In Silico Analysis of Phalaenopsis Orchid Homeobox1 (POH1) Functional Gene for Shoot Development in Phalaenopsis Orchid

Q4 Agricultural and Biological Sciences

Journal of Tropical Biodiversity and Biotechnology Pub Date : 2023-10-16 DOI:10.22146/jtbb.83934

Nuzlan Rasjid, F. Y. Kurniawan, Saifa Usni Putri, Aviesta Linggabuwana, Ireneus Seno Prasojo, E. Semiarti

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引用次数: 0

Abstract

The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved. Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11.

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蝴蝶兰同源染色体 1（POH1）功能基因在蝴蝶兰嫩枝发育中的作用的硅学分析

在印度尼西亚，最受欢迎的观赏作物是兰花，它作为花卉栽培而受益。因此，必须提高这种作物的质量。生物技术适用于提高兰花植物的质量和数量。要采用这种方法，研究人员必须知道哪些基因在植物发育中起作用。在蝴蝶兰中，基因已被确认为同源染色体基因，称为蝴蝶兰同源染色体1（POH1）。本研究旨在对该基因进行硅学分析。研究材料来自 mRNA 和氨基酸数据库。然后，对这些材料进行对齐、可视化、基序位置分析、基序功能发现、系统发育构建和蛋白质三维结构建模。根据 mRNA 和氨基酸的比对，POH1 和其他同源基因中有 4 个结构域是保守的，如 KNOX1、KNOX2、ELK 结构域和 Homeobox KN 结构域，它们作为转录因子参与植物的发育。蛋白质建模使用了 SWISS-MODEL 和 ColabFold。通过 ColabbFold 建模，建模预测使用了 325 个残基，比 SWISS-MODEL 高出 59 个残基。通过 Ramachandra Plot 进行的 ColabFold 验证表明，最喜欢的区域为 68.6%，而 SWISS-MODEL 为 92.3%。另一个验证参数是总体质量因子和 QMEAN 分数。ColabFold 蛋白建模的总体质量因子为 89.252，QMEAN 分数为 0.41 ± 0.05。然而，SWISS-MODEL 三维预测的总体质量因子为 98.039，QMEAN 得分为 0.71 ± 0.11。

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