Analysis and Comparative Characteristics of Codon Preference in Chloroplast Genome of Polygonum genus

doi:10.13304/j.nykjdb.2024.0090

Abstract

Abstract:

To explore the structure， function and evolutionary characteristics of chloroplast genome of Polygonum plants， the software of CodonW， SPSS and online programs Galaxy， Genepioneer Bioinformatics Cloud， mVISTA， GENE DENOVO and other tools were used to analyze the codon usage preferences and phylogenetic relationships of the chloroplast genomes of 28 Polygonum plants. The results showed that the codon adaptation index （CAI） and effective number of codon （ENC） in chloroplast genomes of 28 species of Polygonum plants were low， which indicated weak codon usage preference and being mainly influenced by natural selection. The third base of codon mainly ended in A/U， and 9 optimal codons of chloroplast genome all ended in A/U. The correlation analysis between the GC content at different positions of codon， ENC and GC3s， GC3， GC2 revealed that codon preference in chloroplast genome of Polygonum was weak and mainly influenced by the third base composition， while the length of the chloroplast gene sequence had less influence on base composition and codon preference. The phylogenetic tree based on the relative synonymous codon usage （RSCU） was consist with those besed on matk and rbcl gene sequences， 28 species of Polygonum plants were classified into 3 groups， but there were differences in each group， such as P. maackiana was same group with P. tinctoria in phylogenetic tree based on matk gene， while was same group with P. posumbu in phylogenetic tree based on rbcl gene. Above results provided a reference for the utilization， phylogeny， and chloroplast genetic engineering of Polygonum plants.

Key words: Polygonum genus, chloroplast genome, codon preference, comparative features, phylogeny

摘要：

为探究蓼属植物叶绿体基因组的结构、功能和进化特征，利用CodonW、SPSS软件和在线程序Galaxy、Genepioneer生信云、mVISTA、GENE DENOVO等工具，对28种蓼属植物叶绿体基因组的密码子使用偏好性和系统发育关系进行分析。结果表明，28种蓼属植物叶绿体基因组的密码子适应指数（codon adaptation index，CAI）和有效密码子数（effective number of codon，ENC）均较低，说明其密码子使用偏好性较弱，且主要受自然选择影响；密码子第3位碱基以A/U结尾为主，且叶绿体基因组的9个最优密码子均以A/U结尾；密码子不同位置的GC含量和ENC与密码子GC3s、GC3、GC2之间的相关性分析揭示，蓼属植物叶绿体基因组的密码子偏好性弱，且密码子偏好性主要受第3位碱基组成的影响，叶绿体基因序列长度对碱基组成和密码子偏好性影响较小；基于同义密码子相对使用度（relative synonymous codon usage，RSCU）的系统发育树与基于matk和rbcl基因序列的系统发育树结果相似，28种蓼属植物均被划分为3个类群，但内部存在部分差异，如长戟叶蓼基于matk序列时与蓼蓝聚为一个类群，而基于rbcl序列时与丛枝蓼聚为一个类群。以上研究结果为蓼属植物的资源利用、系统发育和叶绿体基因工程研究提供了参考和依据。

关键词: 蓼属, 叶绿体基因组, 密码子偏好性, 比较特征, 系统发育

CLC Number:

Q943

Qilin LIU, Jinze LI, Jiayu DING, Shuoli WANG, Ziming CHENG, Kangyuan GU, Guangyan FENG. Analysis and Comparative Characteristics of Codon Preference in Chloroplast Genome of Polygonum genus[J]. Journal of Agricultural Science and Technology, 2025, 27(4): 87-98.

刘起麟, 李金泽, 丁佳渝, 王烁理, 程子铭, 古康圆, 冯光燕. 蓼属叶绿体基因组密码子偏好性分析及比较特征[J]. 中国农业科技导报, 2025, 27(4): 87-98.

