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Fine‐scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species


Akiyama, Reiko; Sun, Jianqiang; Hatakeyama, Masaomi; Lischer, Heidi E L; Briskine, Roman V; Hay, Angela; Gan, Xiangchao; Tsiantis, Miltos; Kudoh, Hiroshi; Kanaoka, Masahiro M; Sese, Jun; Shimizu, Kentaro K; Shimizu‐Inatsugi, Rie (2021). Fine‐scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. New Phytologist, 229(6):3587-3601.

Abstract

Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing. We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally. These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.

Abstract

Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors. We quantified soil properties and light availability of habitats of an allotetraploid Cardamine flexuosa and its diploid progenitors Cardamine amara and Cardamine hirsuta in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA sequencing. We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in C. flexuosa varied spatially and temporally. These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Evolution in Action: From Genomes to Ecosystems
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Scopus Subject Areas:Life Sciences > Physiology
Life Sciences > Plant Science
Uncontrolled Keywords:allopolyploid, Cardamine, homeolog expression, temporal fluctuation, transcriptome, water availability
Language:English
Date:1 March 2021
Deposited On:02 Feb 2021 10:14
Last Modified:21 Feb 2021 02:14
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:0028-646X
OA Status:Hybrid
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1111/nph.17101
PubMed ID:33222195
Project Information:
  • : FunderSNSF
  • : Grant ID31003A_159767
  • : Project TitleBreeding systems and germline development - evolutionary genomic analysis using Arabidopsis relatives
  • : FunderSNSF
  • : Grant ID31003A_182318
  • : Project TitleEvolutionary functional genomics of selfing and polyploid speciation
  • : FunderUniversity of Zurich
  • : Grant IDURPP
  • : Project TitleEvolution in Action
  • : FunderJapan Society for the Promotion of Science
  • : Grant ID16H01463, 16H06469, 18H04785, 26113709
  • : Project Title
  • : FunderJapan Science and Technology Agency
  • : Grant IDJPMJCR16O3
  • : Project Title
  • : FunderIndo‐Swiss Collaboration in Biotechnology
  • : Grant ID
  • : Project Title
  • : FunderHuman Frontier Science Program
  • : Grant ID
  • : Project Title

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