Comparison of long-range chromatin interactions at the RCN2 locus from Hi-C data between ZH11 and ZH11-inca2
High-throughput chromosome conformation capture (Hi-C) assaysHi-C libraries were constructed as described elsewhere40, and sequenced using Illumina NovaSeq platform with paired ends (PE150). Trimmomatic 3.0 was used to trim adapters with the same parameters as mentioned above48. The remaining reads were aligned to the rice reference genome sequence (MSU V7.0) with the default settings of Hi-C-Pro. Briefly, a two-step filtering process was undertaken to ensure that the chimeric reads were accurately aligned to the reference sequences. After the adaptor sequences were trimmed, the low-quality reads were filtered out and singletons were discarded. The aligned read pairs were assigned to Mbo I restriction fragments, and the invalid pairs with an overhanging end or those that self-ligated or re-ligated were discarded. AnalyzeHiC function of HOMER (Hypergeometric Optimization of Motif EnRichment) was used to find significant interactions.