Complete chloroplast genome sequence of Rhododendron mariesii and comparative genomics of related species in the family Ericaeae

• Published in: Comparative cytogenetics Vol. 17; no. 1; pp. 163 - 180
• Main Authors: Li, Zhiliang, Huang, Zhiwei, Wan, Xuchun, Yu, Jiaojun, Dong, Hongjin, Zhang, Jialiang, Zhang, Chunyu, Wang, Shuzhen
• Format: Journal Article
• Language: English
• Published: Sofia Pensoft Publishers 18-08-2023
• Subjects: Amino acids; Angiosperms; Chloroplasts; Codons; Genes; Genetic aspects; Genomes; Genomics; Inverted repeat; Leucine; Nucleotide sequence; Phylogenetics; Phylogeny; Rhododendron; RpoB protein; rRNA; tRNA
• ISSN: 1993-0771; 1993-078X
• DOI: 10.3897/compcytogen.17.101427

Rhododendron mariesii
Hemsley et Wilson, 1907, a typical member of the family Ericaeae, possesses valuable medicinal and horticultural properties. In this research, the complete chloroplast (cp) genome of
R. mariesii
was sequenced and assembled, which proved to be a typical quadripartite structure with the length of 203,480 bp. In particular, the lengths of the large single copy region (LSC), small single copy region (SSC), and inverted repeat regions (IR) were 113,715 bp, 7,953 bp, and 40,918 bp, respectively. Among the 151 unique genes, 98 were protein-coding genes, 8 were tRNA genes, and 45 were rRNA genes. The structural characteristics of the
R. mariesii
cp genome was similar to other angiosperms. Leucine was the most representative amino acid, while cysteine was the lowest representative. Totally, 30 codons showed obvious codon usage bias, and most were A/U-ending codons. Six highly variable regions were observed, such as
trnK-pafI
and
atpE-rpoB
, which could serve as potential markers for future barcoding and phylogenetic research of
R. mariesii
species. Coding regions were more conserved than non-coding regions. Expansion and contraction in the IR region might be the main length variation in
R. mariesii
and related Ericaeae species. Maximum-likelihood (ML) phylogenetic analysis revealed that
R. mariesii
was relatively closed to the
R. simsii
Planchon, 1853 and
R. pulchrum
Sweet,1831. This research will supply rich genetic resource for
R. mariesii
and related species of the Ericaeae.