To clarify the process of gene expression changes, we determined the average parental expression (APE) based on the expression of the two parents and compared it with expression in the hybrids, revealing increasing trends in up-regulated expressed genes from F 1 to F 3 , whereas an increasing trend in down-regulated expressed genes was observed from BTF 1 to BTF 3 ( Fig. 3 A; Supplemental Methods ).
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The subgenomes show asymmetric expression of alleles in hybrid lineages of <i>Megalobrama amblycephala</i> × <i>Culter alburnus</i>.
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With respect to cis- and trans- regulatory expression, especially its effects on bone morphology, we detected an increasing trend in “ trans only” genes and a decreasing trend in “ cis + trans ” genes and “ cis × trans ” genes in successive hybrid generations ( Supplemental Table S27 ).