The Review of Bioinformatics Tool for 3D Plant Genomics Research.

Since the genome of the nucleus is a complicated three-dimensional spatial structure but not a single linear structure, biologists consider that 3D structure of plant chromatin is highly correlated with the function of the genome, which can be used to study the regulation mechanisms of genes and their evolutionary process. Because plants are more prone to chromosome structural variation and the 3D structure of plant chromatin are highly correlated with the function of the genome, it is important to investigate the impact of chromosome structural variation on gene expression by analyzing 3D structure. Here, we will briefly review the current bioinformatics tools for 3D plant genome study, which covers Hi-C data processing tools, then are the tools for A and B compartments identification, topologically associated domains (TAD) identification, identification of significant interactions and visualization. And then, we could provide the useful information for the related 3D plant genomics research scientists to select the appropriate tools according to their study. Finally, we discuss how to develop the future 3D genomic plant bioinformatics tools to keep up with the pace of scientific research development.