National Center of Agricultural Technology, Sustainability and Environment, King Abdulaziz City for Science and Technology KACST, Box 6086, Riyadh 11442, Saudi Arabia.
Genes (Basel). 2022 Nov 2;13(11):2014. doi: 10.3390/genes13112014.
This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.
本研究旨在通过分析氨基酸来研究番茄基因组中的热休克蛋白。在序列中，seq19 的长度最长，为 3534 个碱基对。seq19 已被报道，并包含一个被称为 的蛋白质家族，该家族具有转录激活域，可耐受热和其他非生物胁迫。番茄热休克蛋白 mRNA 的密码子适应指数 (CAI) 值范围为 0.80（Seq19）至 0.65（Seq10）。天冬酰胺 (AAT、AAC)、天冬氨酸 (GAT、GAC)、苯丙氨酸 (TTT、TTC) 和酪氨酸 (TAT、TAC) 的相对同义密码子使用 (RSCU) 值大于 0.5。在改良相对密码子偏性 (MRCBS) 中，组氨酸、色氨酸、天冬酰胺、天冬氨酸、赖氨酸、苯丙氨酸、异亮氨酸、半胱氨酸和苏氨酸在热胁迫下的高基因表达。RSCU 值小于 0.5 被认为是稀有密码子，会影响翻译速度，因此在热胁迫下降低表达基因的频率可能会产生有效的选择。RSCU 的正态分布显示，从标准正态分布中抽取的约 68%的值在 0.22 和-0.22 标准差范围内，倾向于围绕平均值聚集。基于主成分分析 (PCA) 的最关键组件是 RSCU。这些发现将有助于植物育种家在番茄育种计划中开发番茄的生长习性。
