title: Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum.
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 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.
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Hardigan
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Emily
authors.initials: E
authors.lastname: Crisovan
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: John P
authors.initials: JP
authors.lastname: Hamilton
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Jeongwoon
authors.identifier: 0000-0002-7102-6799
authors.initials: J
authors.lastname: Kim
authors.affiliation: Department of Horticulture, Virginia Tech, Blacksburg, Virginia 24061.
authors.forename: Parker
authors.initials: P
authors.lastname: Laimbeer
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Courtney P
authors.initials: CP
authors.lastname: Leisner
authors.affiliation: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Norma C
authors.initials: NC
authors.lastname: Manrique-Carpintero
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Linsey
authors.initials: L
authors.lastname: Newton
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Gina M
authors.initials: GM
authors.lastname: Pham
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Brieanne
authors.initials: B
authors.lastname: Vaillancourt
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706 Institute of Biotechnology, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
authors.forename: Xueming
authors.identifier: 0000-0003-3842-2041
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Zixian
authors.initials: Z
authors.lastname: Zeng
authors.affiliation: Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824.
authors.forename: David S
authors.identifier: 0000-0002-0636-5356
authors.initials: DS
authors.lastname: Douches
authors.affiliation: Department of Horticulture, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Jiming
authors.initials: J
authors.lastname: Jiang
authors.affiliation: Department of Horticulture, Virginia Tech, Blacksburg, Virginia 24061.
authors.forename: Richard E
authors.identifier: 0000-0002-7852-4408
authors.initials: RE
authors.lastname: Veilleux
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 buell@msu.edu.
authors.forename: C Robin
authors.identifier: 0000-0002-6727-4677
authors.initials: CR
authors.lastname: Buell
mesh_terms: D056915:DNA Copy Number Variations / Q000235:genetics*; D020440:Gene Duplication; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D017404:In Situ Hybridization, Fluorescence; D010641:Phenotype; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D012100:Reproduction, Asexual / Q000235:genetics; D011198:Solanum tuberosum / Q000235:genetics* / Q000502:physiology; D013045:Species Specificity
chemical_list: D010940:Plant Proteins