人参属植物叶绿体基因组特征及其进化的研究

刘潮; 李敏; 任怡园; 钱柏霖; 韩利红

doi:10.19303/j.issn.1008-0384.2022.007.009

人参属植物叶绿体基因组特征及其进化的研究

doi: 10.19303/j.issn.1008-0384.2022.007.009

曲靖师范学院生物资源与食品工程学院/云南省高校特色果酒技术创新与应用工程研究中心，云南　曲靖　655011

基金项目: 国家自然科学基金项目（32060710、32100010）

详细信息

作者简介:
刘潮：刘潮（1980-），男，博士，副教授，研究方向：植物系统发育与进化（E-mail：liuchao_80@163.com）

通讯作者:
韩利红（1981-），女，博士，副教授，研究方向：真菌系统发育与进化（E-mail：hanlihong9527@126.com）

中图分类号: R 282
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出版历程
- 收稿日期: 2022-03-31
- 录用日期: 2022-03-31
- 修回日期: 2022-05-30
- 网络出版日期: 2022-08-29
- 刊出日期: 2022-07-28

Characteristics and Evolution of Panax Chloroplast Genomes

College of Biological Resource and Food Engineering/Yunnan Engineering Research Center of Fruit Wine，Qujing Normal University，Qujing, Yunnan　655011，China

摘要

摘要: 目的对人参属（Panax L.）物种叶绿体基因组特征及其系统发育进行研究，为我国人参属资源的遗传学研究和开发利用提供理论依据。方法基于14种人参属植物叶绿体基因组序列，利用生物信息学软件，对叶绿体基因组特征、序列重复、结构变异、基因进化和系统发育进行分析。结果人参属物种叶绿体基因组均为典型的四分体结构，包含114个unique基因。长重复序列主要为回文重复和正向重复，30～39 bp的重复序列最多，SSR大多为A/T重复，单核苷酸重复是最丰富的类型。人参属叶绿体基因组未发生基因重排，反向重复区（IR）与单拷贝区边界高度保守，鉴定的12个核苷酸高度可变热点中7个位于大单拷贝（LSC）区，5个位于小单拷贝（SSC）区。根据dN/dS比率，发现功能未知基因clpP、ycf1和ycf2受正选择作用。系统发育分析显示，屏边三七和三叶参位于基部支系，四倍体人参和西洋参与其他二倍体物种聚在不同支系，三七、竹节参和越南参则亲缘关系较近。结论人参属叶绿体基因组基因数目和顺序一致，基因组结构保守，重复序列数目和类型存在差异，单拷贝区核苷酸多态性高于IR区，正选择基因可能与物种的生态适应性有关。
- 人参属 /
- 叶绿体基因组 /
- 重复 /
- 变异 /
- 系统发育
Abstract: Objective Characteristics and phylogeny of chloroplast genomes of the medicinally and economically valuable species in Panax genus were studied. Methods Using bioinformatics software, the properties, repeats, structural variation, evolution, and phylogeny of the genomes of chloroplasts from 14 ginseng species were analyzed. Results The genomes consisted of typical quadripartite structure with 114 unique genes. The long repeats in them were mainly of palindromic and forward types with a length between 30 bp and 39 bp. The simple sequence repeats were largely A/T type and most abundantly mononucleotides. No gene rearrangement occurred in the genomes was observed. The boundary between the inverted repeat region and the single copy region was highly conserved. Of the 12 regions with highly variable nucleotides, 7 were in the large and 5 in the small single copy region. Indicated by the dN/dS ratios, the positive selection could occur on clpP, ycf1, and ycf2 with unknown functions. The phylogenetic analysis showed that P. stipulenatus and P. trifolius were in the basal lineage, the tetraploid P. ginseng and P. quinquefolius separated from other diploid species, while P. notoginseng, P. japonicus, and P. vietnamensis closely related. Conclusion The chloroplasts of the ginseng species examined were basically same in number and order of genomes, conservative in structure, but divert in number and type of repeats. The nucleotide polymorphism of the chloroplasts was higher in single copy region than inverted repeat regions. The positive selection genes identified in the study might result from the ecological adaptation of these Panax species.
- Panax L. /
- chloroplast genome /
- repeat /
- variation /
- phylogeny

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图 1 人参属物种叶绿体基因组长重复序列类型及分布

A：正向、回文、反向、互补重复数量；B：长重复类型及数量。

Figure 1. Types and distribution of long repeats in chloroplast genomes of Panax species

A: Counts of forward, palindromic, reverse and complementary repeats; B: types and counts of long repeats.

