Chloroplast Genome Structure and Interspecies Relationship of Sanicula rubriflora

doi:10.7525/j.issn.1673-5102.2022.03.013

Abstract

Abstract:

As a kind of medicinal herb， Sanicula rubriflora F. Schmidt is easily confused with other medicinal plants of the same genus after drying and interspecific relationship is controversial. The structure and characteristics of the chloroplast genome of S. rubriflora were reported for the first time， the sequencing data was spliced and annotated using bioinformatics methods， and the chloroplast genome structure and phylogeny were further analyzed. The length of the chloroplast genome sequence of S. rubriflora was 155 721 bp， including a large single copy region（LSC） of 85 981 bp and a small single copy region（SSC） of 17 060 bp， and were separated by inverted repeat sequence（IRs） of 26 340 bp. The GC content of the chloroplast genome of S. rubriflora was 38.20% and contained 129 genes， 84 protein-coding genes， 37 tRNA genes and 8 rRNA genes respectively. The chloroplast genome structure of S. rubriflora was highly conservative. The coding genes contained a total of 51 907 codons， with 5 095 leucine and 689 tryptophan. Simple repeated sequence analysis revealed a total of 32 sites， and most of them were single base repeat A/T type. The clustering results of the chloroplast genome supported that the subfamily Hydrocotyloideae was a relatively primitive group in the Umbelliferae family. The subfamily Saniculoideae and Apioideae were sister groups， which were the more close relationship of the Umbelliferae. Sanicula was a relatively natural group. S. rubriflora and S. flavovirens were related sister species， but their morphology and geographical distribution were quite different. The results provid a basis for the interspecies identification of the genus Sanicula and lay the foundation for further study of its phylogenetic relationship and interspecies evolution.

Key words: Sanicula rubriflora, chloroplast genome, interspecies relationship

CLC Number:

Q944.58

Chen YANG, Xueying YAO, Zhixiang CHEN, Qizhi WANG. Chloroplast Genome Structure and Interspecies Relationship of Sanicula rubriflora[J]. Bulletin of Botanical Research, 2022, 42(3): 437-445.

Figures/Tables 6

Table 1

Fig.1

Table 2

Genes contained in S.rubriflora chloroplast genome

分类 Classification	基因家族 Gene Family	基因名称 Gene Name	数量 Quantity
光合作用相关 Genes for photosynthesis	光系统Ⅰ Photosystem Ⅰ	psa A，psa B，psa C，psa I，psa J	5
	光系统Ⅱ Photosystem Ⅱ	psb A，psb B，psb C，psb D，psb E，psb F，psb H，psb I，psb J，psb K， psb L，psb M，psb N，psb T，psb Z	15
	细胞色素b/f 复合物 Cytochrome b/f complex	pet A，pet B^，pet* D，pet G，pet L，pet N	6
	ATP合成酶 ATP synthase	atp A，atp B，atp E，atp F^，atp* H，atp I	6
	NADH脱氢酶 NADH dehydrogenase	ndh A^，ndh* B^a，ndh* C，ndh D，ndh E，ndh F，ndh G，ndh H，ndh I，ndh J，ndh K	12
	二磷酸核酮糖羧化酶大亚基 RubiscoCO large subunit	rbc L	1
自我复制 Self-replication	rRNA	rrn 16^a，rrn 23^a，rrn 4.5^a，rrn 5^a	8
	RNA聚合酶亚基 RNA polymerase	rpo A，rpo B，rpo C1^，rpo* C2	4
	核糖体小亚基（SSU） Ribosomal protein（SSU）	rps 2^，rps* 3，rps 4，rps 7^a，rps 8，rps 11，rps 12^，rps* 14，rps 15，rps 16^，rps* 18，rps 19	13
	核糖体大亚基（LSU） Ribosomal protein （LSU）	rpl 14，rpl 16，rpl 2^a，rpl* 20，rpl 22，rpl 23^a，rpl 32，rpl 33，rpl 36	11
	tRNA	trn A-UGC^a，trn* C-GCA，trn D-GUC，trn E-UUC，trn F-GAA，trn G-GCC^，trn* G-UCC，trn H-GUG，trn I-CAU^a，trn I-GAU^a，trn* K-UUU^，trn* L-CAA^a，trn L-UAA^，trn* L-UAG，trn M-CAU，trn N-GUU^a，trn P-UGG，trn Q-UUG，trn R-ACG^a，trn R-UCU，trn S-GCU，trn S-GGA，trn S-UGA，trn T-GGU，trn T-UGU，trn V-GAC^a，trn V-UAC^，trn* W-CCA，trn Y-GUA，trn fM-CAU	37
其他基因 Other genes	成熟酶Maturase	mat K	1
	被膜蛋白 Envelop membrane protein	cem A	1
	乙酰辅酶A羧化酶 Subunit of acetyl-CoA-carboxylase	acc D	1
	细胞色素C的合成基因 Synthetic gene of cytochrome C	ccs A	1
	蛋白酶Protease	clp P^**	1
	转录启动因子Transcription promoter	inf A	1
未知功能基因 Unknown function gene	保守假定的叶绿体开放阅读框 Hypothetical chloroplast reading frames	ycf 1，ycf 2^a，ycf 3^*，ycf* 4	5

