*2.4. Target Gene Prediction and Coexpression Analysis of lncRNAs with PGs*

WGCNA was used to explore the cis-regulatory relationships between lncRNAs and PGs by calculating the correlations with chromosomal neighboring genes within 100 kb from the middle of a given lncRNA [50,53]. RNAplex software was used to predict the trans-acting lncRNAs and their target PGs (TPGs) [54]. Their coexpression was analyzed using WGCNA (cis-analysis: soft threshold = 21; trans-analysis: soft threshold = 22). R was used to calculate the Spearman correlations for the expression of lncRNAs and their target gene pairs.

The GO Analysis Toolkit and the Database for the Agricultural Community (agriGO; http://bioinfo.cau.edu.cn/agriGO/analysis.php) (accessed on 19 July 2019) were used for the GO analysis of the TPGs. The hypergeometric test was used as the statistical method, while Yekutieli (FDR under dependency) was employed as the multi-test adjustment method [50].
