ChIP-seq of holocentric Chionographis japonica to determine the centromere distribution and genome organization

To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2 Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for chromatin repeat CENH3 as well as conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2. Each CENH3-, H3K4me2-, and H3K9me2-ChIPseq experiments was performed for two biological replicates.