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图 2 人参属物种叶绿体基因组SSR位点类型及分布

A：单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸、六核苷酸重复数量；B：SSR类型及数量。

Figure 2. Types and distribution of SSRs in chloroplast genomes of Panax species

A: Counts of mono-, di-, tri-, tetra-, penta- and hexanucleotides; B: types and counts of SSR.

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图 3 人参属物种叶绿体基因组LSC、SSC和IRs边界比较

Figure 3. Borders of LSC, SSC, and IRs in chloroplast genomes of Panax species

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图 4 人参属物种叶绿体基因组序列比较

Figure 4. Sequences of chloroplast genomes of Panax species

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图 5 人参属物种叶绿体基因组序列多态性分析

Figure 5. Nucleotide diversity of chloroplast genomes of Panax species

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图 6 人参属叶绿体蛋白编码基因dN/dS分析

Figure 6. dN/dS ratios on protein coding genes of chloroplasts of Panax species

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图 7 基于IQ-TREE软件构建的人参属物种叶绿体基因组系统发育树

Figure 7. Phylogenetic tree of chloroplast genes of Panax species based on IQ-TREE

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表 1 人参属物种叶绿体基因组特征

Table 1. Chloroplast genomes of Panax species

物种 Species	登录号 Accession	长度 Length/bp				GC含量 GC content/%
物种 Species	登录号 Accession	基因组 Genome	LSC	SSC	IR	基因组 Genome	LSC	SSC	IR
人参 P. ginseng	MK408938	156 241	86 128	18 077	26 018	38.07	36.27	32.18	43.10
竹节参 P. japonicus	KP036469	156 188	86 199	18 013	25 988	38.07	36.29	32.21	43.05
疙瘩七 P. japonicus var. bipinnatifidus	MK408962	156 244	86 186	18 006	26 026	38.06	36.28	32.21	43.05
珠子参 P. major	MN496312	156 402	86 189	18 007	26 103	38.07	36.28	32.22	43.05
三七 P. notoginseng	MK408945	156 319	86 157	18 004	26 079	38.07	36.27	32.23	43.07
假人参 P. pseudoginseng	MW145449	156 074	86 124	18 008	25 971	38.06	36.27	32.22	43.06
西洋参 P. quinquefolius	MK408953	156 070	86 077	17 993	26 000	38.07	36.27	32.22	43.08
屏边三七 P. stipuleanatus	MK408965	156 007	86 083	18 150	25 887	38.04	36.26	32.07	43.08
三叶参 P. trifolius	MF100782	156 157	86 322	18 047	25 894	38.08	36.27	32.26	43.10
越南参 P. vietnamensis	KP036470	155 993	86 178	17 935	25 940	38.05	36.27	32.22	43.02
野三七 P. vietnamensis var. fuscidiscus	MT798585	156 284	86 171	17 971	26 071	38.06	36.28	32.27	42.98
越南参变种 P. vietnamensis var. langbianensis	MT798583	155 984	86 174	17 934	25 938	38.05	36.27	32.21	43.03
峨眉三七 P. wangianus	MK408964	156 189	86 190	17 969	26 015	38.07	36.29	32.21	43.03
姜状三七 P. zingiberensis	MK408969	156 192	86 116	17 966	26 055	38.07	36.31	32.27	43.00

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表 2 基于位点模型的人参属叶绿体蛋白编码基因正选择分析

Table 2. Potential positive selection test on chloroplast genomes of Panax species based on site model

