Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum
Author(s) -
Michael A. Hardigan,
Emily Crisovan,
John P. Hamilton,
Jeongwoon Kim,
Parker Laimbeer,
Courtney P. Leisner,
Norma C. ManriqueCarpintero,
Linsey Newton,
Gina M. Pham,
Brieanne Vaillancourt,
Yang Xue-ming,
Zixian Zeng,
David S. Douches,
Jiming Jiang,
Richard E. Veilleux,
C. Robin Buell
Publication year - 2016
Publication title -
the plant cell
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.324
H-Index - 341
eISSN - 1532-298X
pISSN - 1040-4651
DOI - 10.1105/tpc.15.00538
Subject(s) - biology , genome , gene , gene duplication , solanum tuberosum , ploidy , genetics , copy number variation , adaptation (eye) , solanum , gene dosage , asexual reproduction , genetic variation , gene family , allele , structural variation , evolutionary biology , botany , gene expression , neuroscience
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 gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways.
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