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

1	XU C, DONG W P, LI W Q, et al.. Comparative analysis of six Lagerstroemia complete chloroplast genomes [J/OL]. Front. Plant Sci., 2017, 8:15 [2021-09-10]. .
2	吴静妍,葛新新,李海英,等.蔷薇科果树组织培养研究进展[J].安徽农业科学,2020,48(21):10-12.
	WU J Y, GE X X, LI H Y, et al.. Research progress on tissue culture of Rosaceae fruit trees [J]. J. Anhui Agric. Sci., 2020, 48(21):10-12.
3	刘玉,刘聚栋.月季在园林布景中的应用[J].乡村科技,2021,12(24):106-107.
4	GUTTERIDGE S. The impact of a changing atmosphere on chloroplast function, photosynthesis, yield, and food security [J]. Essays Biol., 2018, 62(1):1-11.
5	陈柯伊,李朝娜,成敏敏,等.不同叶色矢竹叶绿体结构和光系统特性差异[J].植物学报,2018,53(4):509-518.
	CHEN K Y, LI Z N, CHENG M M, et al.. Chloroplast ultrastructure and chlorophyll fluorescence characteristics of three cultivars of Pseudosasa japonica [J]. Chin. Bull. Bot., 2020, 48(21):10-12.
6	NAKAMURA M, SUGIURA M. Translation efficiencies of synonymous codons for arginine differ dramatically and are not correlated with codon usage in chloroplasts [J]. Gene, 2011, 472(1-2):50-54.
7	DINAKAR C, QINGWEI Z, DOROTHEA B. Protection of photosynthesis in desiccation-tolerant resurrection plants [J]. J. Plant Physiol., 2018, 227:84-92.
8	ANDREW W G, SHEIL A A, LI Z Z, et al.. Comparative genomics of 11 complete chloroplast genomes of Senecioneae (Asteraceae) species: DNA barcodes and phylogenetics [J/OL]. Bot. Stud., 2019, 60(1):17 [2021-09-10]. .
9	WEI Q K, JIN H Y. The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L [J/OL]. Peer J., 2017, 5:e3037 [2021-09-10]. .
10	SUZUKI H, MORTON B R. Codon adaptation of plastid genes [J/OL]. PLoS ONE, 2016, 11(5):e0154306 [2021-09-10]. .
11	NAKAMURA M, SUGIURA M. Translation efficiencies of synonymous codons for arginine differ dramatically and are not correlated with codon usage in chloroplasts [J]. Gene, 2011, 472(1-2):50-54.
12	PURABI M, ROFINA Y B, KATHARINA M N, et al.. Codon usage and codon pair patterns in non-grass monocot genomes [J]. Ann. Bot., 2017, 120:893-909.
13	LIU M Y, DONG H, WANG M, et al.. Evolutionary divergence of function and expression of laccase genes in plants [J/OL]. J. Genet., 2020, 99(1):23 [2021-09-10]. .
14	LIU X Y, LI Y, JI K K, et al.. Genome-wide codon usage pattern analysis reveals the correlation between codon usage bias and gene expression in Cuscuta australis [J]. Genomics, 2020, 112 (4):2695-2702.
15	JENSEN P E, LEISTER D. Chloroplast evolution, structure and functions [J/OL]. F1000Prime Rep., 2014, 6:40 [2021-09-10]. .
16	ZHANG D Z, RABIA B P, LIU J J, et al.. Morphological diversity and correlation analysis of phenotypes and quality traits of proso millet (Panicum miliaceum L.) core collections [J]. J. Integr. Agric., 2019, 18(5):958-969.
17	HD B, DONG H, JIANG C, et al.. Analysis of codon usage patterns in Ginkgo biloba reveals codon usage tendency from A/U-ending to G/C-ending [J/OL]. Sci. Rep., 2016, 6(1):35927 [2021-09-10]. .
18	WRIGHT F. The ‘effective number of codons’ used in a gene [J]. Gene, 1990, 87(1):23-29.
19	SHIVANI G, PATRA P K, YADAV M K. New insights into the factors affecting synonymous codon usage in human infecting Plasmodium species [J]. Acta Trop., 2017, 176:29-33.
20	RENSING S, FRITZOWSKY D, LANG D, et al.. Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens [J/OL]. BMC Genomics., 2005, 6(1):43 [2021-09-10]. .
