http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1060441
MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of medicinal plant Pinellia ternata Limin Han1,2*, Chen Chen1*, Bin Wang1,3, and Zhe-Zhi Wang1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/14/15 For personal use only.
National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi’an, PR China, 2Department of Bioscience and Biotechnology, Shaanxi Xueqian Normal University, Xi’an, PR China, and 3Colleage of Chemistry, Biology and Materias Science, East China Institute of Technology, NanChang, PR China Abstract
Keywords
Pinellia ternata is an important medicinal plant used in the treatment of cough, to dispel phlegm, to calm vomiting and to terminate early pregnancy, as an anti-ulcer and anti-tumor medicine. In this study, we found that the complete chloroplast genome of Pinellia ternata was 164 013 bp in length, containing a pair of inverted repeats of 25 625 bp separated by a large single-copy region and a small single-copy region of 89 783 bp and 22 980 bp, respectively. The chloroplast genome encodes 132 predicted functional genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The chloroplast DNA is GC-rich (36.7%). The phylogenetic analysis showed a strong sister relationship with Colocasia esculenta, which also strongly supports the position of Pinellia ternata. The complete chloroplast genome sequence of Pinellia ternata reported here has the potential to advance population and phylogenetic studies of this medicinal plant.
Chloroplast genome, medicinal plant, Pinellia ternata
Chloroplast genomes are useful for molecular plant breeding, DNA barcoding, population, phylogenetic and trans-plastomics (Bock & Khan, 2004; Liu et al., 2012; Pan et al., 2012). So far, the complete chloroplast genomes about many medicinal plants such as Salvia miltiorrhiza, Clematis terniflora, and Anoectochilus roxburghii (Li et al., 2015; Qian et al., 2013; Yu et al., 2015) have been reported. Pinellia ternata used in traditional Chinese medicine to treat cough, dispel phlegm, and terminate early pregnancy (Chen et al., 2003; Kim et al., 2006; Lu et al., 2013). In this study, we assembled the complete chloroplast genome P. ternata and analyzed its phylogenetic evolution, which will be help for identification, utilization, and protection of pinellia germplasm resources. Total genome DNA was extracted from leaves of P. ternata and used for the shotgun library construction according to the manufacturer’s manual for the Illumina Hiseq 2500 Sequencing System (Illumina, Hayward, CA). The whole-genome sequencing was conducted by Shanghai Genesky Biotechnologies Inc. (Shanghai, China). Using CLC Genomics Workbench v8.0 (CLC Bio, Aarhus, Denmark), the resultant 25.09 M reads were trimmed and then used for the chloroplast genome reconstruction by the program MITObim v1.8 (University of Oslo, Oslo, Norway; Kaiseraugst, Switzerland) (Hahn et al., 2013), with Colocasia esculenta chloroplast genome sequence as reference genome. The chloroplast genome of P. ternata was annotated in Geneious 8.0 (Kearse et al., 2012) and submitted to GenBank with the accession number of KR270823.
History Received 20 May 2015 Revised 31 May 2015 Accepted 6 June 2015 Published online 8 July 2015
The complete chloroplast genome sequence of P. ternata is 164 013 bp in length. It has a large single copy (LSC) region of 89 783 bp and a small single copy (SSC) region of 22 980 bp, is separated by a pair of inverted repeats (IRa and IRb) of 25 625 bp. The GC content of the whole chloroplast genome is 36.7% with the IR regions having a higher GC content (42.5%) than the LSC (34.6%) and the SSC (31.7%) region. The gene-coding regions account for 68.4% of the genome length including 132 genes, composed of 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. About 61 protein-coding genes and 22 tRNA genes are located in the LSC region, while only one tRNA gene and 12 protein-coding genes are located in the SSC region. Seven protein-coding genes, four rRNA genes, and seven tRNA genes are located in the IR regions. Among the identified genes, nine different genes (atpF, ndhA, petD, rpl2, rpl16, rpoC1, rps12, rps16, and ycf68) contain a single intron, and two genes (clpP and ycf3) contain two introns. Sequences of the complete chloroplast genome were used to infer phylogenetic relationships, for which the chloroplast genomes are available from NCBI database, including Liliaceae, Arecaceae, Lemnaceae, Araceae, and Brassicaceae. A neighborjoining analysis was performed with Mega 6.0 (MEGA Inc., Englewood, NJ) (Tamura et al., 2013) using 500 bootstrap replicates. The position of P. ternata was situated as the sister of Colocasia esculenta in the Asteraceae (Figure 1). The characterized chloroplast genome sequence of P. ternata will be helpful for further study on exploration of molecular
*These authors contributed equally to this work. Correspondence: Zhe-Zhi Wang, College of Life Sciences, Shaanxi Normal University, No. 620, Western Chang’an Street, Chang’an District, Xi’an, Shaanxi 710119, P. R. China. Tel: +86 29 85310260. Fax: +86 29 85310623. E-mail: [email protected]
