Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume

Emmanuel Nyongesa Waswa; Elijah Mbandi Mkala; Wyclif Ochieng Odago; Sara Getachew Amenu; Elizabeth Syowai Mutinda; Samuel Wamburu Muthui; Shi-Xiong Ding; Guang-Wan Hu; Qing-Feng Wang

doi:10.3389/fpls.2023.1179510

Comparative chloroplast genome analysis of Sambucus L. (Viburnaceae): inference for phylogenetic relationships among the closely related Sambucus adnata Wall. ex DC Sambucus javanica Blume

Front Plant Sci. 2023 Jun 16:14:1179510. doi: 10.3389/fpls.2023.1179510. eCollection 2023.

Authors

Emmanuel Nyongesa Waswa^{1

2

3}, Elijah Mbandi Mkala^{1

2

3}, Wyclif Ochieng Odago^{1

2

3}, Sara Getachew Amenu^{1

2

3}, Elizabeth Syowai Mutinda^{1

2

3}, Samuel Wamburu Muthui^{1

2

3}, Shi-Xiong Ding^{1

2

3}, Guang-Wan Hu^{1

2

3}, Qing-Feng Wang^{1

2

3}

Affiliations

¹ Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
² Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
³ Botany Department, University of Chinese Academy of Sciences, Beijing, China.

Abstract

Sambucus L. is found in the family Viburnaceae (syn. Adoxaceae) and encompasses approximately 29 accepted species. The complex morphology of these species has caused continued confusion concerning their nomenclature, classification, and identification. Despite previous attempts to resolve taxonomic complexities in the Sambucus genus, there are still unclear phylogenetic relationships among several species. In this study, the newly obtained plastome of Sambucus williamsii Hance. as well as the populations of Sambucus canadensis L., Sambucus javanica Blume, and Sambucus adnata Wall. ex DC were sequenced, and their sizes, structural similarity, gene order, gene number, and guanine-cytosine (GC) contents were analyzed. The phylogenetic analyses were conducted using the whole chloroplast genomes and protein-coding genes (PCGs). The findings revealed that the chloroplast genomes of Sambucus species exhibited typical quadripartite double-stranded DNA molecules. Their lengths ranged from 158,012 base pairs (bp) (S. javanica) to 158,716 bp (S. canadensis L). Each genome comprised a pair of inverted repeats (IRs), which separated the large single-copy (LSC) and small single-copy (SSC) regions. In addition, the plastomes contained 132 genes, encompassing 87 protein-coding, 37 tRNA, and four rRNA genes. In the simple sequence repeat (SSR) analysis, A/T mononucleotides had the highest proportion, with the most repetitive sequences observed in S. williamsii. The comparative genome analyses showed high similarities in structure, order, and gene contents. The hypervariable regions in the studied chloroplast genomes were trnT-GGU, trnF-GAA, psaJ, trnL-UAG, ndhF, and ndhE, which may be used as candidate barcodes for species discrimination in Sambucus genus. Phylogenetic analyses supported the monophyly of Sambucus and revealed the separation of S. javanica and S. adnata populations. Sambucus chinensis Lindl. was nested within S. javanica in the same clade, collaborating their conspecific treatment. These outcomes indicate that the chloroplast genome of Sambucus plants is a valuable genetic resource for resolving taxonomic discrepancies at the lower taxonomic levels and can be applied in molecular evolutionary studies.

Keywords: Sambucus; Viburnaceae; chloroplast; genomes; phylogeny; taxonomy.

Grants and funding

This work was supported by grants from the National Natural Science Foundation of China (31961143026, 31970211), National Science and Technology Fundamental Resources Investigation Program of China (2019FY101800), International Partnership Program of Chinese Academy of Sciences (151853KYSB20190027), and Sino-Africa Joint Research Center, CAS (SAJC202101).