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

dc.contributor.affiliationUniversity of Würzburg - Saul, Franziska
dc.contributor.affiliationUniversity of Potsdam - Scharmann, Mathias
dc.contributor.affiliationUniversity of Würzburg - Wakatake, Takanori
dc.contributor.affiliationUniversity of Helsinki - Rajaraman, Sitaram
dc.contributor.affiliationMax Planck Institute for Plant Breeding Research - Marques, André
dc.contributor.affiliationUniversity of Würzburg - Freund, Matthias
dc.contributor.affiliationUniversity of Würzburg - Bringmann, Gerhard
dc.contributor.affiliationUniversity of Würzburg - Channon, Louisa
dc.contributor.affiliationUniversity of Würzburg - Becker, Dirk
dc.contributor.affiliationUniversity at Buffalo, State University of New York - Carroll, Emily
dc.contributor.affiliationSingapore Botanic Gardens* - Low, Yee Wen
dc.contributor.affiliationUniversity at Buffalo, State University of New York - Lindqvist, Charlotte
dc.contributor.affiliationMichigan State University - Gilbert, Kadeem J.
dc.contributor.affiliationPennsylvania State University - Renner, Tanya
dc.contributor.affiliationRIKEN Center for Sustainable Resource Science - Masuda, Sachiko
dc.contributor.affiliationUniversity at Buffalo, State University of New York - Richter, Michaela
dc.contributor.affiliationUniversity of Würzburg - Vogg, Gerd
dc.contributor.affiliationRIKEN Center for Sustainable Resource Science - Shirasu, Ken
dc.contributor.affiliationSalk Institute for Biological Studies - Michael, Todd P.
dc.contributor.affiliationUniversity of Würzburg - Hedrich, Rainer
dc.contributor.affiliationUniversity at Buffalo, State University of New York - Albert, Victor A.
dc.contributor.affiliationUniversity of Würzburg - Fukushima, Kenji
dc.contributor.authorSaul, Franziska
dc.contributor.authorScharmann, Mathias
dc.contributor.authorWakatake, Takanori
dc.contributor.authorRajaraman, Sitaram
dc.contributor.authorMarques, André
dc.contributor.authorFreund, Matthias
dc.contributor.authorBringmann, Gerhard
dc.contributor.authorChannon, Louisa
dc.contributor.authorBecker, Dirk
dc.contributor.authorCarroll, Emily
dc.contributor.authorLow, Yee Wen
dc.contributor.authorLindqvist, Charlotte
dc.contributor.authorGilbert, Kadeem J.
dc.contributor.authorRenner, Tanya
dc.contributor.authorMasuda, Sachiko
dc.contributor.authorRichter, Michaela
dc.contributor.authorVogg, Gerd
dc.contributor.authorShirasu, Ken
dc.contributor.authorMichael, Todd P.
dc.contributor.authorHedrich, Rainer
dc.contributor.authorAlbert, Victor A.
dc.contributor.authorFukushima, Kenji
dc.date.accessioned2025-03-24T15:26:52Z
dc.date.issued2023-06-21
dc.date.issued2023-06-21
dc.descriptionSubgenome 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.
dc.identifierhttps://doi.org/10.5061/dryad.xsj3tx9mj
dc.identifier.urihttps://hydatakatalogi-test-24.it.helsinki.fi/handle/123456789/11623
dc.rightsOpen
dc.rights.licensecc-zero
dc.subjectNepenthes gracilis
dc.subjectGenome sequencing
dc.subjectPolyploidy
dc.titleData from: Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis
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