小黑麦叶绿体基因组密码子偏好性分析与基因功能相关性分析

doi:10.11733/j.issn.1007-0435.2025.03.005

草地学报 ›› 2025, Vol. 33 ›› Issue (3): 707-718.DOI: 10.11733/j.issn.1007-0435.2025.03.005

• 研究论文 • 上一篇

小黑麦叶绿体基因组密码子偏好性分析与基因功能相关性分析

田甜, 张银霞, 杜文华

甘肃农业大学草业学院/草业生态系统教育部重点实验室/甘肃省草业工程实验室/中-美草地畜牧业可持续发展研究中心, 甘肃兰州 730070

收稿日期:2024-08-26 修回日期:2024-10-13 发布日期:2025-04-07
通讯作者: 杜文华,E-mail:duwh@gasu.edu.cn
作者简介:田甜（1997-）,女,苗族,贵州铜仁人,博士研究生,主要从事草地生物多样性研究,E-mail：1138115730@qq.com
基金资助:
农业生物育种重大专项（2023ZD0402605-02）;国家自然科学基金（32260339）;甘肃省高等学校产业支撑计划（2022CYZC-49）;甘肃省重大专项（21ZD4NA012）;西藏重大专项（XZ202101ZD003N）资助

Correlation Between Codon Usage Patterns and Gene Functions in the Chloroplast Genome of Triticale

TIAN Tian, ZHANG Yin-xia, DU Wen-hua

College of Grassland Science, Gansu Agricultural University/Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Ministry of Education/Pratacultural Engineering Laboratory of Gansu Province/Sino-U. S. Centers for Grazingland Ecosystem Sustainability, Lanzhou, Gansu Province 730070, China

Received:2024-08-26 Revised:2024-10-13 Published:2025-04-07

摘要/Abstract

摘要： 为揭示小黑麦（Triticale）的密码子使用偏好性及其影响因素,用CodonW 1.4.2和在线软件CUSP（Codon Usage and Synonymous Condon Usage Profile）对小黑麦叶绿体基因组中52个编码序列（Coding sequence,CDS）特征进行分析。结果表明：小黑麦叶绿体基因组密码子第三位主要偏向以A/U为主；有效密码子数（Effective number of codon,ENC）值在37.64~61.00之间,平均值为47.31,大于45的有42个；密码子适应指数（Codon adaptation index,CAI）在0.12~0.33之间,平均值为0.17,说明小黑麦叶绿体基因组密码子偏好性较弱；16个均以A/U结尾的密码子被筛选为最优密码子。中性绘图、ENC-GC_3s和偏倚性绘图分析（Parity Rule 2,PR2-plot）结果表明多数功能基因的密码子使用偏好性受自然选择压力影响为主。小黑麦叶绿体基因组中与光合作用密切相关的基因可能受到了突变和选择的强烈作用,使这些基因的密码子使用频率具有共同特征,表现为密码子使用模式与基因功能有较大的相关性。

关键词: 小黑麦, 叶绿体基因组, 密码子偏好性, 最优密码子

Abstract: To investigate the codon usage bias and its influencing factors in triticale （Triticale）, CodonW 1.4.2 and the online tool CUSP （Codon Usage and Synonymous Condon Usage Profile） were used to analyze the characteristics of 52 coding sequences （CDS） in the chloroplast genome of triticale. The results showed that the third codon position in the triticale chloroplast genome predominantly favored A/U bases. The effective number of codons （ENC） ranged from 37.64 to 61.00, with an average of 47.31, and 42 sequences had ENC values greater than 45. The codon adaptation index （CAI） ranged 0.12-0.33, with an average of 0.17, indicating a weak codon usage bias in the triticale chloroplast genome. Sixteen codons ending in A/U were identified as optimal codons. Neutral plotting, ENC-GC3s analysis, and PR2-plot analysis （Parity Rule 2） revealed that the codon usage bias of most functional genes was mainly influenced by natural selection. Genes in the triticale chloroplast genome closely related to photosynthesis were likely subjected to strong mutation and selection pressures, resulting in shared codon usage patterns among these genes. This suggests a significant correlation between codon usage patterns and gene functions.

Key words: Triticale, Chloroplast genome, Codon usage bias, Optimal codon

中图分类号:

S544.9

田甜, 张银霞, 杜文华. 小黑麦叶绿体基因组密码子偏好性分析与基因功能相关性分析[J]. 草地学报, 2025, 33(3): 707-718.

