Abstract
Fruit is essential for plant reproduction and is responsible for protection and dispersal of seeds. The development and maturation of fruit is tightly regulated by numerous genetic factors that respond to environmental and internal stimulation. In this study, we attempted to identify novel fruit-related genes in a model organism, Arabidopsis thaliana, using a computational method. Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds. The identified genes with high probabilities were filtered by the permutation test and linkage tests. In the permutation test, the genes that were selected due to the structure of the PPI network were discarded. In the linkage tests, the importance of each candidate gene was measured from two aspects: (1) its functional associations with validated genes and (2) its similarity with validated genes on gene ontology (GO) terms and KEGG pathways. Finally, 255 inferred genes were obtained, subsequent extensive analysis of important genes revealed that they mainly contribute to ubiquitination (UBQ9, UBQ8, UBQ11, UBQ10), serine hydroxymethyl transfer (SHM7, SHM5, SHM6) or glycol-metabolism (HXKL2_ARATH, CSY5, GAPCP1), suggesting essential roles during the development and maturation of fruit in Arabidopsis thaliana.
Highlights
Fruit, as specialized seed-bearing structures, are designed to protect the reproductive organs of plants [1]
Our method first applied the random walk with restart (RWR) algorithm to the protein-protein interaction (PPI) network constructed in Section “PPI network” using validated fruit-related genes as seed nodes
To reduce the searching scope, we selected genes with probabilities larger than 10−5, obtaining 6,310 RWR genes. These genes and their probabilities yielded by the RWR algorithm are listed in S2 Table
Summary
As specialized seed-bearing structures, are designed to protect the reproductive organs of plants [1]. During the development and maturation of seeds, fruit has been confirmed to play a specific role. There are two main functions of fruit that may contribute to the reproductive processes of plants [2]. Fruits serve as a solid physical barrier between seeds and the external environment, providing a reliable shelter for seed development and maturation [2, 3]. Some fruits may contribute to the dispersal of mature seeds. Not all mature seeds of a plant can grow into fertile plants.
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