[1]许建民,程柳洋,仇学文.红光、蓝光处理下马铃薯转录组特异表达基因密码子的偏好性分析[J].江苏农业学报,2024,(07):1199-1211.[doi:doi:10.3969/j.issn.1000-4440.2024.07.006]
　XU Jianmin,CHENG Liuyang,QIU Xuewen.Analysis of codon usage bias in potato transcriptionally specific expressed genes under red and blue light treatments[J].,2024,(07):1199-1211.[doi:doi:10.3969/j.issn.1000-4440.2024.07.006]
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红光、蓝光处理下马铃薯转录组特异表达基因密码子的偏好性分析()
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江苏农业学报[ISSN:1006-6977/CN:61-1281/TN]

卷:
期数:
2024年07期
页码:
1199-1211
栏目:
遗传育种·生理生化
出版日期:
2024-07-30

文章信息/Info

Title:
Analysis of codon usage bias in potato transcriptionally specific expressed genes under red and blue light treatments
作者:
许建民1; 程柳洋2; 仇学文3
(1.江苏农林职业技术学院,江苏句容212400；2.东台市农业技术推广中心，江苏东台224200；3.江西农业大学,江西南昌330000)
Author(s):
XU Jianmin1; CHENG Liuyang2; QIU Xuewen3
(1.Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, China;2.Agricultural Technology Extension Center of Dongtai City, Dongtai 224200, China;3.Jiangxi Agricultural University, Nanchang 330000, China)
关键词:
红蓝光; 马铃薯; 转录组; 特异表达基因; 密码子; 偏好性
Keywords:
red and blue light; potato; transcriptome; specifically expressed genes; codon; preference
分类号:
S532.01
DOI:
doi:10.3969/j.issn.1000-4440.2024.07.006
文献标志码:
A
摘要:
以红光、蓝光处理下的马铃薯转录组数据为基础,以白光为对照,各筛选出1 206条、691条特异表达基因。通过CodonW、CUSP对筛选出的基因编码序列(CDS)进行密码子使用偏好性分析。结果表明,在红光、蓝光处理下,马铃薯对基因密码子的使用偏好性都较弱,都偏好使用A或T(U)结尾的密码子。在2种光质处理下,特异表达基因序列密码子的GC总量都与同义密码子在第3位的胞嘧啶和鸟嘌呤含量（GC3s）有极显著相关性。在2种光质处理下,高频密码子[相对同义密码子使用度（RSCU）>1.00]均为30个,且高频密码子类型完全一致。从ENc-plot、PR2-plot和中性绘图结果可以看出,2种光质处理下的特异表达基因主要受到自然选择的影响。本研究还分别从蓝光、红光处理的特异表达基因中筛选26个、28个最优密码子。从马铃薯在不同光质处理下特异表达基因与其他生物密码子使用频率的比值及聚类分析结果可以看出,番茄、烟草均可作为红光、蓝光处理下马铃薯特异表达基因的异源表达受体。
Abstract:
In this study, 1 206 and 691 specifically expressed genes were screened based on the transcriptome data of potato under red light treatment and blue light treatment, with white light as control, respectively. The coding sequences (CDS) of the selected genes were analyzed by CodonW and CUSP for codon usage bias. The results showed that the codon usage bias of potato genes under both red and blue light treatments was weak, with both preferring codons ending in A or T (U). The total number of sequence codons GC under two light treatments was highly significantly correlated with GC3s. Codons with relative synonymous codon usage (RSCU) greater than 1.00 were high-frequency codons. The number of high-frequency codons under two light treatments was 30, and the types of high-frequency codons were identical. Based on the results of ENc-plot, PR2-plot and neutral plots, it was found that the specifically expressed genes under two light treatments were mainly affected by natural selection. In this study, the 26 and 28 best codons were also screened from genes specifically expressed under blue and red light treatments, respectively. The ratio of codon usage frequency of specifically expressed genes under different light treatments in potato to that in other organisms and the clustering analysis showed that both tomato and tobacco could be used as receptors for heterologous expression of potato specifically expressed genes under red and blue light treatments.

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备注/Memo

备注/Memo:
收稿日期：2023-06-09基金项目：江苏农林职业技术学院院级科研项目(2022kj46);江苏农林职业技术学院亚夫科技创新与服务项目（2023kj01）作者简介：许建民(1981-),男,甘肃张掖人,硕士,副教授,主要从事设施园艺光环境控制方面的研究。(E-mail)jsnlxjm@vip.163.com
更新日期/Last Update: 2024-09-14