Analysis of chloroplast genome structure and evolutionary development of Metaplexis japonica

doi:10.16178/j.issn.0528-9017.20230432

Abstract

Abstract:

Metaplexis japonica (Thunb.) Makino has certain edible and medicinal value. The purpose of this study is to obtain the chloroplast genome splicing of Metaplexis japonica, analyze the sequence characteristics of the chloroplast genome, and determine its phylogenetic relationship in related species. The research method is to use the Illumina platform for high-throughput sequencing of the chloroplast genome of Metaplexis japonica, using a series of bioinformatics analysis methods to complete genome splicing and gene annotation, and analyze repeat sequence characteristics. Combining multiple closely related species of Metaplexis japonica, analyzing the variation of boundary genes, a multi species phylogenetic tree was constructed. The results showed that the chloroplast genome of Metaplexis japonica is a typical circular tetrad structure, with a total length of 157 081 bp and a GC content of 36.49%. A total of 132 genes were annotated, including 45 photosynthesis related genes, 74 self replication related genes, 6 other genes, and 7 functionally unknown genes. In total, 271 simple repeat sequence (SSR) loci were identified, with single base repeats being the main sequence, followed by triple base repeats. Multiple species comparison and phylogenetic analysis have confirmed that Metaplexis japonica belongs to the genus Cynanchum, and shows a closer relation to the genera Asclepias and Calotropis.

Key words: Metaplexis japonica, chloroplast genome, phylogenetic analysis

CLC Number:

S567

MA Mengmeng, LI Shuxian, WU Huaitong. Analysis of chloroplast genome structure and evolutionary development of Metaplexis japonica[J]. Journal of Zhejiang Agricultural Sciences, 2024, 65(1): 130-138.

Figures/Tables 7

References 38

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物种拉丁名	NCBI登录号	分类属名
Asclepias nivea	NC_022431	马利筋属
Asclepias syriaca	KF386166	马利筋属
Biondia insignis	NC_042760	秦岭藤属
Calotropis gigantea	NC_041431	牛角瓜属
Calotropis procera	NC_041440	牛角瓜属
Cynanchum auriculatum	KU900231	鹅绒藤属
Cynanchum bungei	OK271106	鹅绒藤属
Cynanchum chinense	MW415427	鹅绒藤属
Cynanchum rostellatum	OL689165	鹅绒藤属
Cynanchum thesioides	MW864598	鹅绒藤属
Cynanchum wilfordii	KX352467	鹅绒藤属
Gymnema sylvestre	NC_047175	匙羹藤属
Hoya carnosa	NC_045868	球兰属
Hoya liangii	NC_042245	球兰属
Hoya pottsii	NC_042246	球兰属
Trachelospermum jasminoides	MK783315	络石属
Vincetoxicum hainanense	NC_051946	白前属
Vincetoxicum pycnostelma	OK271107	白前属
Vincetoxicum shaanxiense	NC_046785	白前属
Vincetoxicum versicolor	NC_052877	白前属
Vincetoxicum forrestii	MN383187	白前属
Gongronemopsis tenacissima	MW861760	牛奶菜属
Dischidia australis	OL790122	眼树莲属
Rhazya stricta	KJ123753	端兹亚属
Catharanthus roseus	NC_021423	长春花属

物种拉丁名	NCBI登录号	分类属名
Asclepias nivea	NC_022431	马利筋属
Asclepias syriaca	KF386166	马利筋属
Biondia insignis	NC_042760	秦岭藤属
Calotropis gigantea	NC_041431	牛角瓜属
Calotropis procera	NC_041440	牛角瓜属
Cynanchum auriculatum	KU900231	鹅绒藤属
Cynanchum bungei	OK271106	鹅绒藤属
Cynanchum chinense	MW415427	鹅绒藤属
Cynanchum rostellatum	OL689165	鹅绒藤属
Cynanchum thesioides	MW864598	鹅绒藤属
Cynanchum wilfordii	KX352467	鹅绒藤属
Gymnema sylvestre	NC_047175	匙羹藤属
Hoya carnosa	NC_045868	球兰属
Hoya liangii	NC_042245	球兰属
Hoya pottsii	NC_042246	球兰属
Trachelospermum jasminoides	MK783315	络石属
Vincetoxicum hainanense	NC_051946	白前属
Vincetoxicum pycnostelma	OK271107	白前属
Vincetoxicum shaanxiense	NC_046785	白前属
Vincetoxicum versicolor	NC_052877	白前属
Vincetoxicum forrestii	MN383187	白前属
Gongronemopsis tenacissima	MW861760	牛奶菜属
Dischidia australis	OL790122	眼树莲属
Rhazya stricta	KJ123753	端兹亚属
Catharanthus roseus	NC_021423	长春花属

