| 摘要: |
| 为了解香樟基因密码子偏好性,该文以NCBI网站中香樟转录组数据为材料,利用生物信息学手段评价转录组数据质量,选取高质量数据的转录组,去除低质量序列,组装转录组,预测基因结构,再利用自编perl脚本提取以AUG开头的基因序列37 Mb序列34 931个基因,进一步利用CodonW分析基因密码子偏好性。结果表明:GC含量的变化范围为0.273～0.742,均值为0.452; ENC的范围为26.29～61.00,均值为52.76; CAI的范围为0.064～0.401,均值为0.199; RSCU值大于1的密码子数目为27个,其中以U或A结尾的有22个; 中性分析表明,小部分基因在对角线上,大多数基因偏离对角线; ENC-plot分析表明小部分基因在标准曲线上,大多数基因偏离标准曲线。上述研究结果表明,香樟基因的密码子偏好性比较弱,密码子常以A/U结尾; 突变和选择两者都在密码子偏好中起作用,而选择作用更大; 最终确定了GUU、CAG、GAA、UCU、GCU、GGU为最优密码子,通过对目标基因密码子的校正,提高表达效率,从而为利用基因工程技术改良香樟重要性状奠定了基础。 |
| 关键词: 香樟, 转录组, 基因, 密码子, 偏好性 |
| DOI：10.11931/guihaia.gxzw202003074 |
| 分类号:Q945.4 |
| 文章编号:1000-3142(2021)12-2077-07 |
| Fund project:自治区主席科技资金项目(1517-06); 第八批广西特聘专家专项; 广西林科院基本科研业务费项目(林科201806号); 广西重点实验室开放课题(19-B-04-01)[Supported by the Scientific Program of Chairman in Guangxi(1517-06); the Eighth Batch Guangxi Special Expert Program; Basic Research Fund of Guangxi Forestry Research Institute(LinKe 201806); Open Project of Guangxi Key Laboratory(19-B-04-01)]。 |
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| Codon bias of transcriptomic genes in Cinnamomum camphora |
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LIANG Xiaojing1, ZHU Changsan1, LI Kaixiang1, AN Jiacheng1, WANG Pengliang2*
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1. Guangxi Forestry Research Institute, Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest Crops, Engineering
and Technology Research Center for Anise and Cinnamon of State Forestry Administration, Guangxi Engineering and Technology Research
Center for Woody Spices, Nanning 530002, China;2. Beibu Gulf University, Qinzhou 535011, Guangxi, China
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| Abstract: |
| In order to understand the genes codon bias of transcriptome in Cinnamomum camphora, all transcriptome data of C. camphora were downloaded, screened against their quality. The screened data were assembled and annotated in gene structure after low-quality reads were deleted. Then 37 Mb gene sequences initiated with AUG were extracted by perl script with 34 931 genes. The codon bias was analyzed using CodonW software. The results were as follows: GC content ranged from 0.273 to 0.742 with the average of 0.452; ENC ranged from 26.29 to 61.00 with the average of 52.76; CAI ranged from 0.064 to 0.401 with the average of 0.199; There were 27 genes whose RSCU were greater than 1, of which 22 genes ended with U or A; Neutral plot analysis indicated that a great many genes were not on the line and ENC-plot showed the similar results. The above results elucidate that the gene codon bias of transcriptome was weak, and most ended with U or A; Selection played more important role than mutation in codon bias; Finally, GUU, CAG, GAA, UCU, GCU and GGU were taken as the optimal codons. This will provide a solid foundation for improving traits of C. camphora via the codon revision of the targeted genes. |
| Key words: Cinnamomum camphora, transcriptome, genes, codon, bias |
