睡莲属叶绿体基因组密码子偏好性及系统发育分析

doi:10.13304/j.nykjdb.2021.0768

中国农业科技导报 ›› 2022, Vol. 24 ›› Issue (4): 75-84.DOI: 10.13304/j.nykjdb.2021.0768

睡莲属叶绿体基因组密码子偏好性及系统发育分析

黄祥¹^,²(), 楚光明¹, 郑新开¹, 程锦涛¹, 陈健豪¹, 徐迎春³, 金奇江³, 杨梅花¹^,²()

^1.石河子大学农学院，新疆石河子 832003
^2.石河子大学特色果蔬栽培生理与种质资源利用兵团重点实验室，新疆石河子 832003
^3.南京农业大学园艺学院，南京 210095

收稿日期:2021-09-01 接受日期:2021-10-20 出版日期:2022-04-15 发布日期:2022-04-19
通讯作者: 杨梅花
作者简介:黄祥 E-mail：shzu_hx@163.com；
基金资助:
石河子大学新品种培育专项(YZZX202105);NSFC-新疆联合基金项目(U1803104);石河子大学高层次人才科研启动资金项目(RCZK2018C04)

Analysis of Codon Usage Bias and Phylogenetic of Chloroplast Genome in Nymphaea

Xiang HUANG¹^,²(), Guangming CHU¹, Xinkai ZHENG¹, Jintao CHENG¹, Jianhao CHEN¹, Yingchun XU³, Qijiang JIN³, Meihua YANG¹^,²()

^1.College of Agriculture，Shihezi University，Xinjiang Shihezi 832003，China
^2.Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization，Shihezi University，Xinjiang Shihezi 832003，China
^3.College of Horticulture，Nanjing Agricultural University，Nanjing 210095，China

Received:2021-09-01 Accepted:2021-10-20 Online:2022-04-15 Published:2022-04-19
Contact: Meihua YANG

摘要/Abstract

摘要：

睡莲属植物是具有重要的经济、药用和观赏价值的原始被子植物。分析其叶绿体基因组编码区密码子的使用特征，以22种睡莲的叶绿体基因组为研究对象，对睡莲叶绿体基因组密码子的偏好性及睡莲属植物间的进化关系进行了系统分析。结果表明，22种睡莲植物叶绿体基因组密码子适应指数（codon adaptation index，CAI）为0.168~0.170，有效密码子数（effective number of codon，ENC）为51.301~51.577，表明睡莲属叶绿体基因组密码子偏好性较弱；密码子不同位置的GC含量分别为46.26%（第1位，GC1）、38.67%（第2位，GC2）和32.54%（第3位，GC3），表明睡莲属植物叶绿体密码子偏好使用A/U结尾。ENC-plot、PR2-plot和中性绘图分析表明，选择压力是影响睡莲属叶绿体编码区密码子偏好性的重要因素。相关性分析表明，ENC与GC2、GC3呈显著相关（P<0.05），密码子第2、3位碱基组成对密码子使用模式存在较大影响。最优密码子分析表明，22种睡莲最优密码子存在数量差异（5~11个），共有的2个最优密码子为CCA、AAU。系统发育分析显示，基于同义密码子相对使用度（relative synonymous codon usage，RSCU）和基于叶绿体基因序列（matK、trnL?trnF和编码序列）的分类结果相似，说明睡莲属近缘种之间密码子使用特征相似，基于RSCU将睡莲属划分为3个亚属，为睡莲属植物系统进化、物种分类及叶绿体基因工程的相关研究提供了理论依据。

关键词: 睡莲属, 叶绿体基因组, 密码子偏好性, 系统发育

Abstract:

Nymphaea is primitive angiosperm with important economic， medicinal and ornamental value. The characteries analysis of codons in the coding region of chloroplast genome is of great significance for chloroplast genetic engineering and species phylogeny. The codon usage profiling of chloroplast genomes in Nymphaea was systematically analyzed， and the phylogenetic relationship was decoded among the 22 Nymphaea plants. The results showed that the codon adaptation index of chloroplast genome from total 22 Nymphaea ranged from 0.168 to 0.170， and the effective codon number ranged from 51.301 to 51.577， which indicated weak codon preference in Nymphaea. The GC contents of bases at different positions of codon were 46.26% （GC1）， 38.67% （GC2） and 32.54% （GC3）， respectively， indicating that A and U used in chloroplast codons were rich in Nymphaea. The analysis of ENC plot， PR2 plot and neutral plot showed that the codon bias in the chloroplast genome was mainly affected by selection pressure. Correlation analysis showed that ENC value was significantly correlated with GC2 and GC3 （P<0.05）， which indicated that the composition of bases in the 1^st and 2^nd had great influence on codon using pattern. The optimal codon analysis showed that there were quantitative differences of the optimal codons among these species （5~11）， and two optimal codons （CCA and AAU） were determined. Phylogenetic analysis showed that the classification results based on relative synonymous codon usage （RSCU） value were consistent to those based on chloroplast gene sequences （matK， trnL?trnF and coding sequence）， which indicated that the codon using characteristics among related species of Nymphaea were similar， and the classification results based on codon RSCU value divided Nymphaea into 3 subgenera， which provided a theoretical basis for the phylogeny， species classification and chloroplast genetic engineering of Nymphaea.

Key words: Nymphaea, chloroplast genome, codon usage bias, phylogeny

中图分类号:

S682.32

黄祥, 楚光明, 郑新开, 程锦涛, 陈健豪, 徐迎春, 金奇江, 杨梅花. 睡莲属叶绿体基因组密码子偏好性及系统发育分析[J]. 中国农业科技导报, 2022, 24(4): 75-84.

Xiang HUANG, Guangming CHU, Xinkai ZHENG, Jintao CHENG, Jianhao CHEN, Yingchun XU, Qijiang JIN, Meihua YANG. Analysis of Codon Usage Bias and Phylogenetic of Chloroplast Genome in Nymphaea[J]. Journal of Agricultural Science and Technology, 2022, 24(4): 75-84.

图/表 9

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编号 Number	物种 Species	登录号 Genbank ID	密码子适应指数 CAI	有效密码子数 ENC	GC1/%	GC2/%	GC3/%	GCall/%
1	澳洲巨花睡莲 N. gigantea	MT107637.1	0.170	51.468	46.11	38.66	32.61	39.13
2	白睡莲 N. alba	NC_006050.1	0.169	51.483	46.23	38.69	32.54	39.15
3	齿叶睡莲 N. lotus	NC_041238.1	0.168	51.365	46.34	38.66	32.4	39.13
4	厄德洛睡莲 N. heudelotii	MW802266.1	0.170	51.401	46.22	38.61	32.57	39.13
5	非洲睡莲 N. capensis	NC_040167.1	0.169	51.446	46.25	38.75	32.6	39.20
6	黄睡莲 N. mexicana	NC_024542.1	0.169	51.403	46.19	38.69	32.43	39.10

编号 Number	物种 Species	登录号 Genbank ID	密码子适应指数 CAI	有效密码子数 ENC	GC1/%	GC2/%	GC3/%	GCall/%
1	澳洲巨花睡莲 N. gigantea	MT107637.1	0.170	51.468	46.11	38.66	32.61	39.13
2	白睡莲 N. alba	NC_006050.1	0.169	51.483	46.23	38.69	32.54	39.15
3	齿叶睡莲 N. lotus	NC_041238.1	0.168	51.365	46.34	38.66	32.4	39.13
4	厄德洛睡莲 N. heudelotii	MW802266.1	0.170	51.401	46.22	38.61	32.57	39.13
5	非洲睡莲 N. capensis	NC_040167.1	0.169	51.446	46.25	38.75	32.6	39.20
6	黄睡莲 N. mexicana	NC_024542.1	0.169	51.403	46.19	38.69	32.43	39.10

