Three dimensional Plant Genome Comparative Analysis

Overview


The non-random three-dimensional organization of chromatin plays an important role in regulation of gene expression. However, it remains unclear whether this organization is conserved, and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. Therefore, we developed TPGCA (Three dimensional Plant Genome Comparative Analysis Platform), which is an online service website for data processing of the comparative analysis of plant genome three-dimensional structure. TPGCA introduces mainstream Hi-C data processing integration tools and visualization tools, and provides the following functions: identification of three-dimensional structural units of the genome, calculation of conservative ratios of three-dimensional structural units, statistics of the interaction level and expression level differences of WGD gene pairs, and visualization of three-dimensional structural units, etc.

Improvement of A/B compartment identification tool


The A/B compartments is a prominent three-dimensional structural unit of the genome. The implementation principle of the existing software is to perform PCA on the intrachromosome contact matrix and combine the gene density data to divide the chromosomes into A/B compartment. However, gene data cannot reflect the true chromatin status of the species when doing Hi-C experiments in real time, and methylation data can reflect the true chromatin status. Therefore, the pca.hic algorithm in HiTC, a classic tool for identifying A/B compartments, has been improved. We named the improved tool for identifying chromatin based on methylation level data as MDPH (Methylation data based pca.hic). The workflow is:

Three-dimensional genome comparative analysis process


Three-dimensional genome comparative analysis mainly uses gene mapping algorithms, interval overlap algorithms, and statistical methods, and combines Hi-C sequencing data, DNA methylation data, gene data and gene expression levels for analysis. The whole research process can be divided into three parts: 1. Genome three-dimensional structure analysis; 2. Genome three-dimensional structure conservation analysis; 3. WGD gene spatial structure and expression level difference analysis. The specific process is shown in the figure below.