1
|
Bianco L, Fontana P, Marchesini A, Torre S, Moser M, Piazza S, Alessandri S, Pavese V, Pollegioni P, Vernesi C, Malnoy M, Torello Marinoni D, Murolo S, Dondini L, Mattioni C, Botta R, Sebastiani F, Micheletti D, Palmieri L. The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio. BMC Genom Data 2024; 25:64. [PMID: 38909221 PMCID: PMC11193896 DOI: 10.1186/s12863-024-01245-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024] Open
Abstract
OBJECTIVES The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads. DATA DESCRIPTION The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.
Collapse
Affiliation(s)
- Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Alexis Marchesini
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
| | - Mirko Moser
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Stefano Piazza
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Sara Alessandri
- Dept. of Agricultural and Food Sciences, University of Bologna, Via Zamboni 33, Bologna, BO, 40126, Italy
| | - Vera Pavese
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Paola Pollegioni
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Cristiano Vernesi
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Mickael Malnoy
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Daniela Torello Marinoni
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Sergio Murolo
- Dep. of Agricultural, Food and Env.Sci, Marche Polytechnic University, via Brecce Bianche, Ancona, AN, 60131, Italy
| | - Luca Dondini
- Dept. of Agricultural and Food Sciences, University of Bologna, Via Zamboni 33, Bologna, BO, 40126, Italy
| | - Claudia Mattioni
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Roberto Botta
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
| | - Diego Micheletti
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Luisa Palmieri
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy.
| |
Collapse
|
2
|
Qiao Q, Gao Y, Liu Q. Metabolic and molecular mechanisms of spine color formation in Chinese red chestnut. FRONTIERS IN PLANT SCIENCE 2024; 15:1377899. [PMID: 38835869 PMCID: PMC11148441 DOI: 10.3389/fpls.2024.1377899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 04/11/2024] [Indexed: 06/06/2024]
Abstract
The spines of Chinese red chestnut are red and the depth of their color gradually increases with maturity. To identify the anthocyanin types and synthesis pathways in red chestnut and to identify the key genes regulating the anthocyanin biosynthesis pathway, we obtained and analyzed the transcriptome and anthocyanin metabolism of red chestnut and its control variety with green spines at 3 different periods. GO and KEGG analyses revealed that photosynthesis was more highly enriched in green spines compared with red spines, while processes related to defense and metabolism regulation were more highly enriched in red spines. The analysis showed that the change in spine color promoted photoprotection in red chestnut, especially at the early growth stage, which resulted in the accumulation of differentially expressed genes involved in the defense metabolic pathway. The metabolome results revealed 6 anthocyanins in red spines. Moreover, red spines exhibited high levels of cyanidin, peonidin and pelargonidin and low levels of delphinidin, petunidin and malvidin. Compared with those in the control group, the levels of cyanidin, peonidin, pelargonidin and malvidin in red spines were significantly increased, indicating that the cyanidin and pelargonidin pathways were enriched in the synthesis of anthocyanins in red spines, whereas the delphinidin pathways were inhibited and mostly transformed into malvidin. During the process of flower pigment synthesis, the expression of the CHS, CHI, F3H, CYP75A, CYP75B1, DFR and ANS genes clearly increased, that of CYP73A decreased obviously, and that of PAL, 4CL and LAR both increased and decreased. Notably, the findings revealed that the synthesized anthocyanin can be converted into anthocyanidin or epicatechin. In red spines, the upregulation of BZ1 gene expression increases the corresponding anthocyanidin content, and the upregulation of the ANR gene also promotes the conversion of anthocyanin to epicatechin. The transcription factors involved in color formation included 4 WRKYs.
Collapse
Affiliation(s)
- Qian Qiao
- Shandong Key Laboratory of Fruit Biotechnology Breeding, Shandong Institute of Pomology, Taian, Shandong, China
| | - Yun Gao
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Qingzhong Liu
- Shandong Key Laboratory of Fruit Biotechnology Breeding, Shandong Institute of Pomology, Taian, Shandong, China
| |
Collapse
|
3
|
Liu H, Zhang R, Zhou BF, Shen Z, Chen XY, Gao J, Wang B. Chromosome-scale genome assembly of sweet tea (Lithocarpus polystachyus Rehder). Sci Data 2023; 10:873. [PMID: 38057329 PMCID: PMC10700502 DOI: 10.1038/s41597-023-02791-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
Lithocarpus, with >320 species, is the second largest genus of Fagaceae. However, the lack of a reference genome limits the molecular biology and functional study of Lithocarpus species. Here, we report the chromosome-scale genome assembly of sweet tea (Lithocarpus polystachyus Rehder), the first Lithocarpus species to be sequenced to date. Sweet tea has a 952-Mb genome, with a 21.4-Mb contig N50 value and 98.6% complete BUSCO score. In addition, the per-base consensus accuracy and completeness of the genome were estimated at 60.6 and 81.4, respectively. Genome annotation predicted 37,396 protein-coding genes, with repetitive sequences accounting for 64.2% of the genome. The genome did not undergo whole-genome duplication after the gamma (γ) hexaploidy event. Phylogenetic analysis showed that sweet tea diverged from the genus Quercus approximately at 59 million years ago. The high-quality genome assembly and gene annotation resources enrich the genomics of sweet tea, and will facilitate functional genomic studies in sweet tea and other Fagaceae species.
Collapse
Affiliation(s)
- Hui Liu
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China.
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Biao-Feng Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Zhao Shen
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xue-Yan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden/Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
| | - Baosheng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China.
| |
Collapse
|
4
|
Huang WC, Liao B, Liu H, Liang YY, Chen XY, Wang B, Xia H. A chromosome-scale genome assembly of Castanopsis hystrix provides new insights into the evolution and adaptation of Fagaceae species. FRONTIERS IN PLANT SCIENCE 2023; 14:1174972. [PMID: 37215286 PMCID: PMC10197965 DOI: 10.3389/fpls.2023.1174972] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/22/2023] [Indexed: 05/24/2023]
Abstract
Fagaceae species dominate forests and shrublands throughout the Northern Hemisphere, and have been used as models to investigate the processes and mechanisms of adaptation and speciation. Compared with the well-studied genus Quercus, genomic data is limited for the tropical-subtropical genus Castanopsis. Castanopsis hystrix is an ecologically and economically valuable species with a wide distribution in the evergreen broad-leaved forests of tropical-subtropical Asia. Here, we present a high-quality chromosome-scale reference genome of C. hystrix, obtained using a combination of Illumina and PacBio HiFi reads with Hi-C technology. The assembled genome size is 882.6 Mb with a contig N50 of 40.9 Mb and a BUSCO estimate of 99.5%, which are higher than those of recently published Fagaceae species. Genome annotation identified 37,750 protein-coding genes, of which 97.91% were functionally annotated. Repeat sequences constituted 50.95% of the genome and LTRs were the most abundant repetitive elements. Comparative genomic analysis revealed high genome synteny between C. hystrix and other Fagaceae species, despite the long divergence time between them. Considerable gene family expansion and contraction were detected in Castanopsis species. These expanded genes were involved in multiple important biological processes and molecular functions, which may have contributed to the adaptation of the genus to a tropical-subtropical climate. In summary, the genome assembly of C. hystrix provides important genomic resources for Fagaceae genomic research communities, and improves understanding of the adaptation and evolution of forest trees.
Collapse
Affiliation(s)
- Wei-Cheng Huang
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Borong Liao
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hui Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Yi-Ye Liang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xue-Yan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Hanhan Xia
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|