Molecular Genetics Laboratory, Department of Botany, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001, India.
Genome. 2020 Apr;63(4):215-224. doi: 10.1139/gen-2019-0165. Epub 2020 Jan 27.
Unequal utilization of synonymous codons is a well-known phenomenon among living organisms. This phenomenon plays a major role in the enhancement of the accuracy and efficiency of translation. Gymnosperms are rarely paid attention in this aspect. Understanding the degree of and determining the forces influencing codon usage bias (CUB) in , an endangered Himalayan gymnosperm, will prove useful in interpreting the evolutionary characteristics of this species. Using RNAseq data, 93 790 assembled transcripts were clustered into 32 701 unigenes. Around 13 061 full-length sequences were utilized for the analysis of CUB. Compositional properties showed that GC-content ranged from 28.76% to 65.22%, with an average value of 44.28%, suggesting an AT-rich genome. The mean effective number of codons (ENC) value revealed that CUB is not strong in . The preferred codons tended to be A/U ending, whereas the avoided codons tended to be G/C ending. A P2 index of 0.54 and a Mutation Responsive Index (MRI) value of -0.02 in addition to the results revealed by the neutrality, ENC, and parity plots showed that natural selection is a predominating factor governing CUB. Mutational pressure, gene length, hydropathiciy, aromaticity, and nucleotide composition influence CUB weakly.
同义密码子的使用差异是生物界普遍存在的现象。这种现象在提高翻译的准确性和效率方面起着重要作用。在这方面，裸子植物很少受到关注。了解濒危喜马拉雅裸子植物 中密码子使用偏性（CUB）的程度和确定影响其的力量，将有助于解释该物种的进化特征。利用 RNAseq 数据，将 93790 个组装的转录本聚类为 32701 个非基因。约 13061 个全长序列被用于 CUB 的分析。组成特性表明，GC 含量范围为 28.76%至 65.22%，平均值为 44.28%，表明其基因组富含 AT。平均有效密码子数（ENC）值表明， 的 CUB 不强。偏好的密码子倾向于以 A/U 结尾，而避免的密码子倾向于以 G/C 结尾。P2 指数为 0.54，突变响应指数（MRI）值为-0.02，加上中性、ENC 和奇偶性图的结果表明，自然选择是控制 CUB 的主要因素。突变压力、基因长度、亲水性、芳香性和核苷酸组成对 CUB 的影响较弱。