基因 Gene	M1 vs M2		M7 vs M8		正选择位点 Positively selected sites
基因 Gene	2ΔlnL	P 值	2ΔlnL	P 值	正选择位点 Positively selected sites
accD	2.39	3.0×10^-1	2.47	2.9×10^-1	139 Q, 0.505; 141 S, 0.517; 144 R, 0.528; 209 A, 0.856; 264 E, 0.504; 364 I, 0.507; 372 L, 0.526; 494 Q, 0.855
atpF	3.37	1.9×10^-1	3.42	1.8×10^-1	14 W, 0.541; 77 Q, 0.537; 158 G, 0.854
cemA	7.48	2.4×10^-2	7.48	2.4×10^-2	14 A, 0.547; 22 W, 0.538; 54 K, 0.536; 102 D, 0.533; 103 R, 0.544; 118 V, 0.973*; 205 F, 0.531; 208 W, 0.540
clpP	13.40	1.2×10^-3	13.40	1.2×10^-3	38 P, 0.990*; 39 V, 0.622; 40 A, 0.935; 41 S, 0.612; 138 G, 0.629; 160 Q, 0.626
matK	19.22	6.7×10^-5	19.25	6.6×10^-5	83 R, 0.994**
ndhD	0.77	6.8×10^-1	0.99	6.1×10^-1	22 F, 0.830; 41 I, 0.829
ndhF	19.81	5.0×10^-5	20.29	3.9×10^-5	17 P, 0.597; 123 R, 0.592; 133 T, 0.583; 223 F, 0.959; 421 I, 0.964; 463 Q, 0.591; 483 R, 0.569; 499 H, 0.552; 502 A, 0.965; 511 Q, 0.591; 512 M, 0.526; 532 K, 0.559; 534 I, 0.962; 572 N, 0.543; 598 D, 0.573; 606 F, 0.548; 621 L, 0.630; 641 I, 0.549; 642 G, 0.597; 657 G, 0.594; 670 A, 0.963; 677 I, 0.532; 703 S, 0.548; 737 Y, 0.964; 743 F, 0.537; 745 D, 0.958; 746 L, 1.000*
rbcL	15.94	3.5×10^-4	16.10	3.2×10^-4	225 L, 0.632; 226 Y, 0.969; 230 A, 0.635; 270 I, 0.866; 281 A, 0.644; 328 S, 0.999; 353 F, 0.584; 439 R, 0.968; 472 V, 0.609; 474 I, 0.621; 478 V, 0.714
rpl2	0	1	0	1	99 K, 0.651; 265 D, 0.650; 267 L, 0.652
rpoA	14.53	7.0×10^-4	14.56	6.9×10^-4	34 L, 0.506; 256 E, 0.991; 264 N, 0.999; 272 S, 0.533; 320 A, 0.849; 337 L, 0.537
rpoB	0.90	6.4×10^-1	0.90	6.4×10^-1	37 Y, 0.505; 165 R, 0.502; 193 R, 0.502; 295 I, 0.502; 365 T, 0.504; 459 S, 0.502; 695 K, 0.506; 735 T, 0.504; 935 D, 0.832
rpoC2	0	1	0	1	85 Q, 0.736
rps12	0	1	0.02	9.9×10^-1	25 R, 0.502
ycf1	75.81	0	75.78	0	205 K, 1.000; 206 Y, 0.999; 288 I, 0.876; 532 T, 0.803; 533 K, 0.956; 604 R, 0.801; 624 R, 0.825; 668 I, 0.779; 685 W, 0.837; 699 V, 0.824; 701 Q, 0.802; 706 V, 0.814; 720 V, 0.856; 722 T, 0.814; 723 D, 0.808; 731 R, 0.982; 733 K, 0.809; 734 I, 0.996*; 736 L, 0.855; 737 I, 0.803; 751 N, 0.760; 809 A, 0.828; 906 N, 0.768; 914 E, 0.795; 915 L, 0.788; 929 L, 0.835; 957 K, 0.979; 1030 E, 0.979; 1116 K, 0.804; 1172 M, 0.731; 1186 Q, 0.798; 1206 Q, 0.798; 1502 Q, 0.754; 1601 I, 1.000; 1616 D, 0.773; 1631 R, 0.814; 1652 R, 0.795; 1665 V, 0.738; 1685 E, 0.978; 1710 I, 0.979*; 1739 R, 0.793
ycf2	14.95	5.7×10^-4	14.95	5.7×10^-4	30 R, 0.767; 56 R, 0.770; 103 L, 0.765; 126 S, 0.765; 248 S, 0.769; 285 L, 0.765; 320 L, 0.766; 332 R, 0.764; 432 V, 0.765; 466 Y, 0.765; 573 I, 0.764; 598 L, 0.766; 606 M, 0.759; 759 F, 0.763; 850 S, 0.965; 943 E, 0.764; 1037 P, 0.766; 1050 F, 0.765; 1064 S, 0.763; 1074 I, 0.965; 1093 L, 0.767; 1101 N, 0.964; 1171 W, 0.767; 1173 S, 0.765; 1245 P, 0.766; 1265 D, 0.762; 1309 D, 0.762; 1344 R, 0.764; 1422 L, 0.965; 1431 F, 0.763; 1522 D, 0.767; 1550 Y, 0.766; 1656 N, 0.763; 1717 S, 0.768; 1799 R, 0.769; 2045 E, 0.764
和分别表示正选择位点概率＞ 95%和＞ 99%。 and ** indicate that the probabilities of positively selected sites are ＞ 95% and ＞ 99%, respectively.

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