Figures/Tables 12

References 34

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物种 Species	登陆号 Accession No.	密码子适应指数 CAI	最优密码子使用频率FOP	有效密码子数 ENC	GC含量GC content/％
物种 Species	登陆号 Accession No.	密码子适应指数 CAI	最优密码子使用频率FOP	有效密码子数 ENC	GCall	GC1	GC2	GC3
香蓼 P. viscosa	NC_071834.1	0.164	0.352	51.30	38.38	45.91	37.75	31.49
粘蓼 P. viscofera	NC_082263.1	0.163	0.351	51.15	38.35	45.91	37.77	31.38
蓼蓝 P. tinctoria	OR730799.1	0.165	0.354	51.31	39.26	47.12	38.96	31.68
戟叶蓼 P. thunbergii	NC_082262.1	0.164	0.353	51.32	38.38	45.92	37.82	31.40
刺蓼 P. senticosa	NC_067968.1	0.164	0.352	51.04	38.26	45.74	37.88	31.15
伏毛蓼 P. pubescens	MK234901.1	0.164	0.351	51.18	38.36	45.94	37.74	31.39
丛枝蓼 P. posumbu	NC_082260.1	0.163	0.351	51.23	38.36	45.89	37.76	31.42
扛板归 P. perfoliata	OR730805.1	0.163	0.351	50.88	38.09	45.64	37.67	30.96
红蓼 P. orientalis	NC_065785.1	0.163	0.351	51.25	38.39	46.00	37.74	31.44
尼泊尔蓼 P. nepalensis	NC_082259.1	0.163	0.351	51.22	38.37	45.93	37.75	31.42
春蓼 P. maculosa	NC_082258.1	0.163	0.351	51.22	38.22	45.93	37.75	31.42
长戟叶蓼 P. maackiana	NC_061657.1	0.165	0.353	51.23	38.45	46.17	37.82	31.36
长鬃蓼 P. longiseta	OR730801.1	0.165	0.353	51.23	38.45	46.17	37.82	31.36
酸模叶蓼 P. lapathifolia	OR730804.1	0.163	0.351	51.23	38.38	45.96	37.78	31.42
柔茎蓼 P. kawagoeana	NC_082256.1	0.163	0.351	51.21	38.35	45.90	37.75	31.40
愉悦蓼 P. jucunda	NC_084112.1	0.164	0.352	51.30	38.43	46.04	37.77	31.48
蚕茧草 P. japonica	ON229577.1	0.163	0.351	51.18	38.33	45.85	37.76	31.37
水蓼 P. hydropiper	MK234902.1	0.164	0.352	51.08	38.23	45.80	37.74	31.15
长箭叶蓼 P. hastatosagittata	OR730803.1	0.164	0.352	51.08	38.23	45.80	37.74	31.15
冰川蓼 P. glacialis	NC_082254.1	0.163	0.350	50.88	38.20	45.80	37.74	31.04
光蓼 P. glabra	OR730797.1	0.164	0.352	51.31	38.45	46.11	37.77	31.48
多叶蓼 P. foliosa	ON229572.1	0.163	0.351	51.22	38.35	45.90	37.75	31.41
稀花蓼 P. dissitiflora	ON229570.1	0.164	0.352	51.02	38.23	45.82	37.76	31.11
蓼子草 P. criopolitana	NC_079578.1	0.164	0.351	51.22	38.39	45.99	37.72	31.44
火炭母 P. chinensis	NC_050358.1	0.164	0.351	50.99	38.24	45.92	37.69	31.11
头花蓼 P. capitata	OR730796.1	0.164	0.351	50.99	38.26	45.94	37.74	31.10
柳叶刺蓼 P. bungeana	ON229568.1	0.163	0.350	51.06	38.31	45.91	37.77	31.25
两栖蓼 P. amphibia	ON229566.1	0.163	0.350	51.06	38.31	45.91	37.77	31.25

