Assessing Genetic Diversity in Squash Pumpkin (Cucurbita moschata) Through Computational Analysis of Plastid Genes.

Abstract

<title>Abstract</title> Understanding the genetic diversity of economic crops, including wild relatives of genetic resources is fundamental for the continued improvement of varieties and breeds needed to cope with changes in climatic conditions. Obtaining high plant yield is not always achievable in agricultural activity as it is determined by various factors, including cultivar quality, nutrient and water supplies, degree of infection by pathogens, natural calamities and soil conditions, which affect plant growth and development. The present study was carried out using computational analysis to assess the genetic diversity in the plastid gene of 20 accessions of squash pumpkin (<italic>Cucurbita moschata</italic>). Guanine-cytosine (GC) content, phylogenetic relationship, secondary and tertiary protein structure and domain architecture were assessed. The accessions of the Squash pumpkin were retrieved from the National Centre for Biotechnology Information (NCBI) database. The phylogenetic tree showed a total of 12 clades which had 2 main clades with 4 100% bootstrap in accessions XM_023105445.1, XM_023105444.1, XM_023075850.1 and XM_023075859.1. The GC content was highest in accession XM_021009681.1 and lowest in accession XM_023076698.1. The domain architecture prediction showed the highest number of domains in accession XM_02100968.1 and a single domain in accessions XM_02105444.1, XM_0230758951.1 and XM_023067309.1, suggesting that these sequences may have more specialized functions. The secondary and tertiary protein structure showed variations among the accessions, indicating the possibility of structural differences which could have functional implications in the protein stability or interactions with other molecules.