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

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

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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

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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