Breaking free: The genomics of allopolyploidy-facilitated niche expansion in white clover

Article


Griffiths, Andrew G., Moraga, Roger, Tausen, Marni, Gupta, Vikas, Bilton, Timothy P., Campbell, Matthew A., Ashby, Rachael, Nagy, Istvan, Khan, Anar, Larking, Anna, Anderson, Craig, Franzmayr, Benjamin, Hancock Kerry, Scott, Alicia, Ellison,Nick W., Cox, Murray P., Asp, Torben, Mailund, Thomas, Schierup, Mikkel H. and Andersen, Stig Uggerhøj. 2019. "Breaking free: The genomics of allopolyploidy-facilitated niche expansion in white clover." The Plant Cell. 31 (7), pp. 1466-1487. https://doi.org/10.1105/tpc.18.00606
Article Title

Breaking free: The genomics of allopolyploidy-facilitated niche expansion in white clover

ERA Journal ID2274
Article CategoryArticle
AuthorsGriffiths, Andrew G., Moraga, Roger, Tausen, Marni, Gupta, Vikas, Bilton, Timothy P., Campbell, Matthew A., Ashby, Rachael, Nagy, Istvan, Khan, Anar, Larking, Anna, Anderson, Craig, Franzmayr, Benjamin, Hancock Kerry, Scott, Alicia, Ellison,Nick W., Cox, Murray P., Asp, Torben, Mailund, Thomas, Schierup, Mikkel H. and Andersen, Stig Uggerhøj
Journal TitleThe Plant Cell
Journal Citation31 (7), pp. 1466-1487
Number of Pages22
Year2019
Place of PublicationUnited States
ISSN1040-4651
1532-298X
Digital Object Identifier (DOI)https://doi.org/10.1105/tpc.18.00606
Web Address (URL)https://academic.oup.com/plcell/article/31/7/1466/5985684
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.

KeywordsWhite Clover; genomes; allopolyploidization
ANZSRC Field of Research 2020310803. Plant cell and molecular biology
PubMed ID31023841
FunderAgResearch
Byline AffiliationsAgResearch, New Zealand
Aarhus University, Denmark
Massey University, New Zealand
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