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Liu W, Xu S, Ou C, Liu X, Zhuang F, Deng XW. T2T genomes of carrot and Alternaria dauci and their utility for understanding host-pathogen interactions during carrot leaf blight disease. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39374101 DOI: 10.1111/tpj.17049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 09/09/2024] [Accepted: 09/12/2024] [Indexed: 10/09/2024]
Abstract
Carrot (Daucus carota) is one of the most popular and nutritious vegetable crops worldwide. However, significant yield losses occur every year due to leaf blight, a disease caused by a fungal pathogen (Alternaria dauci). Past research on resistance to leaf blight disease in carrots has been slow because of the low-quality genome assemblies of both carrot and the pathogen. Here, we report the greatly improved assemblies and annotations of telomere-to-telomere (T2T) reference genomes of carrot DH13M14 (451.04 Mb) and A. dauci A2016 (34.91 Mb). Compared with the previous carrot genome versions, our assembly featured notable improvements in genome size, continuity, and completeness of centromeres and telomeres. In addition, we generated a time course transcriptomic atlas during the infection of carrots by A. dauci and captured their dynamic gene expression reprogramming during the interaction process. During infection, A. dauci genes encoding effectors and enzymes responsible for the degradation of plant cell wall components, e.g., cellulose and pectin, were identified, which appeared to increase pathogenic ability through upregulation. In carrot, the coordinated gene expression of components of pattern- and effector-triggered immunity (PTI and ETI) in response to A. dauci attack was characterized. The biosynthesis or signal transduction of plant hormones, including JA, SA, and ethylene, was also involved in the carrot response to A. dauci. This work provides a foundation for understanding A. dauci pathogenic progression and carrot defense mechanisms to improve carrot resistance to leaf blight disease. The Carrot Database (CDB) developed also provides a useful resource for the carrot community.
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Affiliation(s)
- Wenwen Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Shiyao Xu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chenggang Ou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xing Liu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Feiyun Zhuang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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2
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Duan AQ, Deng YJ, Liu H, Xu ZS, Xiong AS. An anthocyanin activation gene underlies the purple central flower pigmentation in wild carrot. PLANT PHYSIOLOGY 2024; 196:1147-1162. [PMID: 39046113 DOI: 10.1093/plphys/kiae391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/07/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024]
Abstract
Many organisms have complex pigmentation patterns. However, how these patterns are formed remains largely unknown. In wild carrot (Daucus carota subsp. carota), which is also known as Queen Anne's lace, one or several purple central flowers occur in white umbels. Here, we investigated the unique central flower pigmentation pattern in wild carrot umbels. Using wild and cultivated carrot (D. carota subsp. sativus L.) accessions, transcriptome analysis, protein interaction, stable transformation, and CRISPR/Cas9-mediated knockout, an anthocyanin-activating R2R3-myeloblastosis (MYB) gene, Purple Central Flower (DcPCF), was identified as the causal gene that triggers only central flowers to possess the purple phenotype. The expression of DcPCF was only detected in tiny central flowers. We propose that the transition from purple to nonpurple flowers in the center of the umbel occurred after 3 separate adverse events: insertion of transposons in the promoter region, premature termination of the coding sequence (caused by a C-T substitution in the open reading frame), and the emergence of unknown anthocyanin suppressors. These 3 events could have occurred either consecutively or independently. The intriguing purple central flower pattern and its underlying mechanism may provide evidence that it is a remnant of ancient conditions of the species, reflecting the original appearance of Umbelliferae (also called Apiaceae) when a single flower was present.