Table 2

Fig.2

Table 3

Fig.3

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植物名 Plant name	亚科名 Subfamily Name	序列号 Serial number
穗序鹅掌柴 Schefflera delavayi（Franch.） Harms ex Diels	五加科 Araliaceae	NC_022813.1
Hydrocotyle verticillata Thunb	天胡荽亚科 Hydrocotyloideae Drude	HM596070.1
天胡荽 Hydrocotyle sibthorpioides Lam	天胡荽亚科 Hydrocotyloideae Drude	KT589392.1
紫花阔叶柴胡 Bupleurum boissieuanum H. Wolff	芹亚科 Apioideae Drude	NC_036017.1
Bupleurum falcatum L.		NC_027834
川明参 Chuanminshen violaceum Sheh et Shan		KU921430.2
野胡萝卜 Daucus carota L.		DQ898156.1
Hansenia oviformis（R.H.Shan） Pimenov & Kljuykov		NC_035055.1
Hansenia weberbaueriana（Fedde ex H.Wolff） Pimenov & Kljuykov		NC_035053.1
Peucedanum insolens Kitag		NC_033344.1
棱子芹 Pleurospermum camtschaticum Hoffm		NC_033343.1
茴香 Foeniculum vulgare Mill		NC_029469
旱芹 Apium graveolens L.		NC_041087.1
鸭儿芹 Cryptotaenia japonica Hassk		NC_046737.1
首阳变豆菜 Sanicula giraldii Wolff	变豆菜亚科 Saniculoideae Drude	MT528256
黄花变豆菜 Sanicula flavovirens Z.H.Chen，D.D.Ma et W.Y.Xie		MT528257
Sanicula odorata（Raf.） Pryer & Phillippe		MT528258
薄片变豆菜 Sanicula lamelligera Hance		MN966729
红花变豆菜 Sanicularubriflora F. Schmidt		MT528260
变豆菜 Sanicula chinensis Bunge		MK208987.1
直刺变豆菜 Sanicula orthacantha S. Moore		MK293943

编号 No.	类型 Type	简单重复序列 SSR	大小 Size	起始 Start	终止 End	所属区域 Area	编号 No.	类型 Type	简单重复序列 SSR	大小 Size	起始 Start	终止 End	所属区域 Area
1	P1	（A）10	10	3 931	3 940	LSC	17	P1	（T）11	11	67 017	67 027	LSC
2	P1	（A）10	10	5 140	5 149	LSC	18	P1	（A）10	10	67 383	67 392	LSC
3	P2	（AT）9	18	10 586	10 603	LSC	19	P1	（A）10	10	72 305	72 314	LSC
4	P1	（T）10	10	13 205	13 214	LSC	20	P1	（A）11	11	72 945	72 955	LSC
5	P1	（A）14	14	13 831	13 844	LSC	21	P1	（T）10	10	79 926	79 935	LSC
6	P1	（T）11	11	19 593	19 603	LSC	22	P1	（T）13	13	81 858	81 870	LSC
7	P1	（T）12	12	27 323	27 334	LSC	23	P1	（T）11	11	84 358	84 368	LSC
8	P2	（AT）9	18	30 725	30 742	LSC	24	P1	（T）14	14	86 052	86 065	IRa
9	P1	（A）13	13	32 475	32 487	LSC	25	P1	（T）11	11	100 139	100 149	IRa
10	P2	（TA）7	14	46 111	46 124	LSC	26	P1	（T）10	10	104 129	104 138	IRa
11	P2	（TA）6	12	48 190	48 201	LSC	27	P2	（AT）9	18	121 034	121 051	SSC
12	P1	（T）10	10	55 915	55 924	LSC	28	P1	（T）15	15	127 760	127 774	SSC
13	P1	（T）10	10	61 948	61 957	LSC	29	P1	（T）11	11	128 044	128 054	SSC
14	P2	（TA）7	14	63 379	63 392	LSC	30	P1	（A）10	10	137 565	137 574	IRb
15	c	（A）11tattacatata（AT）9	40	65 045	65 084	LSC	31	P1	（A）11	11	141 554	141 564	IRb
16	P1	（A）10	10	66 835	66 844	LSC	32	P1	（A）14	14	155 638	155 651	IRb

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