[1]龙婷,董万鹏,曹萌,等. 梓叶槭基因组密码子偏好性分析[J].西北林学院学报,2023,38(6):61-66.[doi:10.3969/j.issn.1001-7461.2023.06.08]
　LONG Ting,DONG Wan-peng,CAO Meng,et al. Codon Usage Bias Analysis in the Acer amplum subsp.catalpifolium Genome[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2023,38(6):61-66.[doi:10.3969/j.issn.1001-7461.2023.06.08]
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 梓叶槭基因组密码子偏好性分析()
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《西北林学院学报》[ISSN:1001-7461/CN:61-1202/S]

卷:
第38卷
期数:
2023年第6期
页码:
61-66
栏目:
出版日期:
2023-11-30

文章信息/Info

Title:
 Codon Usage Bias Analysis in the Acer amplum subsp.catalpifolium Genome
文章编号:
1001-7461(2023)06-0061-06
作者:
 龙婷1; 董万鹏1; 曹萌2; 马文宝3; 于涛4*
 （1.贵州省植物园，贵州 贵阳 550001；2.中国消防救援学院，北京 102202；3.四川省林业科学研究院，四川 成都 610081；4.中节能生态产品发展研究中心，北京 100089）
Author(s):
 LONG Ting1; DONG Wan-peng1; CAO Meng2; MA Wen-bao3; YU Tao4*
 (1.Guizhou Botanical Garden,Guiyang 550001,Guizhou,China; 2.China Fire and Rescue College,Beijing 102202,China; 3.Sichuan Academy of Forestry,Chengdu 610081,Sichuan,China; 4.CECEP Eco-Product Development Research Center,Beijing 100089,China)
关键词:
 ; 梓叶槭; 基因组; 密码子偏好性; 最优密码子
Keywords:
Acer amplum subsp.catalpifolium;  genome;  codon usage bias;  optimal codon
分类号:
Q949.755
DOI:
10.3969/j.issn.1001-7461.2023.06.08
文献标志码:
A
摘要:
 为确定槭属极小种群野生植物梓叶槭的基因组密码子使用模式和可能成因，以梓叶槭基因组中筛选的33 034个编码基因为对象，利用Codon W 1.4.2、CUSP在线程序和R 4.1.1分别进行中性绘图、PR2-plot与ENC-plot分析，揭示梓叶槭基因组密码子使用偏好性及其影响因素，确定最优密码子。结果表明，1）梓叶槭基因组密码子GC含量在0.278~0.697，不同位置上的GC平均含量为GC1（0.494）>GC3（0.417）>GC2（0.397），表明梓叶槭基因组密码子末位碱基偏好以A和U结尾；2）基因组中有效密码子数（ENC）在25.530~61.000，且大部分基因的ENC值>35，表明密码子偏好性较弱；3）PR2-plot与ENC-plot绘图分析结果显示，突变和选择等因素都在梓叶槭基因组密码子偏好性中起到了影响作用，但梓叶槭基因组受到突变压力的影响更大；4）最终确定UUU，UGU，CAA等29个密码子为梓叶槭基因组的最优密码子。研究结果为梓叶槭基因功能解析与后续利用基因工程技术改良槭属植物重要性状奠定了研究基础。
Abstract:
 In order to determine the genomic codon usage patterns and possible causes of the minimal population of Acer amplum subsp.catalpifolium,33 034 coding genes of the A.amplum subsp.catalpifolium genome were used for analysis.Codon W 1.4.2,CUSP online program,R 4.1.1 were used for the analysis of neutral plot,PR2-plot,and ENC-plot.The objectives of this study were to reveal the codon usage bias of the A.amplum subsp.catalpifolium genome and the potential causing factors,and to determine the optimal codons.The results showed that 1) the GC content in the codon genes of the genome ranged from 0.278 to 0.697,and the average GC content in different positions was GC1(0.494)>GC3(0.417)>GC2(0.397),indicating that the third base of the genome codon prefers to end with A and U.2) ENC varied from 25.530 to 61.000.The ENC value of most genes was more than 35,indicating that codon usage bias is weak.3) PR2-plot and ENC-plot analysis showed that the mutation and selection both had contributions to the codon preference,but mutation stress may be a more important causing factor in the genome.4) The 29 optimal codons such as UUU,UGU,and CAA were determined.These results provide a basis for the further studies in the gene function of A.amplum subsp.catalpifolium and for the improvement of important traits in Acer species through genetic engineering.

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备注/Memo

备注/Memo:
 收稿日期：2022-10-21修回日期：2023-01-13
基金项目：贵州科学院博士科研启动基金项目(黔科院R字［2022］02号)；贵州科学院省级科研专项(黔科院科专合字［2022］03号)；内蒙古自治区自然科学基金项目（2020BS03044）。
第一作者：龙婷，博士。研究方向：生物多样性保护。E-mail:741241478@qq.com
*通信作者：于涛，博士。研究方向：生物多样性保护。E-mail:yutao123@bjfu.edu.cn
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