae), a valuable horticultural and medicinal plant species widely used in Western Europe and the US. Despite its importance, this is the first member to have its cpGenome sequenced. Conclusions: The phylogenetic relationships among eight Ericaceae species suggested that R. pulchrum is closely related to Vaccinium oldhamii Miq. and Vaccinium macrocarpon Aiton

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Discussion

Conclusion