Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.
The complete chloroplast (cp) genome ofLonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of theL. japonicacp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, theL. japonicacp genome had a unique rearrangement between trnI-CAU and trnN-GUU. InL. japonicacpDNA,rps19,rpl2, andrpl23move to the LSC region, from the IR region. Theycf1pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses ofL. japonicawith other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns inycf2andrps18genes are found for the first time. Four genes (clpP,petB,petD, andrpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea thatL. japonicais a sister of the Araliaceae species. This study identified unique characteristics of theL. japonicacp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. lhe@implad.ac.cn.
Liu
L
He
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. jqian@implad.ac.cn.
Jun
J
Qian
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. xwli@icmm.ac.cn.|Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China. xwli@icmm.ac.cn.
Xiwen
X
Li
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. zysun@implad.ac.cn.
Zhiying
Z
Sun
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. xlxu@implad.ac.cn.
Xiaolan
X
Xu
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China. slchen@icmm.ac.cn.|Institute of Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China. slchen@icmm.ac.cn.
Shilin
S
Chen
D001482:Base Composition; D018742:DNA, Chloroplast / Q000235:genetics*; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D054628:Genome, Chloroplast; D007438:Introns; D031239:Lonicera / Q000235:genetics*; D010802:Phylogeny; D010946:Plants, Medicinal / Q000235:genetics; D017422:Sequence Analysis, DNA
D018742:DNA, Chloroplast
Lonicera japonica; chloroplast genome; contraction