物种 Species	登陆号 Accession No.	密码子适应指数 CAI	最优密码子使用频率FOP	有效密码子数 ENC	GC含量GC content/％
物种 Species	登陆号 Accession No.	密码子适应指数 CAI	最优密码子使用频率FOP	有效密码子数 ENC	GCall	GC1	GC2	GC3
香蓼 P. viscosa	NC_071834.1	0.164	0.352	51.30	38.38	45.91	37.75	31.49
粘蓼 P. viscofera	NC_082263.1	0.163	0.351	51.15	38.35	45.91	37.77	31.38
蓼蓝 P. tinctoria	OR730799.1	0.165	0.354	51.31	39.26	47.12	38.96	31.68
戟叶蓼 P. thunbergii	NC_082262.1	0.164	0.353	51.32	38.38	45.92	37.82	31.40
刺蓼 P. senticosa	NC_067968.1	0.164	0.352	51.04	38.26	45.74	37.88	31.15
伏毛蓼 P. pubescens	MK234901.1	0.164	0.351	51.18	38.36	45.94	37.74	31.39
丛枝蓼 P. posumbu	NC_082260.1	0.163	0.351	51.23	38.36	45.89	37.76	31.42
扛板归 P. perfoliata	OR730805.1	0.163	0.351	50.88	38.09	45.64	37.67	30.96
红蓼 P. orientalis	NC_065785.1	0.163	0.351	51.25	38.39	46.00	37.74	31.44
尼泊尔蓼 P. nepalensis	NC_082259.1	0.163	0.351	51.22	38.37	45.93	37.75	31.42
春蓼 P. maculosa	NC_082258.1	0.163	0.351	51.22	38.22	45.93	37.75	31.42
长戟叶蓼 P. maackiana	NC_061657.1	0.165	0.353	51.23	38.45	46.17	37.82	31.36
长鬃蓼 P. longiseta	OR730801.1	0.165	0.353	51.23	38.45	46.17	37.82	31.36
酸模叶蓼 P. lapathifolia	OR730804.1	0.163	0.351	51.23	38.38	45.96	37.78	31.42
柔茎蓼 P. kawagoeana	NC_082256.1	0.163	0.351	51.21	38.35	45.90	37.75	31.40
愉悦蓼 P. jucunda	NC_084112.1	0.164	0.352	51.30	38.43	46.04	37.77	31.48
蚕茧草 P. japonica	ON229577.1	0.163	0.351	51.18	38.33	45.85	37.76	31.37
水蓼 P. hydropiper	MK234902.1	0.164	0.352	51.08	38.23	45.80	37.74	31.15
长箭叶蓼 P. hastatosagittata	OR730803.1	0.164	0.352	51.08	38.23	45.80	37.74	31.15
冰川蓼 P. glacialis	NC_082254.1	0.163	0.350	50.88	38.20	45.80	37.74	31.04
光蓼 P. glabra	OR730797.1	0.164	0.352	51.31	38.45	46.11	37.77	31.48
多叶蓼 P. foliosa	ON229572.1	0.163	0.351	51.22	38.35	45.90	37.75	31.41
稀花蓼 P. dissitiflora	ON229570.1	0.164	0.352	51.02	38.23	45.82	37.76	31.11
蓼子草 P. criopolitana	NC_079578.1	0.164	0.351	51.22	38.39	45.99	37.72	31.44
火炭母 P. chinensis	NC_050358.1	0.164	0.351	50.99	38.24	45.92	37.69	31.11
头花蓼 P. capitata	OR730796.1	0.164	0.351	50.99	38.26	45.94	37.74	31.10
柳叶刺蓼 P. bungeana	ON229568.1	0.163	0.350	51.06	38.31	45.91	37.77	31.25
两栖蓼 P. amphibia	ON229566.1	0.163	0.350	51.06	38.31	45.91	37.77	31.25

指标 Index	GC1	GC2	GC3	GC3s	GCall	有效密码子数ENC
GC2	0.475^**
GC3	0.171	0.223
GC3s	0.177	0.252	0.985^**
GCall	0.829^**	0.812^**	0.505^**	0.517^**
有效密码子数ENC	0.094	-0.071	0.343^*	0.348^*	0.121
基因数量Genes number	-0.076	-0.211	0.201	0.199	-0.083	0.213

指标 Index	GC1	GC2	GC3	GC3s	GCall	有效密码子数ENC
GC2	0.475^**
GC3	0.171	0.223
GC3s	0.177	0.252	0.985^**
GCall	0.829^**	0.812^**	0.505^**	0.517^**
有效密码子数ENC	0.094	-0.071	0.343^*	0.348^*	0.121
基因数量Genes number	-0.076	-0.211	0.201	0.199	-0.083	0.213

物种Species	最优密码子Optimal codon
扛板归 P. perfoliata	GCUCGUUGU GAA GGU AUU UUA AAA UUU CCU AGU UCU ACA GUAGUU
两栖蓼 P. amphibia	GCU CGA CGU AAC UGU GAA GGU AUU CUU UUA AAA CCA CCU AGU UCU ACA ACC GUAGUU
光蓼 P. glabra	GCUCGUUGU GAA GGU AUU UUA AAA UUU CCU AGU UCU ACA ACU GUAGUU
火炭母 P. chinensis	GCU CGA CGUUGU GAA GGU CAU AUU UUA AAA UUU CCU AGU UCU ACU GUAGUU
柔茎蓼 P. kawagoeana	GCUCGUUGU CAA GAA GGU AUU CUU UUA AAA UUU CCA CCU AGU UCU ACA GUAGUU
蚕茧草 P. japonica	GCUCGUUGU CAA GAA GGU AUU CUU UUA AAA CCA CCU AGU UCU ACA GUAGUU
冰川蓼 P. glacialis	GCU AGA CGUUGU CAA GGU CUU UUG AAACCUUCU ACA ACU GUA GUU
头花蓼 P. capitata	GCUCGUUGU CAA GAA GGU CAU AUU CUU UUA AAA UUU CCU AGU UCU ACA ACU GUAGUU