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Plant Cell. 2019 Jul;31(7):1466-1487. doi: 10.1105/tpc.18.00606. Epub 2019 Apr 25.

Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover.

Author information

1
AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand andrew.griffiths@agresearch.co.nz sua@mbg.au.dk.
2
AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand.
3
Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.
4
Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C, Denmark.
5
AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand.
6
Bioinformatics and Statistics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand.
7
Department of Molecular Biology and Genetics, Aarhus University, 200 Slagelse, Denmark.
8
Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
9
Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark andrew.griffiths@agresearch.co.nz sua@mbg.au.dk.

Abstract

The merging of distinct genomes, allopolyploidization, is a widespread phenomenon in plants. It generates adaptive potential through increased genetic diversity, but examples demonstrating its exploitation remain scarce. White clover (Trifolium repens) is a ubiquitous temperate allotetraploid forage crop derived from two European diploid progenitors confined to extreme coastal or alpine habitats. We sequenced and assembled the genomes and transcriptomes of this species complex to gain insight into the genesis of white clover and the consequences of allopolyploidization. Based on these data, we estimate that white clover originated ∼15,000 to 28,000 years ago during the last glaciation when alpine and coastal progenitors were likely colocated in glacial refugia. We found evidence of progenitor diversity carryover through multiple hybridization events and show that the progenitor subgenomes have retained integrity and gene expression activity as they traveled within white clover from their original confined habitats to a global presence. At the transcriptional level, we observed remarkably stable subgenome expression ratios across tissues. Among the few genes that show tissue-specific switching between homeologous gene copies, we found flavonoid biosynthesis genes strongly overrepresented, suggesting an adaptive role of some allopolyploidy-associated transcriptional changes. Our results highlight white clover as an example of allopolyploidy-facilitated niche expansion, where two progenitor genomes, adapted and confined to disparate and highly specialized habitats, expanded to a ubiquitous global presence after glaciation-associated allopolyploidization.

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