生物技术通报2024，Vol.40Issue(3)：202-214,13.DOI:10.13560/j.cnki.biotech.bull.1985.2023-0982
甘蔗属种及其近缘属种蔗茅的全基因组密码子偏好性分析
Genome-wide Analysis of Codon Usage Bias in Saccharum Species and Its Phylogenetically Related Species Erianthus fulvus
摘要
Abstract
[Objective]To clarify the codon usage characteristics and improve expression efficiency of exogenous genes in sugarcane.[Method]Codon usage bias were analyzed by Python and CodonW1.4.2 tools based on their genomes data of three species including Saccharum officinarum(LA-purple),S.sponaneum(NP-X and AP85-441),and Erianthus fulvus(Yunnan2009-3).Neutrality-plot,ENC-plot,and Parity Rule 2(PR2)-plot analysis were also used to explore the possible factors that affect the formation of codon usage bias.Simultaneously,correlation analysis between gene expressions and codon usage bias parameters was carryd out based on transcriptome data.Finally,a comparison analysis of codon usage patterns were performed between sugarcane and the other seven main model organisms,namely,Zea mays,Sorghum bicolor,Oryza sativa,Arabidopsis thaliana,Nicotiana tabacum,Escherichia coli,and Saccharomyces cerevisiae based on the average RSCU value of three species.[Result]S.officinarum,S.sponaneum,and E.fulvus were rich in GC base pairs,the average GC content was 56.3%,and GC3 was the highest,followed by GC1 and GC2,indicating that sugarcane preferred to use synonymous codons ending with a C/G base.The average ENC value was 48.45,suggesting that sugarcane had a lower codon usage bias.According to the results of neutral-plot,ENC-plot,and PR2-plot analysis,the codon usage bias of four genomes was affected by natural selection,mutation pressure,and so on,and the natural selection dominated in them.Correlation analysis showed that codon preference parameters were significantly correlated with the actual transcription expressions of genes,but the correlation was not strong.Based on the RSCU and ∆RSCU values,thirteen identical optimal codons were confirmed,and all of them were ended with C/G base pairs.The codon usage characteristics were not different at genome-wide and chromosome level.In addition,the codon usage bias of sugarcane was similar to that of Z.mays,S.bicolor,and O.sativa,while it had a significant difference with A.thaliana,N.tabacum,E.coli,and S.cerevisiae.[Conclusion]The codon usage bias among S.officinarum,S.sponaneum and E.fulvus was highly similar,and its formation was affected by natural selection and mutation pressure factors.Meanwhile,Z.mays,O.sativa and S.bicolor could be used for elite gene function research on sugarcane as a exogenous expression system on account of their codon usage bias patterns.关键词
甘蔗属/蔗茅/基因组/密码子使用偏好性/最优密码子Key words
Saccharum/Erianthus fulvus/genome/codon usage bias/optimal codons引用本文复制引用
田春艳,李旭娟,李纯佳,毛钧,刘新龙..甘蔗属种及其近缘属种蔗茅的全基因组密码子偏好性分析[J].生物技术通报,2024,40(3):202-214,13.基金项目
云南种子种业联合实验室(202205AR070001-09),云南省科技人才与平台计划(202205AM070001) （202205AR070001-09）