基因功能分类	基因种类	基因名称
光合作用相关基因	光合系统Ⅰ	psaA,psaB,psaC,psaI,psaJ
	光合系统Ⅱ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ
	NADH脱氢酶	ndhA^,ndhB^(2),ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	细胞色素b/f复合物	petA,petB^,petD^,petG,petL,petN
	ATP合成酶	atpA,atpB,atpE,atpF^,atpH,atp*I
	RubisCO大亚基	rbcL
自我复制相关基因	核糖体大亚基	rpl14,rpl16^,rpl2^(2),rpl20,rpl22,rpl23(2),rpl32,rpl33,rpl36
	核糖体小亚基	rps11,rps12^*(2),rps14,rps15,rps16^,rps18,rps19,rps2,rps3,rps4,rps7(2),rps8
	RNA聚合酶亚基基因	rpoA,rpoB,rpoC1^,rpo*C2
	核糖体RNA基因	rrn16(2),rrn23(2),rrn4.5(2),rrn5(2)
	转运RNA基因	trnA-UGC^(2),trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,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-UUG,trnR-ACG(2),trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC(2),trnV-UAC^,trnW-CCA,trnY-GUA,trnfM-CAU
其他功能基因	成熟酶	matK
	蛋白酶	clpP^**
	囊膜蛋白基因	cemA
	乙酰辅酶A羧化酶亚基基因	accD
	C型细胞色素合成基因	ccsA
	转录起始因子	infA
未知功能基因	叶绿体阅读框	ycf1,ycf15(2),ycf2(2),ycf3^*,ycf*4

基因功能分类	基因种类	基因名称
光合作用相关基因	光合系统Ⅰ	psaA,psaB,psaC,psaI,psaJ
	光合系统Ⅱ	psbA,psbB,psbC,psbD,psbE,psbF,psbH,psbI,psbJ,psbK,psbL,psbM,psbN,psbT,psbZ
	NADH脱氢酶	ndhA^,ndhB^(2),ndhC,ndhD,ndhE,ndhF,ndhG,ndhH,ndhI,ndhJ,ndhK
	细胞色素b/f复合物	petA,petB^,petD^,petG,petL,petN
	ATP合成酶	atpA,atpB,atpE,atpF^,atpH,atp*I
	RubisCO大亚基	rbcL
自我复制相关基因	核糖体大亚基	rpl14,rpl16^,rpl2^(2),rpl20,rpl22,rpl23(2),rpl32,rpl33,rpl36
	核糖体小亚基	rps11,rps12^*(2),rps14,rps15,rps16^,rps18,rps19,rps2,rps3,rps4,rps7(2),rps8
	RNA聚合酶亚基基因	rpoA,rpoB,rpoC1^,rpo*C2
	核糖体RNA基因	rrn16(2),rrn23(2),rrn4.5(2),rrn5(2)
	转运RNA基因	trnA-UGC^(2),trnC-GCA,trnD-GUC,trnE-UUC,trnF-GAA,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-UUG,trnR-ACG(2),trnR-UCU,trnS-GCU,trnS-GGA,trnS-UGA,trnT-GGU,trnT-UGU,trnV-GAC(2),trnV-UAC^,trnW-CCA,trnY-GUA,trnfM-CAU
其他功能基因	成熟酶	matK
	蛋白酶	clpP^**
	囊膜蛋白基因	cemA
	乙酰辅酶A羧化酶亚基基因	accD
	C型细胞色素合成基因	ccsA
	转录起始因子	infA
未知功能基因	叶绿体阅读框	ycf1,ycf15(2),ycf2(2),ycf3^*,ycf*4