2
L. Han et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/14/15 For personal use only.
Figure 1. The NJ phylogenetic tree of Pinellia ternata and other species based on the complete chloroplast genomes. Numbers above each node were bootstrap support values. Lobularia maritima, Raphanus sativus, and Brassica napus were set as the outgroup. Genebank accession numbers for each plant are as follows: Fritillaria taipaiensis (NC_023247), Fritillaria cirrhosa (NC_024728), Fritillaria hupehensis (KF712486), Lilium longiflorum (KC968977), Cocos nucifera (KF285453), Phoenix dactylifera (GU811709), Elaeis guineensis (JF274081), Spirodela polyrhiza (NC_01589), Lemna minor (NC_010109), Pinellia ternata (KR270823), Colocasia esculenta (NC_016753), Lobularia maritima (NC_009274), Raphanus sativus (NC_024469), and Brassica napus (NC_016734).
markers, genetic diversity, molecular breeding, and genetic engineering.
Declaration of interest The authors declare that there is no conflict of interest regarding the publication of this article. The authors alone are responsible for the content and writing of the paper. The authors were financially supported by Scientific and Technological Research and Development Projects of Tech&Science Department of Shaanxi Provincial Government (2012K19-02-04), Natural Science Foundation of Education Department of Shaanxi Provincial Government (14JK1178), Innovation Funds of Graduate Programs, Shaanxi Normal University (CXS20120048), and the ‘‘Foundation for Excellent Doctoral Degree Dissertation’’ of Shaanxi Normal University (X2012YB01), Shaanxi, PR China.
References Bock R, Khan MS. (2004). Taming plastids for a green future. Trends Biotechnol 6:311–18. Chen JH, Cui GY, Liu JY, Tan RX. (2003). Pinelloside, an antimicrobial cerebroside from Pinellia ternata. Phytochemistry 4:903–6. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucleic Acids Res 41: e129. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, et al. (2012). Geneious Basic: An integrated and extendable
desktop software platform for the organization and analysis of sequence data. Bioinformatics 12:1647–9. Kim YJ, Shin YO, Ha YW, Lee S, Oh JK, Kim YS. (2006). Anti-obesity effect of Pinellia ternata extract in Zucker rats. Biol Pharm Bull 6: 1278–81. Li M, Yang B, Chen Q, Zhu W, Ma J, Tian J. (2015). The complete chloroplast genome sequence of Clematis terniflora DC. (Ranunculaceae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2015.1033702. Liu Z, Zeng X, Yang D, Chu G, Yuan Z, Chen S. (2012). Applying DNA barcodes for identification of plant species in the family Araliaceae. Gene 1:76–80. Lu H, Xue T, Zhang A, Sheng W, Zhu Y, Chang L, Song Y, Xue J. (2013). Construction of an SSH library of Pinellia ternata under heat stress, and expression analysis of four transcripts. Plant Mol Biol Rep 1: 185–94. Pan IC, Liao DC, Wu FH, Daniell H, Singh ND, Chang C, Shih MC, et al. (2012). Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding. PLoS One 4:e34738. Qian J, Song J, Gao H, Zhu Y, Xu J, Pang X, Yao H, et al. (2013). The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One 2:e57607. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 12:2725–9. Yu CW, Lian Q, Wu KC, Yu SH, Xie LY, Wu ZJ. (2015). The complete chloroplast genome sequence of Anoectochilus roxburghii. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2015.1033706.
MITOGENOME ANNOUNCEMENT
The complete chloroplast genome sequence of medicinal plant Pinellia ternata Limin Han1,2*, Chen Chen1*, Bin Wang1,3, and Zhe-Zhi Wang1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/14/15 For personal use only.
