12种蔷薇科植物叶绿体基因组密码子偏好性分析

doi:10.13304/j.nykjdb.2021.0876

摘要/Abstract

摘要：

为研究蔷薇科植物叶绿体基因组密码子偏好性，对12种蔷薇科植物进行叶绿体基因组密码子使用模式分析。结果表明，12种蔷薇科植物叶绿体基因组的GC含量为 36.54%~37.23%，密码子第3位碱基的平均GC含量为28.27%~28.61%，平均有效密码子数为47.87~49.17。筛选到32个高频密码子，主要以A/U结尾。中性绘图分析、ENC-plot分析、PR2-plot分析表明自然选择是蔷薇科植物密码子偏好性形成的主要因素。基于同义密码子相对使用度（relative synonymous codon usage，RSCU）构建的进化树与基于编码基因和叶绿体基因组构建的进化树聚类差异较大，说明基于密码子偏好特征的进化关系可能损失了一些信息。以上结果为深入探究蔷薇科植物进化规律奠定了理论基础。

关键词: 蔷薇科, 叶绿体基因组, 密码子使用特征, 系统进化树

Abstract:

To study the structure characteristics， phylogeny and codon usage bias of chloroplast genome in Rosaceae plants， 12 Rosaceae species were selected for pattern analysis of chloroplast genome codon usage. The results showed that the GC contents of chloroplast genome in 12 Rosaceae species were 36.54%~37.23%， and the average GC contents of the third base in codon were 28.27%~28.61%， and the average effective number of codons was 47.87~49.17. 32 high-frequency codons were screened， which mainly ended with A/U. The neutral plot analysis， ENC-plot analysis and PR2-plot analysis showed that natural selection was the main factor for codon bias formation in Rosaceae plants. The clustering tree constructed based on RSCU（relative synonymous codon usage） value was different with the evolutionary trees constructed based on coding genes and chloroplast genome， which indicated some informations was lost based on codon preference characteristics. The above results laid foundation for further exploration of the evolution law of Rosaceae plants.

Key words: Rosaceae, chloroplast genome, codon usage characteristics, phylogenetic tree

中图分类号:

张冬冬, 韩宏伟, 余镇藩, 曾斌, 杨佳惠, 高雯雯, 马昕彤. 12种蔷薇科植物叶绿体基因组密码子偏好性分析[J]. 中国农业科技导报, 2023, 25(8): 65-75.

Dongdong ZHANG, Hongwei HAN, Zhenfan YU, Bin ZENG, Jiahui YANG, Wenwen GAO, Xintong MA. Codon Preference Analysis of Chloroplast Genome in 12 Rosaceae Plants[J]. Journal of Agricultural Science and Technology, 2023, 25(8): 65-75.

图/表 9

参考文献 36

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属 Genus	物种 Species	NCBI登录号 Accession number in the NCBI database	长度 Length/bp
木瓜属Chaenomeles	木瓜Chaenomeles sinensis	KT932967.1	159 351
枇杷属Eriobotrya Lindl.	枇杷Eriobotrya japonica	KT633951.1	159 137
草莓属Fragaria L.	草莓Fragaria × ananassa	KY358226.1	155 549
苹果属Malus Mill.	苹果Malus domestica	MK434916.1	159 926
苹果属Malus Mill.	西府海棠Malus micromalus	MF062434.1	159 834
杏属Armeniaca Mill.	杏Prunus armeniaca	MH700954.1	158 070
杏属Armeniaca Mill.	梅花Prunus mume	MH727486.1	157 783
桃属Amygdalus L.	扁桃Prunus dulcis	MH700953.1	157 916
桃属Amygdalus L.	桃Prunus persica	HQ336405.1	157 790
樱属Cerasus Mill.	樱桃Prunus pseudocerasus	KX255667.1	157 834
李属Prunus L.	中国李Prunus salicina	MH700952.1	157 916
梨属Pyrus	西洋梨Pyrus communis	MN577870.1	160 171

