Assessing Genetic Diversity in Squash Pumpkin (Cucurbita moschata) through Computational Analysis of Plastid Genes
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Abstract
Grasping the genetic variation of economically significant crops, along with their Wild counterparts that serve as genetic assets, is essential for advancing the development of cultivars and strains capable of adapting to shifting climate conditions. Achieving high crop yields in agriculture is often challenging due to multiple influencing factors, such as cultivar quality, availability of nutrients and water, pathogen infection levels, natural disasters, and soil quality, all of which play a role in plant growth and development. This research evaluated the genetic diversity of 20 accessions of squash pumpkin (Cucurbita moschata) by analysing its’ plastid genes using bioinformatics mechanism. Twenty Cucurbita moschata accessions were sourced from the National Center for Biotechnology Information (NCBI) database. Phylogenetic association, Guanine-cytosine (GC) composition, secondary and three-dimensional protein structure, and domain structure were evaluated. The phylogenetic assessment identified 12 clades in total, with two main clades containing four accessions; XM_023105445.1, XM_023105444.1, XM_023075850.1, and XM_023075859.1 each showing 100% bootstrap support. Accession XM_021009681.1 showed the peak Guanine-cytosine composition, whereas XM_023076698.1 showed the least performance. The analysis of domain structure indicated that accession XM_02100968.1 contained the highest number of domains, while XM_023067309.1, XM_02105444.1, and XM_0230758951.1, each had only one domain, implying that they could have a more specific role. Variations in secondary and three-dimensional protein structures were observed across the accessions, suggesting potential structural differences that may affect protein robustness or their ability to interact with other molecules.
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