National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi’an, PR China, 2Department of Bioscience and Biotechnology, Shaanxi Xueqian Normal University, Xi’an, PR China, and 3Colleage of Chemistry, Biology and Materias Science, East China Institute of Technology, NanChang, PR China Abstract
Keywords
Pinellia ternata is an important medicinal plant used in the treatment of cough, to dispel phlegm, to calm vomiting and to terminate early pregnancy, as an anti-ulcer and anti-tumor medicine. In this study, we found that the complete chloroplast genome of Pinellia ternata was 164 013 bp in length, containing a pair of inverted repeats of 25 625 bp separated by a large single-copy region and a small single-copy region of 89 783 bp and 22 980 bp, respectively. The chloroplast genome encodes 132 predicted functional genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The chloroplast DNA is GC-rich (36.7%). The phylogenetic analysis showed a strong sister relationship with Colocasia esculenta, which also strongly supports the position of Pinellia ternata. The complete chloroplast genome sequence of Pinellia ternata reported here has the potential to advance population and phylogenetic studies of this medicinal plant.
Chloroplast genome, medicinal plant, Pinellia ternata
Chloroplast genomes are useful for molecular plant breeding, DNA barcoding, population, phylogenetic and trans-plastomics (Bock & Khan, 2004; Liu et al., 2012; Pan et al., 2012). So far, the complete chloroplast genomes about many medicinal plants such as Salvia miltiorrhiza, Clematis terniflora, and Anoectochilus roxburghii (Li et al., 2015; Qian et al., 2013; Yu et al., 2015) have been reported. Pinellia ternata used in traditional Chinese medicine to treat cough, dispel phlegm, and terminate early pregnancy (Chen et al., 2003; Kim et al., 2006; Lu et al., 2013). In this study, we assembled the complete chloroplast genome P. ternata and analyzed its phylogenetic evolution, which will be help for identification, utilization, and protection of pinellia germplasm resources. Total genome DNA was extracted from leaves of P. ternata and used for the shotgun library construction according to the manufacturer’s manual for the Illumina Hiseq 2500 Sequencing System (Illumina, Hayward, CA). The whole-genome sequencing was conducted by Shanghai Genesky Biotechnologies Inc. (Shanghai, China). Using CLC Genomics Workbench v8.0 (CLC Bio, Aarhus, Denmark), the resultant 25.09 M reads were trimmed and then used for the chloroplast genome reconstruction by the program MITObim v1.8 (University of Oslo, Oslo, Norway; Kaiseraugst, Switzerland) (Hahn et al., 2013), with Colocasia esculenta chloroplast genome sequence as reference genome. The chloroplast genome of P. ternata was annotated in Geneious 8.0 (Kearse et al., 2012) and submitted to GenBank with the accession number of KR270823.
History Received 20 May 2015 Revised 31 May 2015 Accepted 6 June 2015 Published online 8 July 2015
The complete chloroplast genome sequence of P. ternata is 164 013 bp in length. It has a large single copy (LSC) region of 89 783 bp and a small single copy (SSC) region of 22 980 bp, is separated by a pair of inverted repeats (IRa and IRb) of 25 625 bp. The GC content of the whole chloroplast genome is 36.7% with the IR regions having a higher GC content (42.5%) than the LSC (34.6%) and the SSC (31.7%) region. The gene-coding regions account for 68.4% of the genome length including 132 genes, composed of 87 protein-coding genes, 37 tRNA genes and eight rRNA genes. About 61 protein-coding genes and 22 tRNA genes are located in the LSC region, while only one tRNA gene and 12 protein-coding genes are located in the SSC region. Seven protein-coding genes, four rRNA genes, and seven tRNA genes are located in the IR regions. Among the identified genes, nine different genes (atpF, ndhA, petD, rpl2, rpl16, rpoC1, rps12, rps16, and ycf68) contain a single intron, and two genes (clpP and ycf3) contain two introns. Sequences of the complete chloroplast genome were used to infer phylogenetic relationships, for which the chloroplast genomes are available from NCBI database, including Liliaceae, Arecaceae, Lemnaceae, Araceae, and Brassicaceae. A neighborjoining analysis was performed with Mega 6.0 (MEGA Inc., Englewood, NJ) (Tamura et al., 2013) using 500 bootstrap replicates. The position of P. ternata was situated as the sister of Colocasia esculenta in the Asteraceae (Figure 1). The characterized chloroplast genome sequence of P. ternata will be helpful for further study on exploration of molecular
*These authors contributed equally to this work. Correspondence: Zhe-Zhi Wang, College of Life Sciences, Shaanxi Normal University, No. 620, Western Chang’an Street, Chang’an District, Xi’an, Shaanxi 710119, P. R. China. Tel: +86 29 85310260. Fax: +86 29 85310623. E-mail: [email protected]