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Affiliation(s)
- Ao-Qi Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Yuan-Jie Deng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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3
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Uncu AT, Patat AS, Uncu AO. Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species. Funct Integr Genomics 2024; 24:142. [PMID: 39187716 DOI: 10.1007/s10142-024-01423-x] [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: 07/04/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
Parsley is a commonly cultivated Apiaceae species of culinary and medicinal importance. Parsley has several recognized health benefits and the species has been utilized in traditional medicine since ancient times. Although parsley is among the most commonly cultivated members of Apiaceae, no systematic genomic research has been conducted on parsley. In the present work, parsley genome was sequenced using the long-read HiFi (high fidelity) sequencing technology and a draft contig assembly of 1.57 Gb that represents 80.9% of the estimated genome size was produced. The assembly was highly repeat-rich with a repetitive DNA content of 81%. The assembly was phased into a primary and alternate assembly in order to minimize redundant contigs. Scaffolds were constructed with the primary assembly contigs, which were used for the identification of AMP (antimicrobial peptide) genes. Characteristic AMP domains and 3D structures were used to detect and verify antimicrobial peptides. As a result, 23 genes (PcAMP1-23) representing defensin, snakin, thionin, lipid transfer protein and vicilin-like AMP classes were identified. Bioinformatic analyses for the characterization of peptide physicochemical properties indicated that parsley AMPs are extracellular peptides, therefore, plausibly exert their antimicrobial effects through the most commonly described AMP action mechanism of membrane attack. AMPs are attracting increasing attention since they display their fast antimicrobial effects in small doses on both plant and animal pathogens with a significantly reduced risk of resistance development. Therefore, identification and characterization of AMPs is important for their incorporation into plant disease management protocols as well as medicinal research for the treatment of multi-drug resistant infections.
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Affiliation(s)
- Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey
| | - Aysenur Soyturk Patat
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey
| | - Ayse Ozgur Uncu
- Department of Biotechnology, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey.
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4
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Huang XC, Tang H, Wei X, He Y, Hu S, Wu JY, Xu D, Qiao F, Xue JY, Zhao Y. The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae. Nat Commun 2024; 15:6864. [PMID: 39127760 PMCID: PMC11316762 DOI: 10.1038/s41467-024-51285-x] [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: 01/15/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
Complex coumarins (CCs) represent characteristic metabolites found in Apiaceae plants, possessing significant medical value. Their essential functional role is likely as protectants against pathogens and regulators responding to environmental stimuli. Utilizing genomes and transcriptomes from 34 Apiaceae plants, including our recently sequenced Peucedanum praeruptorum, we conduct comprehensive phylogenetic analyses to reconstruct the detailed evolutionary process of the CC biosynthetic pathway in Apiaceae. Our results show that three key enzymes - p-coumaroyl CoA 2'-hydroxylase (C2'H), C-prenyltransferase (C-PT), and cyclase - originated successively at different evolutionary nodes within Apiaceae through various means of gene duplications: ectopic and tandem duplications. Neofunctionalization endows these enzymes with novel functions necessary for CC biosynthesis, thus completing the pathway. Candidate genes are cloned for heterologous expression and subjected to in vitro enzymatic assays to test our hypothesis regarding the origins of the key enzymes, and the results precisely validate our evolutionary inferences. Among the three enzymes, C-PTs are likely the primary determinant of the structural diversity of CCs (linear/angular), due to divergent activities evolved to target different positions (C-6 or C-8) of umbelliferone. A key amino acid variation (Ala161/Thr161) is identified and proven to play a crucial role in the alteration of enzymatic activity, possibly resulting in distinct binding forms between enzymes and substrates, thereby leading to different products. In conclusion, this study provides a detailed trajectory for the establishment and evolution of the CC biosynthetic pathway in Apiaceae. It explains why only a portion, not all, of Apiaceae plants can produce CCs and reveals the mechanisms of CC structural diversity among different Apiaceae plants.
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Affiliation(s)
- Xin-Cheng Huang
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Huanying Tang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China
| | - Xuefen Wei
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shuaiya Hu
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jia-Yi Wu
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dingqiao Xu
- School of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712046, Shaanxi, China
| | - Fei Qiao
- National Key Laboratory for Tropical Crop Breeding, Sanya, 572024, Hainan, China.
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Jia-Yu Xue
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
- Medical Botanical Garden, China Pharmaceutical University, Nanjing, 210009, Jiangsu, China.
