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Characterization of stilbene synthase genes by comparative genome sequencing of Vitis flexuosa with high contents of stilbene compounds to Vitis vinifera genome

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Abstract

Grapevine is an economically important fruit crop with high secondary metabolite content. The stilbene contents in ripe berries were significantly higher in Vitis flexuosa than in ‘Pinot Noir’ (V. vinifera) and ‘Campbell Early’ (V. labruscana). A phylogenetic tree analysis of STS family showed high similarity between V. flexuosa and V. vinifera. The draft genome sequence of a heterozygous V. flexuosa, were assembled from ~ 172-fold sequencing data. The assembled genome has a total length of 511 Mb and contains 18,515 orthologous genes. Moreover, there was high structural variation in V. flexuosa compared to cultivated grapevines, which are contributed to genetic variation involved in expression of characteristics such as disease resistance and high content of stilbene compound in V. flexuosa. The V. flexuosa genome sequence will facilitate exploration of the biological discovery and breeding-related applications of this useful resource plant, Korea native wild grapevine V. flexuosa.

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Data Availability

All raw reads of genome and transcriptome assembly of V. flexuosa obtained from Illumina Hi seq 2000 are available in the Sequence Read Archive (SRA) database under the BioProject id PRJNA445217 in NCBI with the accession name “Draft genome of Vitis flexuosa” (www.ncbi.nlm.nih.gov/sra/PRJNA445217).

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Acknowledgements

This research was funded by the Next-Generation BioGreen 21 program, grant number PJ008213.

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Authors and Affiliations

  1. Department of Horticulture and Life Science, Yeungnam University, Gyeongsan, 38541, Korea

    Soon Young Ahn & Hae Keun Yun

  2. Apple Research Institute, National Institute of Horticultural & Herbal Science, RDA, Gunwi, 39000, Korea

    Seon Ae Kim

  3. SEEDERS Inc, Daejeon, 34015, Korea

    Sung Hwan Jo

  4. Department of Plant Science, Seoul National University, Seoul, Korea

    Doil Choi

  5. Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea

    Doil Choi

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Conceptualization, SYA and HKY: methodology, SAK and SHC: formal analysis, SYA and HKY: writing-draft preparation, review and edition, SYA and HKY. All authors have read and agreed to the published version of the manuscript.

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Ahn, S.Y., Kim, S.A., Jo, S.H. et al. Characterization of stilbene synthase genes by comparative genome sequencing of Vitis flexuosa with high contents of stilbene compounds to Vitis vinifera genome. Hortic. Environ. Biotechnol. 64, 283–298 (2023). https://doi.org/10.1007/s13580-022-00471-1

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