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Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the Gossypium genus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

To construct a fine 3D genome map of cotton, we produced an ultra-high-resolution (3 Kb) Hi-C library (233 Gb) and a Pore-C library (113 Gb) with appropriate resolution (20 Kb) using leaves of I G. hirsutum i (Figure 1b, Tables S1 and S2). Multi-omics mapping of chromatin interaction resolves the fine hierarchy of 3D genome in allotetraploid cotton Keywords: Pore-C; Hi-C; ChIA-PET; 3D genome; cotton EN Pore-C Hi-C ChIA-PET 3D genome cotton 1639 1641 3 08/25/22 20220901 NES 220901 Allotetraploid cotton ( I Gossypium hirsutum i ) is cultivated globally as an important fibre and oil crop, and also serves as a model for genomic analysis of allopolyploidization. [Extracted from the article]