Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

The Plant Cell
Michael A HardiganC Robin Buell

Abstract

Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gen...Continue Reading

Citations

Feb 24, 2017·The Plant Journal : for Cell and Molecular Biology·Juan D MontenegroDavid Edwards
Apr 25, 2018·Genome Génome / Conseil National De Recherches Canada·Maxime BastienFrançois Belzile
Nov 1, 2017·Proceedings of the National Academy of Sciences of the United States of America·Michael A HardiganC Robin Buell
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Nov 27, 2020·Scientific Reports·Zhen LiaoChristina Dixelius

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