编号 Number	物种 Species	登录号 Genbank ID	密码子适应指数 CAI	有效密码子数 ENC	GC1/%	GC2/%	GC3/%	GCall/%
均值Mean			0.169	51.401	46.26	38.67	32.54	35.16
8	蓝星睡莲 N. colorata	MT107631.1	0.170	51.466	46.13	38.61	32.65	39.13
9	鲁吉娜睡莲 N. rudgeana	MW802268.1	0.169	51.320	46.25	38.53	32.41	39.06
10	睡莲（子午莲） N. tetragona	MT107634.1	0.169	51.577	46.82	39.24	32.88	39.65
11	特尼日洼睡莲 N. tenerinervia	MW802269.1	0.170	51.317	46.21	38.54	32.39	39.05
12	细瓣睡莲 N. gracilis	MW802265.1	0.170	51.391	46.21	38.57	32.53	39.10
13	香睡莲 N. oborata	MT107636.1	0.170	51.500	47.03	39.33	33.00	39.79
14	小花睡莲 N. micrantha	MT107635.1	0.170	51.466	46.11	38.65	32.61	39.12
15	小腺睡莲 N. glandulifera	MW802264.1	0.170	51.303	46.19	38.52	32.37	39.03
16	亚马孙睡莲 N. amazonum	MW802262.1	0.170	51.317	46.21	38.53	32.41	39.05
17	延药睡莲 N. stellata	MT991061.1	0.170	51.410	46.19	38.60	32.57	39.12
18	夜雪睡莲 N. potamophila	MT107633.1	0.170	51.365	46.07	38.60	32.46	39.04
19	印度红睡莲 N. rubra	MT107632.1	0.169	51.399	46.17	38.51	32.44	39.04
20	永恒睡莲 N. immutabilis	MW802267.1	0.170	51.349	46.2	38.59	32.52	39.10
21	詹姆森睡莲 N. jamesoniana	NC_031826.2	0.169	51.362	46.25	38.67	32.44	39.12
22	侏儒卢旺达睡莲 N. thermarum	MW143076.1	0.170	51.419	46.19	38.61	32.60	39.13

编号 Number	物种 Species	登录号 Genbank ID	密码子适应指数 CAI	有效密码子数 ENC	GC1/%	GC2/%	GC3/%	GCall/%
均值Mean			0.169	51.401	46.26	38.67	32.54	35.16
8	蓝星睡莲 N. colorata	MT107631.1	0.170	51.466	46.13	38.61	32.65	39.13
9	鲁吉娜睡莲 N. rudgeana	MW802268.1	0.169	51.320	46.25	38.53	32.41	39.06
10	睡莲（子午莲） N. tetragona	MT107634.1	0.169	51.577	46.82	39.24	32.88	39.65
11	特尼日洼睡莲 N. tenerinervia	MW802269.1	0.170	51.317	46.21	38.54	32.39	39.05
12	细瓣睡莲 N. gracilis	MW802265.1	0.170	51.391	46.21	38.57	32.53	39.10
13	香睡莲 N. oborata	MT107636.1	0.170	51.500	47.03	39.33	33.00	39.79
14	小花睡莲 N. micrantha	MT107635.1	0.170	51.466	46.11	38.65	32.61	39.12
15	小腺睡莲 N. glandulifera	MW802264.1	0.170	51.303	46.19	38.52	32.37	39.03
16	亚马孙睡莲 N. amazonum	MW802262.1	0.170	51.317	46.21	38.53	32.41	39.05
17	延药睡莲 N. stellata	MT991061.1	0.170	51.410	46.19	38.60	32.57	39.12
18	夜雪睡莲 N. potamophila	MT107633.1	0.170	51.365	46.07	38.60	32.46	39.04
19	印度红睡莲 N. rubra	MT107632.1	0.169	51.399	46.17	38.51	32.44	39.04
20	永恒睡莲 N. immutabilis	MW802267.1	0.170	51.349	46.2	38.59	32.52	39.10
21	詹姆森睡莲 N. jamesoniana	NC_031826.2	0.169	51.362	46.25	38.67	32.44	39.12
22	侏儒卢旺达睡莲 N. thermarum	MW143076.1	0.170	51.419	46.19	38.61	32.60	39.13

参数Parameter	ENC	GC1	GC2	GC12	GC3	GC3s
GC1	0.04
GC2	0.77^**	0.38
GC12	0.52	0.74^**	0.82^**
GC3	0.90^**	-0.01	0.64^*	0.42
GC3s	0.89^**	-0.04	0.63^*	0.40	0.97^**
GCall	0.83^**	0.46	0.86^**	0.82^**	0.78^**	0.74^**

睡莲属叶绿体基因组密码子偏好性及系统发育分析

Analysis of Codon Usage Bias and Phylogenetic of Chloroplast Genome in Nymphaea

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