TIAN Tian, ZHANG Yin-xia, DU Wen-hua. Correlation Between Codon Usage Patterns and Gene Functions in the Chloroplast Genome of Triticale[J]. Acta Agrestia Sinica, 2025, 33(3): 707-718.

0
/ 收藏文章 0 / 推荐

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://manu40.magtech.com.cn/Jweb_cdxb/CN/10.11733/j.issn.1007-0435.2025.03.005

https://manu40.magtech.com.cn/Jweb_cdxb/CN/Y2025/V33/I3/707

参考文献

[1] VIDI P A,KANWISCHER M,BAGINSKY S,et al. Tocopherol cyclase (VTE1) localization and vitamin E accumulation in chloroplast plastoglobule lipoprotein particles[J]. Journal of Biological Chemistry,2006,281(16):11225-11234
[2] LIPPOLD F,DORP K VOM,ABRAHAM M,et al. Fatty acid phytyl ester synthesis in chloroplasts of Arabidopsis[J]. The Plant Cell,2012,24(5):2001-2014
[3] DANIELL H,JIN S X,ZHU X G,et al. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins:history and phylogeny[J]. Plant Biotechnology Journal,2021,19(3):430-447
[4] DOBROGOJSKI J,ADAMIEC M,LUCIŃSKI R. The chloroplast genome:a review[J]. Acta Physiologiae Plantarum,2020,42(6):98
[5] SUGIURA M. History of chloroplast genomics[J]. Photosynthesis Research,2003,76(1/2/3):371-377
[6] GREVICH J J,DANIELL H. Chloroplast genetic engineering:recent advances and future perspectives[J]. Critical Reviews in Plant Sciences,2005,24(2):83-107
[7] DANIELL H,LIN C S,YU M,et al. Chloroplast genomes:diversity,evolution,and applications in genetic engineering[J]. Genome Biology,2016,17(1):134
[8] KWAK S Y,LEW T T S,SWEENEY C J,et al. Chloroplast-selective gene delivery and expression in planta using chitosan-complexed single-walled carbon nanotube carriers[J]. Nature Nanotechnology,2019,14(5):447-455
[9] RUF S,HERMANN M,BERGER I J,et al. Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit[J]. Nature Biotechnology,2001,19(9):870-875
[10] RAUBESON L A,PEERY R,CHUMLEY T W,et al. Comparative chloroplast genomics:analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus[J]. BMC Genomics,2007,8:174
[11] 高守舆,李钰莹,杨志青,等.白羊草叶绿体基因组密码子使用偏好性分析[J].草业学报,2023,32(7):85-95
[12] IKEMURA T. Codon usage and tRNA content in unicellular and multicellular organisms[J]. Molecular Biology and Evolution,1985,2(1):13-34
[13] QUAX T E F,CLAASSENS N J,SÖLL D,et al. Codon bias as a means to fine-tune gene expression[J]. Molecular Cell,2015,59(2):149-161
[14] WANG Z J,XU B B,LI B,et al. Comparative analysis of Codon usage patterns in chloroplast genomes of six Euphorbiaceae species[J]. PeerJ,2020,8:e8251
[15] SHENG J J,SHE X,LIU X Y,et al. Comparative analysis of Codon usage patterns in chloroplast genomes of five Miscanthus species and related species[J]. PeerJ,2021,9:e12173
[16] MAZUMDAR P,BINTI OTHMAN R,MEBUS K,et al. Codon usage and Codon pair patterns in non-grass monocot genomes[J]. Annals of Botany,2017,120(6):893-909
[17] CHEN S L,LEE W,HOTTES A K,et al. Codon usage between genomes is constrained by genome-wide mutational processes[J]. Proceedings of the National Academy of Sciences of the United States of America,2004,101(10):3480-3485
[18] 刘慧,王梦醒,岳文杰,等.糜子叶绿体基因组密码子使用偏性的分析[J].植物科学学报,2017,35(3):362-371
[19] 原晓龙,李云琴,张劲峰,等.降香黄檀叶绿体基因组密码子偏好性分析[J].广西植物,2021,41(4):622-630
[20] 刘晶,赵明月,郭宏玉,等.高寒牧区小黑麦研究进展[J].青海科技,2021,28(4):23-26
