直刺变豆菜叶绿体全基因组及其特征

doi:10.17520/biods.2018332

生物多样性 ›› 2019, Vol. 27 ›› Issue (4): 366-372. DOI: 10.17520/biods.2018332

• 研究报告: 植物多样性 • 上一篇下一篇

直刺变豆菜叶绿体全基因组及其特征

陈志祥¹, 姚雪莹¹, Stephen R.Downie², 王奇志¹^,^*()

¹ 华侨大学化工学院园艺系, 福建厦门 361021
² Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801

收稿日期:2018-12-18 接受日期:2019-01-09 出版日期:2019-04-20 发布日期:2019-06-05
通讯作者: 王奇志
基金资助:
国家自然科学基金(31500162);国家标本平台教学标本子平台项目(2005DKA21403-JK);华侨大学研究生科研创新能力培育计划资助项目(1611315007);中国大学校园植物网的构建与示范Ⅱ(20180947)

Assembling and analysis of Sanicula orthacantha chloroplast genome

Zhixiang Chen¹, Xueying Yao¹, R. Downie Stephen², Qizhi Wang¹^,^*()

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:2019-04-20 Published:2019-06-05
Contact: Qizhi Wang

摘要/Abstract

摘要：

直刺变豆菜(Sanicula orthacantha)是中国广泛分布的多年生草本植物, 也是一味著名的民族药。本文通过二代高通量测序平台Illumina HiSeq PE150对直刺变豆菜叶绿体全基因组进行测序, 并通过生物信息学方法对其结构特征进行分析。结果表明: 直刺变豆菜叶绿体全基因组大小为157,163 bp, 包括大单拷贝区(large single copy, LSC)、小单拷贝区(small single copy, SSC)和2个反向重复序列(inverted repeat sequence, IRa和IRb), 长度分别为87,547 bp、17,122 bp和26,247 bp, 具有典型被子植物叶绿体基因组环状四分体结构; 共注释得到129个基因, 包括8个核糖体RNA (rRNA)基因、37个转运RNA (tRNA)基因和84个蛋白质编码基因。直刺变豆菜在叶绿体基因组结构、基因种类、排列顺序上与其他伞形科植物基本一致。直刺变豆菜叶绿体全基因组测序的成功为变豆菜属植物完整叶绿体基因组组装及其特征分析提供了新的方法。

关键词: 高通量测序, 变豆菜属, 基因组装, 系统发育分析

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

陈志祥, 姚雪莹, Stephen R.Downie, 王奇志 (2019) 直刺变豆菜叶绿体全基因组及其特征. 生物多样性, 27, 366-372. DOI: 10.17520/biods.2018332.

Zhixiang Chen, Xueying Yao, R. Downie Stephen, Qizhi Wang (2019) Assembling and analysis of Sanicula orthacantha chloroplast genome. Biodiversity Science, 27, 366-372. DOI: 10.17520/biods.2018332.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2018332

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

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参考文献 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

直刺变豆菜叶绿体全基因组及其特征

Assembling and analysis of Sanicula orthacantha chloroplast genome

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