Qing Du1,2,3, Mei Jiang1,4, Sihui Sun5, Liqiang Wang6, Shengyu Liu7, Chuanbei Jiang8, Haidong Gao8, Haimei Chen1, Yong Li5, Bin Wang9, Chang Liu10. 1. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China. 2. College of Pharmacy, Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau, Qinghai Minzu University, Xining, Qinghai, 810007, People's Republic of China. 3. Fresh Sky-Right (Beijing) International Science and Technology Co. Ltd, Beijing, 100187, People's Republic of China. 4. School of Pharmaceutical Sciences, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, People's Republic of China. 5. College of Pharmacy, Xiangnan University, Chenzhou, Hunan, 423000, People's Republic of China. 6. College of Pharmacy, Heze University, Heze, Shandong, 274015, People's Republic of China. 7. Institute of Medical Information & Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, People's Republic of China. 8. Genepioneer Biotechnologies Inc., Nanjing, Jiangsu, 210023, People's Republic of China. 9. College of Pharmacy, Xiangnan University, Chenzhou, Hunan, 423000, People's Republic of China. beinwang@126.com. 10. Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China. cliu6688@yahoo.com.
Abstract
BACKGROUND: Clerodendranthus spicatus (Thunb.) C. Y. Wu ex H. W. Li is one of the most important medicines for the treatment of nephrology in the southeast regions of China. To understand the taxonomic classification of Clerodendranthus species and identify species discrimination markers, we sequenced and characterized its chloroplast genome in the current study. METHODS AND RESULTS: Total genomic DNA were isolated from dried leaves of C. spicatus and sequenced using an Illumina sequencing platform. The data were assembled and annotated by the NOVOPlasty software and CpGAVAS2 web service. The complete chloroplast genome of C. spicatus was 152,155 bp, including a large single-copy region of 83,098 bp, a small single-copy region of 17,665 bp, and a pair of inverted repeat regions of 25,696 bp. The Isoleucine codons are the most abundant, accounting for 4.17% of all codons. The codons of AUG, UUA, and AGA demonstrated a high degree of usage bias. Twenty-eight simple sequence repeats, thirty-six tandem repeats, and forty interspersed repeats were identified. The distribution of the specific rps19, ycf1, rpl2, trnH, psbA genes were analyzed. Analysis of the genetic distance of the intergenic spacer regions shows that ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD regions have high K2p values. Phylogenetic analysis showed that C. spicatu is closely related to two Lamiaceae species, Tectona grandis, and Glechoma longituba. CONCLUSIONS: In this study, we sequenced and characterized the chloroplast genome of C. spicatus. Phylogenomic analysis has identified species closely related to C. spicatus, which represent potential candidates for the development of drugs improving renal functions.
BACKGROUND: Clerodendranthus spicatus (Thunb.) C. Y. Wu ex H. W. Li is one of the most important medicines for the treatment of nephrology in the southeast regions of China. To understand the taxonomic classification of Clerodendranthus species and identify species discrimination markers, we sequenced and characterized its chloroplast genome in the current study. METHODS AND RESULTS: Total genomic DNA were isolated from dried leaves of C. spicatus and sequenced using an Illumina sequencing platform. The data were assembled and annotated by the NOVOPlasty software and CpGAVAS2 web service. The complete chloroplast genome of C. spicatus was 152,155 bp, including a large single-copy region of 83,098 bp, a small single-copy region of 17,665 bp, and a pair of inverted repeat regions of 25,696 bp. The Isoleucine codons are the most abundant, accounting for 4.17% of all codons. The codons of AUG, UUA, and AGA demonstrated a high degree of usage bias. Twenty-eight simple sequence repeats, thirty-six tandem repeats, and forty interspersed repeats were identified. The distribution of the specific rps19, ycf1, rpl2, trnH, psbA genes were analyzed. Analysis of the genetic distance of the intergenic spacer regions shows that ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD regions have high K2p values. Phylogenetic analysis showed that C. spicatu is closely related to two Lamiaceae species, Tectona grandis, and Glechoma longituba. CONCLUSIONS: In this study, we sequenced and characterized the chloroplast genome of C. spicatus. Phylogenomic analysis has identified species closely related to C. spicatus, which represent potential candidates for the development of drugs improving renal functions.
Authors: Catherine J Nock; Daniel L E Waters; Mark A Edwards; Stirling G Bowen; Nicole Rice; Giovanni M Cordeiro; Robert J Henry Journal: Plant Biotechnol J Date: 2010-08-27 Impact factor: 9.803
Authors: Richard Cronn; Aaron Liston; Matthew Parks; David S Gernandt; Rongkun Shen; Todd Mockler Journal: Nucleic Acids Res Date: 2008-08-27 Impact factor: 16.971