Assembling and analysis of Sanicula orthacantha chloroplast genome

doi:10.17520/biods.2018332

Abstract

Abstract:

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

Chen Zhixiang,Yao Xueying,Stephen R. Downie,Wang Qizhi. Assembling and analysis of Sanicula orthacantha chloroplast genome[J]. Biodiv Sci, 2019, 27(4): 366-372.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.17520/biods.2018332

https://www.biodiversity-science.net/EN/Y2019/V27/I4/366

Figures/Tables 3

References 28

[1]	Andrews S ( 2013) Babraham Bioinformatics FastQC: A Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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 URL
[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.

基因分类 Category for genes	基因分组 Group of genes	基因名称 Name of genes
表达相关基因 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
	核糖体小亚基基因 Ribosomal small subunit (SSU)	rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15
	核糖体大亚基基因 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
光合作用相关基因 Genes for photosynthesis	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
	依赖ATP的蛋白酶单元p基因 ATP-dependent protease subunit p gene	clpP
	二磷酸核酮糖羧化酶大亚基基因 RubiscoCO large subunit	rbcL
	NADH脱氢酶基因 NADH dehydrogenase	ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH
其他基因 Other genes	成熟酶基因 Maturase	matK
	包裹膜蛋白基因 Envelop membrane protein	cemA
	乙酰辅酶A羧化酶亚基基因 Subunit of acetyl-CoA-carboxylase	accD
	c型细胞色素合成基因 c-type cytochrome synthesis ccsA gene	ccsA
	转录起始因子基因 Transcription initiation factor IF-1	InfA
未知功能基因 Genes of unknown function	保守开放阅读框 Conserved open reading frames	ycf1, ycf2(×2), ycf3, ycf4

基因分类 Category for genes	基因分组 Group of genes	基因名称 Name of genes
表达相关基因 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
	核糖体小亚基基因 Ribosomal small subunit (SSU)	rps16, rps2, rps14, rps4, rps18, rps11, rps8, rps3, rps19, rps7(×2), rps12, rps15
	核糖体大亚基基因 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
光合作用相关基因 Genes for photosynthesis	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
	依赖ATP的蛋白酶单元p基因 ATP-dependent protease subunit p gene	clpP
	二磷酸核酮糖羧化酶大亚基基因 RubiscoCO large subunit	rbcL
	NADH脱氢酶基因 NADH dehydrogenase	ndhJ, ndhK, ndhC, ndhB(×2), ndhF, ndhD, ndhE, ndhG, ndhI, ndhA, ndhH
其他基因 Other genes	成熟酶基因 Maturase	matK
	包裹膜蛋白基因 Envelop membrane protein	cemA
	乙酰辅酶A羧化酶亚基基因 Subunit of acetyl-CoA-carboxylase	accD
	c型细胞色素合成基因 c-type cytochrome synthesis ccsA gene	ccsA
	转录起始因子基因 Transcription initiation factor IF-1	InfA
未知功能基因 Genes of unknown function	保守开放阅读框 Conserved open reading frames	ycf1, ycf2(×2), ycf3, ycf4