The spatial arrangement of chromosomes in the nucleus is important for gene expression and genome function both in animals and plants.The recently developed Hi-C technology is an effective method to investigate the chromosome interaction.In order to probe the function of polyploidy levels in genome packing,Arabidopsis autotetraploid was used in our study to build three-dimensional structure of the genome with Hi-C analysis.We found that tetraploidy Arabidopsis shows a similar local chromatin packing compared to the wide type,most interactions are within chromosomes.However,it also has its specific conformations: intra-arm interaction frequencies reducein coincidence with that inter-arm interactions increase.In addition,increased inter-arm interactions were mainly found within the two pericentromeric domains flanking each centromere.The interaction matrix revealed that all telomeres interact with each other with reduced interaction frequency in autotetraploidy Arabidopsis compared to that of the wide type.These data suggested that duplicated genome prefers long-range inter-arm interactions,resulting in more compact nuclei.Further,we preformed transcriptome sequencing to address the relationship between three-dimensional structure of the genome and gene transcription.Our results indicated that gene clusters found in different interaction bins were mapped to different transcription "factory",suggesting the correlation between chromosomal organization and gene expression.