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

Abstract

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. mariesiicp 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.

Comparative Study on Codon Usage Patterns across Chloroplast Genomes of Eighteen Taraxacum Species

“…Additionally, the negative correlation between CAI and axis 1, and between ENc and axis 2 in T. xinyuanicum, further demonstrates the dual inhibition of codon adaptation and diversity. On the other hand, in T. amplum, T. mongolicum, T. multiscaposum, T. officinale, T. parvulum, and T. xinyuanicum, the positive correlation between ENc and GC3s with axis 1 reveals a positive relationship between GC content at the third codon position and the number of effective codons, potentially enhancing gene expression efficiency to better meet though this relationship has not been conclusively proven [25][26][27]. Further research should explore how environmental conditions could influence changes in codon usage preferences and their impact on plant survival.…”