Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover
- 25 April 2019
- journal article
- research article
- Published by Oxford University Press (OUP) in THE PLANT CELL ONLINE
- Vol. 31 (7), 1466-1487
- https://doi.org/10.1105/tpc.18.00606
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.Keywords
Funding Information
- Pastoral Genomics
- Ministry of Business, Innovation and Employment, New Zealand (C10X1306, ‘Genomics for Production & Security in a Biological Economy’)
- Innovation Fund Denmark (4105-00007A)
- The Danish Council for Independent Research/Technology and Production Sciences (10-081677)
This publication has 126 references indexed in Scilit:
- An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to MedicagoBMC Genomics, 2013
- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusionsGenome Biology, 2013
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and CufflinksNature Protocols, 2012
- Inference of human population history from individual whole-genome sequencesNature, 2011
- A framework for variation discovery and genotyping using next-generation DNA sequencing dataNature Genetics, 2011
- Evolution of the mutation rateTrends in Genetics, 2010
- Hybridization, polyploidy and invasion: lessons from Spartina (Poaceae)Biological Invasions, 2008
- Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plantProceedings of the National Academy of Sciences of the United States of America, 2008
- Molecular phylogenetics of the clover genus (Trifolium—Leguminosae)Molecular Phylogenetics and Evolution, 2006