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Li H, Liu Y, Fan P, Dai Z, Hao J, Duan W, Liang Z, Wang Y. The Genome of Vitis zhejiang-adstricta Strengthens the Protection and Utilization of the Endangered Ancient Grape Endemic to China. PLANT & CELL PHYSIOLOGY 2024; 65:216-227. [PMID: 37930871 PMCID: PMC10873524 DOI: 10.1093/pcp/pcad140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/08/2023]
Abstract
Vitis zhejiang-adstricta (V. zhejiang-adstricta) is one of the most important and endangered wild grapes. It is a national key protected wild, rare and endangered ancient grape endemic to China and used as a candidate material for resistance breeding owing to its excellent significant disease resistance. Here, we present a high-quality chromosome-level assembly of V. zhejiang-adstricta (IB-VB-01), comprising 506.66 Mb assembled into 19 pseudo-chromosomes. The contig N50 length is 3.91 Mb with 31,196 annotated protein-coding genes. Comparative genome and evolutionary analyses illustrated that V. zhejiang-adstricta has a specific position in the evolution of East Asian Vitis and shared a common ancestor with Vitis vinifera during the divergence of the two species about 10.42 (between 9.34 and 11.12) Mya. The expanded gene families compared with those in plants were related to disease resistance, and constructed gene families were related to plant growth and primary metabolism. With the analysis of gene family expansion and contraction, the evolution of environmental adaptability and especially the NBS-LRR gene family of V. zhejiang-adstricta was elucidated based on the pathways of resistance genes (R genes), unique genes and structural variations. The near-complete and accurate diploid V. zhejiang-adstricta reference genome obtained herein serves as an important complement to wild grape genomes and will provide valuable genomic resources for investigating the genomic architecture of V. zhejiang-adstricta as well as for improving disease resistance breeding strategies in grape.
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Affiliation(s)
- Huayang Li
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing 100012, PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Jiachen Hao
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- China National Botanical Garden, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
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Pahayo DG, Cadorna CAE, Quimado MO, Rey JD. The complete chloroplast genome of Calophyllum soulattri Burm. f. (Calophyllaceae). Mitochondrial DNA B Resour 2023; 8:607-611. [PMID: 37250208 PMCID: PMC10215020 DOI: 10.1080/23802359.2023.2215350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Calophyllum soulattri Burm. f. (1768) is an evergreen tree native to Southeast Asia, Australia, and the Solomon Islands. It is known for its medicinal uses and has been utilized in traditional folk medicine. However, genomic resources for this species are still unavailable. In this study, we sequenced and assembled the first complete chloroplast genome of C. soulattri using next-generation sequencing data. The chloroplast genome of C. soulattri is 161,381 bp in length with a total GC content of 36.36%. The chloroplast genome contains a large single copy (LSC) region of 88,680 bp, a small single copy (SSC) region of 17,453 bp, and two inverted repeat (IR) regions of 27,624 bp each. Furthermore, the chloroplast genome has 131 genes, which include 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis indicated that C. soulattri is clustered in the same branch with C. inophyllum and is closely related to Mesua ferrea.
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Affiliation(s)
- Dexter G. Pahayo
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Charles Anthon E. Cadorna
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
| | - Marilyn O. Quimado
- Forest Biological Sciences, College of Forestry and Natural Resources, University of the Philippines, Los Baños, Laguna, Philippines
| | - Jessica D. Rey
- Plant Molecular Phylogenetics Laboratory, Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, Philippines
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Wee CC, Nor Muhammad NA, Subbiah VK, Arita M, Nakamura Y, Goh HH. Plastomes of Garcinia mangostana L. and Comparative Analysis with Other Garcinia Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:930. [PMID: 36840278 PMCID: PMC9966718 DOI: 10.3390/plants12040930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
The two varieties of mangosteen (Garcinia mangostana L.) cultivated in Malaysia are known as Manggis and Mesta. The latter is preferred for its flavor, texture, and seedlessness. Here, we report a complete plastome (156,580 bp) of the Mesta variety that was obtained through a hybrid assembly approach using PacBio and Illumina sequencing reads. It encompasses a large single-copy (LSC) region (85,383 bp) and a small single-copy (SSC) region (17,137 bp) that are separated by 27,230 bp of inverted repeat (IR) regions at both ends. The plastome comprises 128 genes, namely, 83 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The plastome of the Manggis variety (156,582 bp) obtained from reference-guided assembly of Illumina reads was found to be nearly identical to Mesta except for two indels and the presence of a single-nucleotide polymorphism (SNP). Comparative analyses with other publicly available Garcinia plastomes, including G. anomala, G. gummi-gutta, G. mangostana var. Thailand, G. oblongifolia, G. paucinervis, and G. pedunculata, found that the gene content, gene order, and gene orientation were highly conserved among the Garcinia species. Phylogenomic analysis divided the six Garcinia plastomes into three groups, with the Mesta and Manggis varieties clustered closer to G. anomala, G. gummi-gutta, and G. oblongifolia, while the Thailand variety clustered with G. pedunculata in another group. These findings serve as future references for the identification of species or varieties and facilitate phylogenomic analysis of lineages from the Garcinia genus to better understand their evolutionary history.
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Affiliation(s)
- Ching-Ching Wee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Vijay Kumar Subbiah
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia
| | - Masanori Arita
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Yasukazu Nakamura
- Department of Informatics, National Institute of Genetics, Mishima 411-8540, Shizuoka, Japan
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
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