Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis
Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against t...
| Main Authors: | , , , , , , , , |
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| Format: | Journal Article |
| Language: | English |
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2022
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| Online Access: | https://hdl.handle.net/10356/161024 |
| _version_ | 1824455177243983872 |
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| author | Cui, Fuqiang Ye, Xiaoxue Li, Xiaoxiao Yang, Yifan Hu, Zhubing Overmyer, Kirk Brosché, Mikael Yu, Hong Salojärvi, Jarkko |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Cui, Fuqiang Ye, Xiaoxue Li, Xiaoxiao Yang, Yifan Hu, Zhubing Overmyer, Kirk Brosché, Mikael Yu, Hong Salojärvi, Jarkko |
| author_sort | Cui, Fuqiang |
| collection | NTU |
| description | Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and we predicted 41 815 genes using RNA-sequencing evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and Vaccinium corymbosum. This conserved genome structure may explain the high fertility observed during crossbreeding of V. darrowii with other blueberry cultivars. Analysis of gene expansion and tandem duplication indicated possible roles for defense- and flowering-associated genes in the adaptation of V. darrowii to the subtropics. Putative SOC1 genes in V. darrowii were identified based on phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA sequencing, we delineated the cuticle biosynthesis pathways of Vaccinium species in V. darrowii. This result can serve as a reference for breeding berries whose colors are appealing to customers. The V. darrowii reference genome, together with the unique traits of this species, including its diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species. |
| first_indexed | 2025-02-19T03:34:03Z |
| format | Journal Article |
| id | ntu-10356/161024 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T03:34:03Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | ntu-10356/1610242023-02-28T17:13:20Z Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis Cui, Fuqiang Ye, Xiaoxue Li, Xiaoxiao Yang, Yifan Hu, Zhubing Overmyer, Kirk Brosché, Mikael Yu, Hong Salojärvi, Jarkko School of Biological Sciences Science::Biological sciences Vaccinium Darrowii Blueberry Vaccinium darrowii is a subtropical wild blueberry species that has been used to breed economically important southern highbush cultivars. The adaptive traits of V. darrowii to subtropical climates can provide valuable information for breeding blueberry and perhaps other plants, especially against the background of global warming. Here, we assembled the V. darrowii genome into 12 pseudochromosomes using Oxford Nanopore long reads complemented with Hi-C scaffolding technologies, and we predicted 41 815 genes using RNA-sequencing evidence. Syntenic analysis across three Vaccinium species revealed a highly conserved genome structure, with the highest collinearity between V. darrowii and Vaccinium corymbosum. This conserved genome structure may explain the high fertility observed during crossbreeding of V. darrowii with other blueberry cultivars. Analysis of gene expansion and tandem duplication indicated possible roles for defense- and flowering-associated genes in the adaptation of V. darrowii to the subtropics. Putative SOC1 genes in V. darrowii were identified based on phylogeny and expression analysis. Blueberries are covered in a thick cuticle layer and contain anthocyanins, which confer their powdery blue color. Using RNA sequencing, we delineated the cuticle biosynthesis pathways of Vaccinium species in V. darrowii. This result can serve as a reference for breeding berries whose colors are appealing to customers. The V. darrowii reference genome, together with the unique traits of this species, including its diploid genome, short vegetative phase, and high compatibility in hybridization with other blueberries, make V. darrowii a potential research model for blueberry species. Nanyang Technological University Published version These studies were supported by the Natural Science Foundation of Zhejiang Province (grant LY22C160005), the National Natural Science Foundation of China (grant 31700224), Innovative Scientific and Technological Talents in Henan Province (no. 20HASTIT041), and the Outstanding Youth Foundation of Henan Province (no. 202300410041), as well as a Nanyang Technological University startup grant and the Academy of Finland (decisions 318288 and 319947) to J.S. 2022-08-12T02:59:33Z 2022-08-12T02:59:33Z 2022 Journal Article Cui, F., Ye, X., Li, X., Yang, Y., Hu, Z., Overmyer, K., Brosché, M., Yu, H. & Salojärvi, J. (2022). Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. Plant Communications, 3(4), 100307-. https://dx.doi.org/10.1016/j.xplc.2022.100307 2590-3462 https://hdl.handle.net/10356/161024 10.1016/j.xplc.2022.100307 35605198 2-s2.0-85126862847 4 3 100307 en Plant Communications © 2022 The Author(s). Published by the Plant Communications Shanghai Editorial Office in association with Cell Press, an imprint of Elsevier Inc., on behalf of CSPB and CEMPS, CAS. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). application/pdf |
| spellingShingle | Science::Biological sciences Vaccinium Darrowii Blueberry Cui, Fuqiang Ye, Xiaoxue Li, Xiaoxiao Yang, Yifan Hu, Zhubing Overmyer, Kirk Brosché, Mikael Yu, Hong Salojärvi, Jarkko Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| title | Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| title_full | Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| title_fullStr | Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| title_full_unstemmed | Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| title_short | Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| title_sort | chromosome level genome assembly of the diploid blueberry vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis |
| topic | Science::Biological sciences Vaccinium Darrowii Blueberry |
| url | https://hdl.handle.net/10356/161024 |
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