De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas

we report a chromosome-scale de novo genome assembly of the woody plant Jatropha curcas with a total length of 379.5 Mb and scaffold N50 of 30.7 Mb using PacBio long-reads combined with genome-wide chromosome conformation capture (Hi-C) technology. Based on this high-quality reference genome, we detected chromatin architecture differences between the monoecious and gynoecious inflorescence buds of Jatropha. Differentially expressed genes (DEGs) were significantly enriched in the changed A/B compartments and topologically associated domain (TAD) regions and occurred preferentially in differential contact regions between monoecious and gynoecious inflorescence buds. Twelve DEGs related to flower development or hormone synthesis displayed significantly different genomic interaction patterns in monoecious and gynoecious inflorescence buds. These results demonstrate that chromatin organization participates in the regulation of gene transcription during the process of sex differentiation in Jatropha.