[21] 王伟强,刘晶,田新会,等.“甘农4号”小黑麦品种在青海省不同区域的适应性评价[J].草地学报,2020,28(6):1626-1634
[22] 裴亚斌,杜文华,刘汉成,等.甘南高寒牧区3种饲草不同种植模式下的生产性能及经济效益[J].草业科学,2020,37(4):791-799
[23] 杨晓,宋谦,余小亮,等.陇东旱塬区秋播小黑麦与青贮玉米的复种效果[J].草业科学,2019,36(8):2127-2134
[24] 杨永强,尹玉林,杜文华.青藏高原川西北牧区一年两季饲草种植模式对土壤理化性质及酶活性的影响[J].草原与草坪,2024,44(2):57-66
[25] 宋谦,马淑梅,张兰,等.陇东地区秋播小黑麦茬后复种青贮玉米品种的筛选[J].中国饲料,2024(7):140-145
[26] 倪典墨,李冉郡,郭忠静,等.百合科植物psbA基因密码子偏好性分析[J].生物学杂志,2020,37(6):68-72
[27] BIN PEK H,KLEMENT M,ANG K S,et al. Exploring Codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli[J]. Enzyme and Microbial Technology,2015,75:57-63
[28] 时欢,林玉玲,赖钟雄,等. CRISPR/Cas9介导的植物基因编辑技术研究进展[J].应用与环境生物学报,2018,24(3):640-650
[29] DOUDNA J A,CHARPENTIER E. The new frontier of genome engineering with CRISPR-Cas9[J]. Science, 2014,346(6213):1258096
[30] JIANG F G,DOUDNA J A. CRISPR-Cas9 structures and mechanisms[J]. Annual Review of Biophysics, 2017,46(1):505-529
[31] MA X L,ZHANG Q Y,ZHU Q L,et al. A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants[J]. Molecular Plant,2015,8(8):1274-1284
[32] SHAN Q W,WANG Y P,LI J,et al. Targeted genome modification of crop plants using a CRISPR-Cas system[J]. Nature Biotechnology,2013,31(8):686-688
[33] ZHANG H,ZHANG J S,WEI P L,et al. The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation[J]. Plant Biotechnology Journal,2014,12(6):797-807
[34] SUEOKA N. Directional mutation pressure and neutral molecular evolution[J]. Proceedings of the National Academy of Sciences of the United States of America,1988,85(8):2653-2657
[35] KAWABE A,MIYASHITA N T. Patterns of Codon usage bias in three dicot and four monocot plant species[J]. Genes& Genetic Systems,2003,78(5):343-352
[36] WRIGHT F. The'effective number of codons'used in a gene[J]. Gene,1990,87(1):23-29
[37] SUEOKA N. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third Codon position[J]. Gene,1999,238(1):53-58
[38] WANG L J,ROOSSINCK M J. Comparative analysis of expressed sequences reveals a conserved pattern of optimal Codon usage in plants[J]. Plant Molecular Biology,2006,61(4/5):699-710
[39] 洪森荣,林顺来,李盈萍,等.甜高粱叶绿体基因组特征及密码子偏好性分析[J].草地学报,2023,31(12):3636-3650
[40] ZHANG Y R,NIE X J,JIA X O,et al. Analysis of Codon usage patterns of the chloroplast genomes in the Poaceae family[J]. Australian Journal of Botany,2012,60(5):461
[41] 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
[42] YANG S W,LI G,LI H. Molecular characterizations of genes in chloroplast genomes of the genus Arachis L.(Fabaceae) based on the Codon usage divergence[J]. PLoS One,2023,18(3):e0281843
[43] CAMPBELL W H,GOWRI G. Codon usage in higher plants,green algae,and cyanobacteria[J]. Plant Physiology,1990,92(1):1-11
[44] SHARP P M,LI W H. An evolutionary perspective on synonymous Codon usage in unicellular organisms[J]. Journal of Molecular Evolution,1986,24(1/2):28-38
[45] SALIM H M W,CAVALCANTI A R O. Factors influencing Codon usage bias in genomes[J]. Journal of the Brazilian Chemical Society,2008,19(2):257-262
[46] LIU Q P. Mutational bias and translational selection shaping the Codon usage pattern of tissue-specific genes in rice[J]. PLoS One,2012,7(10):e48295
[47] PLOTKIN J B,KUDLA G. Synonymous but not the same:the causes and consequences of Codon bias[J]. Nature Reviews Genetics,2011,12(1):32-42