21	吴宪明,吴松锋,任大明,等.密码子偏性的分析方法及相关研究进展[J].遗传,2007(4):420-426.
	WU X M, WU S F, REN D M, et al.. The analysis method and progress in the study of codon bias [J]. Hereditas., 2007(4):420-426.
22	SONG H, LIU J, SONG Q, et al.. Comprehensive analysis of codon usage bias in seven Epichloë species and their peramine-coding genes [J/OL]. Front. Microbiol., 2017, 8:1419 [2021-09-10]. .
23	ZHANG Y, NIE X, JIA X, et al.. Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family [J/OL]. Aust. J. Bot., 2012, 60 (5):461 [2021-09-10]. .
24	MCLEAN M J, WOLFE K H, DEVINE K M. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes [J]. J. Mol. Evol., 1998, 47(6):691-696.
25	唐玉娟,赵英,黄国弟,等.芒果叶绿体基因组密码子使用偏好性分析[J].热带作物学报,2021,42(8):2143-2150.
	TANG Y J, ZHAO Y, HUANG G D, et al.. Analysis on codon usage bias of chloroplast genes from mango [J]. Chin. J. Tropical Crop, 2021, 42(8):2143-2150.
26	王鹏良,杨利平,吴红英,等.普通油茶叶绿体基因组密码子偏好性分析[J].广西植物,2018,38(2):135-144.
	WANG P L, YANG L P, WU H Y, et al.. Condon preference of chloroplast genome in Camellia oleifera [J]. Guihaia, 2018, 38(2):135-144.
27	刘汉梅,赵耀,顾勇,等.几种植物waxy基因的密码子用法特性分析[J].核农学报,2010,24(3):476-481.
	LIU H M, ZHAO Y, GU Y, et al.. Characterization of codon usage of waxy genes in several plants [J]. J. Nucl. Agric. Sci., 2010, 24(3):476-481.
28	KUMAR S, STECHER G, LI M, et al.. MEGA X: molecular evolutionary genetics analysis across computing platforms [J]. Mol. Biol. Evol., 2018, 35(6):1547-1549.
29	LI S C, CHANG L, ZHANG J. Advancing organelle genome transformation and editing for crop improvement [J/OL]. Plant Commun., 2021, 2(2):100141 [2021-09-10]. .
30	CHAKRABORTY S, NAG D, MAZUMDER T H, et al.. Codon usage pattern and prediction of gene expression level in Bungarus species [J]. Gene, 2017, 604:48-60.
31	朱婷婷,张磊,陈万生,等.1342个植物叶绿体基因组分析[J].基因组学与应用生物学, 2017,36(10):4323-4333.
	ZHU T T, ZHANG L, CHEN W S, et al.. Analysis of chloroplast genomes in 1342 plants [J]. Genomics Appl. Biol., 2017, 36(10):4323-4333.
32	季凯凯,宋希强,陈春国,等.木兰科叶绿体基因组的密码子使用特征分析[J].中国农业科技导报,2020,22(11):52-62.
	JI K K, SONG X Q, CHEN C G, et al.. Codon usage profiling of chloroplast genome in Magnoliaceae [J]. J. Agric. Sci. Technol., 2020, 22(11):52-62.
33	WANG Z, XU B, LI B, et al.. Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species [J/OL]. Peer J., 2020, 8:e8251 [2021-09-10]. .
34	LI N, LI Y, ZHENG C, et al.. Genome-wide comparative analysis of the codon usage patterns in plants [J]. Genes Genom., 2016, 38:723-731.
35	吴妙丽,陈世品,陈辉.竹亚科叶绿体基因组的密码子使用偏性分析[J].森林与环境学报,2019,39(1):9-14.
	WU M L, CHEN S P, CHEN H. Condon preference of chloroplast genome of Bambusoideae [J]. J. Fores. Env. 2019, 39(1):9-14.
36	傅建敏,索玉静,刘慧敏,等.柿属植物叶绿体蛋白质编码基因密码子用法[J].经济林研究,2017,35(2):38-44.
	FU J M, SUO Y J, LIU H M, et al.. Analysis on codon usage in the chloroplast protein-coding genes of Diospyros spp [J]. Nonwood Forest Res., 2017, 35(2):38-44.

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

[1]	严其伟, 梁湘兰, 陶秋云, 罗秋香, 郭松. 老班瑶药牛耳风叶绿体基因组特征及其密码子使用偏好性分析[J]. 中国农业科技导报, 2022, 24(8): 74-86.
[2]	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.
[3]	苏玥§, 刘娟娟§, 完斌, 张鹏举, 陈正根, 宿俊吉, 王彩香. 乳苣叶绿体基因组特征及其系统发育分析[J]. 中国农业科技导报, 2021, 23(6): 33-42.
[4]	季凯凯1,宋希强1,陈春国2,李革2,谢尚潜1*. 木兰科叶绿体基因组的密码子使用特征分析[J]. 中国农业科技导报, 2020, 22(11): 52-62.