Data from: Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploidal karyotype with a complete set of syntenic chromosomes (2n=10x=80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and harbored three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with the specific expression in the digestive zone, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent there because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in pitcher-specific tissues. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.