2
L. Han et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Nyu Medical Center on 07/14/15 For personal use only.
Figure 1. The NJ phylogenetic tree of Pinellia ternata and other species based on the complete chloroplast genomes. Numbers above each node were bootstrap support values. Lobularia maritima, Raphanus sativus, and Brassica napus were set as the outgroup. Genebank accession numbers for each plant are as follows: Fritillaria taipaiensis (NC_023247), Fritillaria cirrhosa (NC_024728), Fritillaria hupehensis (KF712486), Lilium longiflorum (KC968977), Cocos nucifera (KF285453), Phoenix dactylifera (GU811709), Elaeis guineensis (JF274081), Spirodela polyrhiza (NC_01589), Lemna minor (NC_010109), Pinellia ternata (KR270823), Colocasia esculenta (NC_016753), Lobularia maritima (NC_009274), Raphanus sativus (NC_024469), and Brassica napus (NC_016734).
markers, genetic diversity, molecular breeding, and genetic engineering.
Declaration of interest The authors declare that there is no conflict of interest regarding the publication of this article. The authors alone are responsible for the content and writing of the paper. The authors were financially supported by Scientific and Technological Research and Development Projects of Tech&Science Department of Shaanxi Provincial Government (2012K19-02-04), Natural Science Foundation of Education Department of Shaanxi Provincial Government (14JK1178), Innovation Funds of Graduate Programs, Shaanxi Normal University (CXS20120048), and the ‘‘Foundation for Excellent Doctoral Degree Dissertation’’ of Shaanxi Normal University (X2012YB01), Shaanxi, PR China.
References Bock R, Khan MS. (2004). Taming plastids for a green future. Trends Biotechnol 6:311–18. Chen JH, Cui GY, Liu JY, Tan RX. (2003). Pinelloside, an antimicrobial cerebroside from Pinellia ternata. Phytochemistry 4:903–6. Hahn C, Bachmann L, Chevreux B. (2013). Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads – A baiting and iterative mapping approach. Nucleic Acids Res 41: e129. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, et al. (2012). Geneious Basic: An integrated and extendable
desktop software platform for the organization and analysis of sequence data. Bioinformatics 12:1647–9. Kim YJ, Shin YO, Ha YW, Lee S, Oh JK, Kim YS. (2006). Anti-obesity effect of Pinellia ternata extract in Zucker rats. Biol Pharm Bull 6: 1278–81. Li M, Yang B, Chen Q, Zhu W, Ma J, Tian J. (2015). The complete chloroplast genome sequence of Clematis terniflora DC. (Ranunculaceae). Mitochondrial DNA. [Epub ahead of print]. doi:10.3109/19401736.2015.1033702. Liu Z, Zeng X, Yang D, Chu G, Yuan Z, Chen S. (2012). Applying DNA barcodes for identification of plant species in the family Araliaceae. Gene 1:76–80. Lu H, Xue T, Zhang A, Sheng W, Zhu Y, Chang L, Song Y, Xue J. (2013). Construction of an SSH library of Pinellia ternata under heat stress, and expression analysis of four transcripts. Plant Mol Biol Rep 1: 185–94. Pan IC, Liao DC, Wu FH, Daniell H, Singh ND, Chang C, Shih MC, et al. (2012). Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding. PLoS One 4:e34738. Qian J, Song J, Gao H, Zhu Y, Xu J, Pang X, Yao H, et al. (2013). The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza. PLoS One 2:e57607. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 12:2725–9. Yu CW, Lian Q, Wu KC, Yu SH, Xie LY, Wu ZJ. (2015). The complete chloroplast genome sequence of Anoectochilus roxburghii. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736. 2015.1033706.