编辑推荐 0

Metrics

阅读次数

全文

HTML			PDF

最新录用	在线预览	正式出版	最新录用	在线预览	正式出版
0	0	0	0	0	24

	来源	本网站

	次数	24
	比例	100%

摘要

最新录用	在线预览	正式出版

0	0	36

	来源	本网站

	次数	36
	比例	100%

小黑麦叶绿体基因组密码子偏好性分析与基因功能相关性分析

Correlation Between Codon Usage Patterns and Gene Functions in the Chloroplast Genome of Triticale

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐 0

Metrics

本文评价

[1]	李琳, 徐明志, 刘燕蓉, 张万军. 苜蓿基因组密码子偏好性分析[J]. 草地学报, 2024, 32(9): 2695-2706.
[2]	余志伟, 陈垣, 郭凤霞, 董鹏斌, 王红燕. 菘蓝叶绿体基因组密码子使用偏好性分析[J]. 草地学报, 2024, 32(8): 2374-2385.
[3]	邓鸟絮, 罗中元, 孙志轩, 孟静, 赵雁. 螺旋果苜蓿组叶绿体基因组进化和系统发育分析[J]. 草地学报, 2024, 32(8): 2394-2407.
[4]	王涛, 徐成体, 唐楚煜, 曹正飞, 肖梦君, 何敏, 李秀璋, 李玉玲. 基于祖先性状演化和叶绿体基因组的马先蒿形态特征分析[J]. 草地学报, 2024, 32(7): 2039-2053.
[5]	岳竞之, 孙迷平, 陈丽, 张庆社, 牛小沛, 张月玲, 杜文华, 肖兴中, 蔡友敏. 刈割方式对豫西北地区小黑麦草产量和营养品质的影响[J]. 草地学报, 2024, 32(7): 2297-2304.
[6]	花梅, 吕丽娟, 穆赢通, 张晓明, 郝宁, 王俊杰, 刘媛. 基于转录组数据的红三叶密码子使用偏好性分析[J]. 草地学报, 2024, 32(6): 1752-1759.
[7]	杜明川, 王伟, 鲍海娟, 格措, 张蕊, 王久利, 刘晶. 葫芦巴叶绿体基因组密码子偏好性分析[J]. 草地学报, 2024, 32(2): 409-418.
[8]	王毓, 李奇铮, 马小东, 王斌, 王腾飞, 兰剑, 张宇. 播种期及收获期对饲用小黑麦生产性能和营养品质的影响[J]. 草地学报, 2024, 32(2): 637-645.
[9]	郭松, 梁湘兰, 彭姿, 卢全, 曾珍贵. 莓叶委陵菜叶绿体基因组特征及其系统发育分析[J]. 草地学报, 2024, 32(11): 3383-3390.
[10]	卢政阳, 于凤扬, 肖月娥, 石钰, 毕晓颖. 北陵鸢尾叶绿体基因组及其特征分析[J]. 草地学报, 2023, 31(6): 1656-1664.
[11]	郝新艳, 赵淑文, 刘嘉伟, 石蕊, 王晓龙, 李迎, 王晓宇, 米福贵. 杂花苜蓿叶绿体基因组特征及系统发育分析[J]. 草地学报, 2023, 31(6): 1665-1672.
[12]	武瑞鑫, 石霞, 贾文娟, 游永亮, 赵海明, 李源. 华北平原区饲用小黑麦与褐色中脉高丹草复种模式研究[J]. 草地学报, 2023, 31(5): 1571-1577.
[13]	权欣, 武俊喜, 杨培志, 余成群, 钟志明, 呼天明. 拉萨河谷禾豆混播草地生产力与种间关系研究[J]. 草地学报, 2023, 31(3): 657-667.
[14]	郭蕊, 金星娜, 常丹丹, 杜文华. 基于小黑麦RIL群体的草产量相关性状QTL分析[J]. 草地学报, 2023, 31(3): 710-718.
[15]	洪森荣, 林顺来, 李盈萍, 李芸芸, 李和月, 张庆宝. 甜高粱叶绿体基因组特征及密码子偏好性分析[J]. 草地学报, 2023, 31(12): 3636-3650.