Biodiversity Science ›› 2019, Vol. 27 ›› Issue (4): 366-372.doi: 10.17520/biods.2018332

• Original Papers • Previous Article     Next Article

Assembling and analysis of Sanicula orthacantha chloroplast genome

Chen Zhixiang1, Yao Xueying1, Stephen R. Downie2, Wang Qizhi1, *()   

  1. 1 Department of Horticulture, Huaqiao University, Xiamen, Fujian 361021, China
    2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801
  • Received:2018-12-18 Accepted:2019-01-09 Online:2019-06-05
  • Wang Qizhi

Sanicula orthacantha is a perennial herb widely distributed in China and is a widely used for medicinal purposes. In this study, the whole chloroplast genome was sequenced and analyzed using bioinformatics methods. The results showed that it was a circular molecule 157,163 bp in length with a typical quadripartite structure including a pair of inverted repeats (IRa and IRb) of 26,247 bp that were separated by large and small single copy regions (LSC and SSC) of 87,547 bp and 17,122 bp, respectively. A total of 129 predicted genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes were identified. Compared with other Apiaeceae species, the S. orthacantha chloroplast genome had few differences in size, order and structure. The success of sequencing the S. orthacantha chloroplast genome provides a new method for the complete chloroplast genome assembly and characterization of Sanicula species, providing a methodological guide for the study of Sanicula plant evolution and phylogeny.

Key words: high-throughput sequencing, Sanicula L., gene assembly, phylogenetic analysis

Fig. 1

Sequence map of the Sanicula orthacantha chloroplast genome. Genes drawn outside of the circle are transcribed counter-clockwise, while genes shown on the inside of the circle are transcribed clockwise. Genes belonging to different functional groups are color-coded. The dark gray in the inner circle indicates GC content, while the light gray corresponds to AT content."

Table 1

List of genes found in Sanicula orthacantha chloroplast genome"

Category for genes
Group of genes
Name of genes
Self replication
核糖体RNA基因 Ribosomal RNAs rrn4.5(×2), rrn5(×2), rrn16(×2), rrn 23(×2)
转运RNA基因 Transfer RNAs trnA-UGC(×2), trnC-GCA, trnD-GUG, trnE-UCC, trnF-GAA, trnfM-CAU, trnG-GCC, trnG-UCC, trnH-GUG, trnI-CAU(×2), trnI-GAU(×2), trnK- UUU, trnL-CAA(×2), trnL-UAA, trnL-UAG, trnM-CAU, trnN-GUU (×2) trnP-UGG, trnQ-UUC, trnR-ACG(×2) trnR-UCU, trnS-GCU, trnS-GGA, trnS-UGA, trnT-GGU, trnT-UGU, trnV-GAC(×2), trnV-UAC, trnW-CCA, trnY-GUA
Ribosomal small subunit (SSU)
rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15
Ribosomal large subuni (LSU)
rpl33, rpl20, rpl36, rpl14, rpl16, rpl22, rpl2(×2), rpl23(×2), rpl32
RNA聚合酶亚基基因 RNA polymerase rpoA, rpoB, rpoC1, rpoC2
Genes for
光合系统I基因 Photosystem I psaA, psaB, psaC, psaI, psaJ
光合系统II基因 Photosystem II psbA, psbB, psbK, psbI, psbM, psbD, psbC, psbE, psbJ, psbL, psbT, psbH, psbN, psbF, psbZ, psbJ
细胞色素复合物基因 Cytochrome b/f complex petA, petD, petG, petL, petN
ATP合酶基因 ATP synthase atpA, atpF, atpH, atpI, atpE, atpB
ATP-dependent protease subunit p gene
RubiscoCO large subunit
NADH脱氢酶基因 NADH dehydrogenase ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH
Other genes
成熟酶基因 Maturase matK
包裹膜蛋白基因 Envelop membrane protein cemA
Subunit of acetyl-CoA-carboxylase
c-type cytochrome synthesis ccsA gene
Transcription initiation factor IF-1
Genes of unknown
Conserved open reading frames
ycf1, ycf2(×2), ycf3, ycf4

Fig. 2

Phylogenetic tree of 15 species based on chloroplast genome using Maximum Likelihood method"

