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Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)

Yongfeng Zhou, Andrea Minio, Mélanie Massonnet, Edwin Solares, Yuanda Lyu, Tengiz Beridze, View ORCID ProfileDario Cantu, Brandon S. Gaut
doi: https://doi.org/10.1101/508119
Yongfeng Zhou
1Dept. Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92617
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Andrea Minio
2Dept. Viticulture and Enology, UC Davis, Davis, CA 95616
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Mélanie Massonnet
2Dept. Viticulture and Enology, UC Davis, Davis, CA 95616
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Edwin Solares
1Dept. Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92617
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Yuanda Lyu
1Dept. Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92617
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Tengiz Beridze
3Institute of Molecular Genetics, Agricultural University of Georgia, Tbilisi, Georgia
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Dario Cantu
2Dept. Viticulture and Enology, UC Davis, Davis, CA 95616
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  • For correspondence: dacantu@ucdavis.edu bgaut@uci.edu
Brandon S. Gaut
1Dept. Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92617
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  • For correspondence: dacantu@ucdavis.edu bgaut@uci.edu
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ABSTRACT

Little is known about the type and numbers of structural variants (SVs) in plant genomes, the evolutionary processes that shape SV variation, or their effects on phenotypes. Here we assembled the 605Mb genome of the Chardonnay grape (Vitis vinifera ssp. sativa), which we use to catalog SVs within and between genomes and also across 69 cultivars and wild accessions. SVs underlie widespread hemizygosity of protein coding genes within Chardonnay and genic presence-absence variation between cultivars. Negative selection acts against all SV types, but they also accrue as heterozygous, recessive mutations in clonally propagated grapevines. SV hotspots in the sex determination region and the berry color locus illustrate their impact on phenotype and the role of SVs as drivers of convergent phenotypic evolution.

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Posted December 31, 2018.
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Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)
Yongfeng Zhou, Andrea Minio, Mélanie Massonnet, Edwin Solares, Yuanda Lyu, Tengiz Beridze, Dario Cantu, Brandon S. Gaut
bioRxiv 508119; doi: https://doi.org/10.1101/508119
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Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)
Yongfeng Zhou, Andrea Minio, Mélanie Massonnet, Edwin Solares, Yuanda Lyu, Tengiz Beridze, Dario Cantu, Brandon S. Gaut
bioRxiv 508119; doi: https://doi.org/10.1101/508119

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