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Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium
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Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium
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Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium
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Journal Article
Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium
2022
Overview
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.
Pan-genome and pan-3D genome analyses of the
Gossypium
genus reveal evolutionary relationships among transposon-driven genome expansion and chromatin topology innovation and regulatory variations for cotton fiber development.