属 Genus	物种 Species	NCBI登录号 Accession number in the NCBI database	长度 Length/bp
木瓜属Chaenomeles	木瓜Chaenomeles sinensis	KT932967.1	159 351
枇杷属Eriobotrya Lindl.	枇杷Eriobotrya japonica	KT633951.1	159 137
草莓属Fragaria L.	草莓Fragaria × ananassa	KY358226.1	155 549
苹果属Malus Mill.	苹果Malus domestica	MK434916.1	159 926
苹果属Malus Mill.	西府海棠Malus micromalus	MF062434.1	159 834
杏属Armeniaca Mill.	杏Prunus armeniaca	MH700954.1	158 070
杏属Armeniaca Mill.	梅花Prunus mume	MH727486.1	157 783
桃属Amygdalus L.	扁桃Prunus dulcis	MH700953.1	157 916
桃属Amygdalus L.	桃Prunus persica	HQ336405.1	157 790
樱属Cerasus Mill.	樱桃Prunus pseudocerasus	KX255667.1	157 834
李属Prunus L.	中国李Prunus salicina	MH700952.1	157 916
梨属Pyrus	西洋梨Pyrus communis	MN577870.1	160 171

物种Specie	CP	T3	C3	A3	G3	GC1	GC2	GC3	GCall
木瓜Chaenomeles sinensis	31.22	27.91	45.57	37.76	29.74	46.98	39.47	28.28	36.66
枇杷Eriobotrya japonica	31.19	27.92	45.56	37.79	29.73	46.94	39.50	28.27	36.72
草莓Fragaria × ananassa	31.66	28.57	45.60	37.73	30.62	47.06	39.45	29.29	37.23
苹果Malus domestica	31.22	27.90	45.56	37.75	29.73	47.00	39.43	28.32	36.57
西府海棠Malus micromalus	31.77	28.29	45.46	37.66	29.80	46.97	39.44	28.28	36.61
杏Prunus armeniaca	31.76	28.20	45.36	37.62	29.81	46.86	39.40	28.43	36.72
梅花Prunus mume	31.26	27.86	45.48	37.76	29.89	46.90	39.40	28.61	36.76
扁桃Prunus dulcis	31.75	28.20	45.34	37.60	29.83	46.88	39.34	28.45	36.73
桃Prunus persica	31.26	27.86	45.48	37.74	29.86	46.90	39.37	28.58	36.75
樱桃Prunus pseudocerasus	31.70	28.21	45.35	37.61	29.88	46.80	39.38	28.45	36.73
中国李Prunus salicina	31.74	28.21	45.39	37.61	29.80	46.90	39.36	28.45	36.75
西洋梨Pyrus communis	31.75	28.30	45.47	37.67	29.83	46.98	39.46	28.35	36.54

物种Specie	CP	T3	C3	A3	G3	GC1	GC2	GC3	GCall
木瓜Chaenomeles sinensis	31.22	27.91	45.57	37.76	29.74	46.98	39.47	28.28	36.66
枇杷Eriobotrya japonica	31.19	27.92	45.56	37.79	29.73	46.94	39.50	28.27	36.72
草莓Fragaria × ananassa	31.66	28.57	45.60	37.73	30.62	47.06	39.45	29.29	37.23
苹果Malus domestica	31.22	27.90	45.56	37.75	29.73	47.00	39.43	28.32	36.57
西府海棠Malus micromalus	31.77	28.29	45.46	37.66	29.80	46.97	39.44	28.28	36.61
杏Prunus armeniaca	31.76	28.20	45.36	37.62	29.81	46.86	39.40	28.43	36.72
梅花Prunus mume	31.26	27.86	45.48	37.76	29.89	46.90	39.40	28.61	36.76
扁桃Prunus dulcis	31.75	28.20	45.34	37.60	29.83	46.88	39.34	28.45	36.73
桃Prunus persica	31.26	27.86	45.48	37.74	29.86	46.90	39.37	28.58	36.75
樱桃Prunus pseudocerasus	31.70	28.21	45.35	37.61	29.88	46.80	39.38	28.45	36.73
中国李Prunus salicina	31.74	28.21	45.39	37.61	29.80	46.90	39.36	28.45	36.75
西洋梨Pyrus communis	31.75	28.30	45.47	37.67	29.83	46.98	39.46	28.35	36.54

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