Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa)
Abstract The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this...
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| Format: | Article |
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Nature Portfolio
2023-02-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-023-02006-4 |
| _version_ | 1797865614216265728 |
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| author | Hui Xia Honghong Deng Mingzhang Li Yue Xie Lijin Lin Huifen Zhang Xian Luo Xiulan Lv Jin Wang Dong Liang |
| author_facet | Hui Xia Honghong Deng Mingzhang Li Yue Xie Lijin Lin Huifen Zhang Xian Luo Xiulan Lv Jin Wang Dong Liang |
| author_sort | Hui Xia |
| collection | DOAJ |
| description | Abstract The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. ‘Red5’ and ‘Hongyang’ (11.1–27.7 mya) was more recent compared with the divergence time of them and Acd (19.9–41.2 mya), with the divergence time of A. eriantha cv. ‘White’ being the earliest (22.9–45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd. |
| first_indexed | 2024-04-09T23:10:55Z |
| format | Article |
| id | doaj.art-91d15989f2304f2d94183cba63cbce0a |
| institution | Directory Open Access Journal |
| issn | 2052-4463 |
| language | English |
| last_indexed | 2024-04-09T23:10:55Z |
| publishDate | 2023-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj.art-91d15989f2304f2d94183cba63cbce0a2023-03-22T10:23:29ZengNature PortfolioScientific Data2052-44632023-02-011011910.1038/s41597-023-02006-4Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa)Hui Xia0Honghong Deng1Mingzhang Li2Yue Xie3Lijin Lin4Huifen Zhang5Xian Luo6Xiulan Lv7Jin Wang8Dong Liang9Institute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityKey Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource SciencesKey Laboratory of Breeding and Utilization of Kiwifruit in Sichuan Province, Sichuan Provincial Academy of Natural Resource SciencesInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityInstitute of Pomology and Olericulture, College of Horticulture, Sichuan Agricultural UniversityAbstract The most commercialized kiwifruit, Actinidia chinensis var. deliciosa (Acd), is an allohexaploid (2n = 6x = 174), making high-quality assemblage genome challenging. We previously discovered a rare naturally occurring diploid Acd plant. Here, chromosome-level de novo genome assembly for this diploid Acd was reported, reaching approximately 621.98 Mb in length with contig and scaffold N50 values of 10.08 and 21.09 Mb, respectively, 99.66% of the bases anchored to 29 pseudochromosomes, and 38,990 protein-coding genes and 42.29% repetitive elements annotated. The divergence time of A. chinensis cv. ‘Red5’ and ‘Hongyang’ (11.1–27.7 mya) was more recent compared with the divergence time of them and Acd (19.9–41.2 mya), with the divergence time of A. eriantha cv. ‘White’ being the earliest (22.9–45.7 mya) among that of the four Actinidia species. The 4DTv distance distribution highlighted three recent whole-genome duplication events in Acd. This is the first high-quality diploid Acd genome, which lays an important foundation for not only kiwifruit functional genomics studies but also further elucidating genome evolution of allohexaploid Acd.https://doi.org/10.1038/s41597-023-02006-4 |
| spellingShingle | Hui Xia Honghong Deng Mingzhang Li Yue Xie Lijin Lin Huifen Zhang Xian Luo Xiulan Lv Jin Wang Dong Liang Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa) Scientific Data |
| title | Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa) |
| title_full | Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa) |
| title_fullStr | Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa) |
| title_full_unstemmed | Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa) |
| title_short | Chromosome-scale genome assembly of a natural diploid kiwifruit (Actinidia chinensis var. deliciosa) |
| title_sort | chromosome scale genome assembly of a natural diploid kiwifruit actinidia chinensis var deliciosa |
| url | https://doi.org/10.1038/s41597-023-02006-4 |
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