[1] Andrews S ( 2013) Babraham Bioinformatics FastQC: A Quality Control Tool for High Throughput Sequence Data.
[2] Bayly MJ, Rigault P, Spokevicius A, Ladiges PY, Ades PK, Anderson C, Bossinger G, Merchant A, Udovicic F, Woodrow IE ( 2013) Chloroplast genome analysis of Australian eucalypts—Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae). Molecular Phylogenetics & Evolution, 69, 704-716.
[3] Clegg MT, Gaut BS, Learn G, Morton BR ( 1994) Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences, USA, 91, 6795-6801.
doi: 10.1073/pnas.91.15.6795
[4] Daniell H, Lin CS, Ming Y, Chang WJ ( 2016) Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biology, 17, 134-163.
doi: 10.1186/s13059-016-1004-2
[5] Dierckxsens N, Mardulyn P, Smits G ( 2017) NOVO-Plasty: De novo assembly of organelle genomes from whole genome data. Nucleic Acids Research, 45, e18.
doi: 10.1093/nar/gkw1060
[6] Downie SR, Jansen RK ( 2015) A comparative analysis of whole plastid genomes from the Apiales: Expansion and contraction of the inverted repeat, mitochondrial to plastid transfer of DNA, and identification of highly divergent noncoding regions. Systematic Botany, 40, 336-351.
doi: 10.1600/036364415X686620
[7] Ge L, Shen LQ, Chen QY, Li XM, Zhang L ( 2017) The complete chloroplast genome sequence of Hydrocotyle sibthorpioides (Apiales: Araliaceae). Mitochondrial DNA Part B, 2, 29-30.
doi: 10.1080/23802359.2016.1241676
[8] Jansen RK, Raubeson LA, Boore JL, Depamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ ( 2005) Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology, 395, 348-384.
doi: 10.1016/S0076-6879(05)95020-9
[9] Kazutaka K, Kazuharu M, Kei-Ichi K, Takashi M ( 2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 30, 3059-3066.
doi: 10.1093/nar/gkf436
[10] Kearse M, Moir R, Wilson A, Stoneshavas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C ( 2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28, 1647-1649.
doi: 10.1093/bioinformatics/bts199
[11] Kim KJ, Lee HL ( 2005) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research, 11, 247-261.
[12] Kumar S, Stecher G, Tamura K ( 2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology & Evolution, 33, 1870-1874.
[13] Lohse M, Drechsel O, Kahlau S, Bock R ( 2013) OrganellarGenomeDRAW—A suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Research, 41, W575.
doi: 10.1093/nar/gkt289
[14] Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Qi P, Liu Y ( 2012) SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler. GigaScience, 1, 18.
doi: 10.1186/2047-217X-1-18
[15] McCauley DE, Stevens JE, Peroni PA, Raveill JA ( 1996) The spatial distribution of chloroplast DNA and allozyme polymorphisms within a population of Silene alba (Caryophyllaceae). American Journal of Botany, 83, 727-731.
doi: 10.1002/j.1537-2197.1996.tb12761.x
[16] Peden JF ( 1999) CodonW. PhD Dissertation, University of Nottingham, Nottinghamshire, UK.
[17] Ruhlman T, Lee SB, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H ( 2006) Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms. BMC Genomics, 7, 222-235.
doi: 10.1186/1471-2164-7-222
[18] Shan RH, She ML ( 1979) Flora Reipublicae Popularis Sinicae, Tomus 14, pp. 12-67. Science Press, Beijing. (in Chinese)
[ 单人骅, 佘孟兰 ( 1979) 中国植物志, 第十四卷, 12-67页. 科学出版社, 北京.]
[19] Sichuan Provincial Health Department (1979) Sichuan Chinese Herbal Medicine Standard (Trial Draft). Sichuan Provincial Health Department, Chengdu. (in Chinese)
[ 四川省卫生局 ( 1979) 四川省中草药标准(试行稿). 四川省卫生局, 成都.]
[20] Small RL, Cronn RC, Wendel JF ( 2004) Use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Botany, 17, 145-170.
doi: 10.1071/SB03015
[21] Soltis PS, Soltis DE ( 2000) The role of genetic and genomic attributes in the success of polyploids. Proceedings of the National Academy of Sciences, USA, 97, 7051-7057.
doi: 10.1073/pnas.97.13.7051
[22] Thiel T, Michalek W, Varshney R, Graner A ( 2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical & Applied Genetics, 106, 411-422.
[23] Wang L, Dong WP, Zhou SL ( 2012) Structural mutations and reorganizations in chloroplast genomes of flowering plants. Acta Botanica Boreali-Occidentalia Sinica. 32, 1282-1288. (in Chinese with English abstract)
[ 王玲, 董文攀, 周世良 ( 2012) 被子植物叶绿体基因组的结构变异研究进展. 西北植物学报, 32, 1282-1288.]
[24] Xie ZW ( 1996) The Compilation of Chinese Herbal Medicine. People’s Medical Publishing House, Beijing. (in Chinese)
[ 谢宗万 ( 1996) 全国中草药汇编. 人民卫生出版社, 北京.]
[25] Xing SC, Clarke JL ( 2008) Process in chloroplast genome analysis. Progress in Biochemistry and Biophysics, 35, 21-28. (in Chinese with English abstract)
[ 邢少辰 , Clarke JL ( 2008) 叶绿体基因组研究进展. 生物化学与生物物理进展, 35, 21-28.]
[26] Zhang HY ( 1994) Annals of Chinese Traditional Medicine Resources. Science Press, Beijing. (in Chinese)
[ 张惠源 ( 1994) 中国中药资源志要. 科学出版社, 北京.]
[27] Zhang T, Fang Y, Wang X, Deng X, Zhang X, Hu S, Yu J ( 2012) The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: Insights into the evolution of plant organellar genomes. PLoS ONE, 7, e30531.
doi: 10.1371/journal.pone.0030531
[28] Zhao YB, Yin JL, Guo HY, Zhang YY, Xiao W, Sun C, Wu JY, Qu XB, Yu J, Wang XM, Xiao JF ( 2015) The complete chloroplast genome provides insight into the evolution and polymorphism of Panax ginseng. Frontiers in Plant Science, 5, 696-709.
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