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5
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Li Q, Dai Y, Huang XC, Sun L, Wang K, Guo X, Xu D, Wan D, An L, Wang Z, Tang H, Qi Q, Zeng H, Qin M, Xue JY, Zhao Y. The chromosome-scale assembly of the Notopterygium incisum genome provides insight into the structural diversity of coumarins. Acta Pharm Sin B 2024; 14:3760-3773. [PMID: 39220882 PMCID: PMC11365381 DOI: 10.1016/j.apsb.2024.04.005] [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: 12/07/2023] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 09/04/2024] Open
Abstract
Coumarins, derived from the phenylpropanoid pathway, represent one of the primary metabolites found in angiosperms. The alignment of the tetrahydropyran (THP) and tetrahydrofuran (THF) rings with the lactone structure results in the formation of at least four types of complex coumarins. However, the mechanisms underlying the structural diversity of coumarin remain poorly understood. Here, we report the chromosome-level genome assembly of Notopterygium incisum, spanning 1.64 Gb, with a contig N50 value of 22.7 Mb and 60,021 annotated protein-coding genes. Additionally, we identified the key enzymes responsible for shaping the structural diversity of coumarins, including two p-coumaroyl CoA 2'-hydroxylases crucial for simple coumarins basic skeleton architecture, two UbiA prenyltransferases responsible for angular or linear coumarins biosynthesis, and five CYP736 cyclases involved in THP and THF ring formation. Notably, two bifunctional enzymes capable of catalyzing both demethylsuberosin and osthenol were identified for the first time. Evolutionary analysis implies that tandem and ectopic duplications of the CYP736 subfamily, specifically arising in the Apiaceae, contributed to the structural diversity of coumarins in N. incisum. Conclusively, this study proposes a parallel evolution scenario for the complex coumarin biosynthetic pathway among different angiosperms and provides essential synthetic biology elements for the heterologous industrial production of coumarins.
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Affiliation(s)
- Qien Li
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Yiqun Dai
- School of Pharmacy, Bengbu Medical University, Bengbu 233030, China
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xin-Cheng Huang
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Lanlan Sun
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Kaixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Guo
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Dingqiao Xu
- Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xi'an 712046, China
| | - Digao Wan
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Latai An
- Tibetan Medicine Research Center of Qinghai University, Tibetan Medical College, Qinghai University, Xining 810016, China
| | - Zixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huanying Tang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qi Qi
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Huihui Zeng
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Minjian Qin
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Yu Xue
- College of Horticulture, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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6
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Wang YG, Zhang YM, Wang YH, Zhang K, Ma J, Hang JX, Su YT, Tan SS, Liu H, Xiong AS, Xu ZS. The Y locus encodes a REPRESSOR OF PHOTOSYNTHETIC GENES protein that represses carotenoid biosynthesis via interaction with APRR2 in carrot. THE PLANT CELL 2024; 36:2798-2817. [PMID: 38593056 PMCID: PMC11289637 DOI: 10.1093/plcell/koae111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Little is known about the factors regulating carotenoid biosynthesis in roots. In this study, we characterized DCAR_032551, the candidate gene of the Y locus responsible for the transition of root color from ancestral white to yellow during carrot (Daucus carota) domestication. We show that DCAR_032551 encodes a REPRESSOR OF PHOTOSYNTHETIC GENES (RPGE) protein, named DcRPGE1. DcRPGE1 from wild carrot (DcRPGE1W) is a repressor of carotenoid biosynthesis. Specifically, DcRPGE1W physically interacts with DcAPRR2, an ARABIDOPSIS PSEUDO-RESPONSE REGULATOR2 (APRR2)-like transcription factor. Through this interaction, DcRPGE1W suppresses DcAPRR2-mediated transcriptional activation of the key carotenogenic genes phytoene synthase 1 (DcPSY1), DcPSY2, and lycopene ε-cyclase (DcLCYE), which strongly decreases carotenoid biosynthesis. We also demonstrate that the DcRPGE1W-DcAPRR2 interaction prevents DcAPRR2 from binding to the RGATTY elements in the promoter regions of DcPSY1, DcPSY2, and DcLCYE. Additionally, we identified a mutation in the DcRPGE1 coding region of yellow and orange carrots that leads to the generation of alternatively spliced transcripts encoding truncated DcRPGE1 proteins unable to interact with DcAPRR2, thereby failing to suppress carotenoid biosynthesis. These findings provide insights into the transcriptional regulation of carotenoid biosynthesis and offer potential target genes for enhancing carotenoid accumulation in crop plants.
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Affiliation(s)
- Ying-Gang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu-Min Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ya-Hui Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Ma
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Jia-Xin Hang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu-Ting Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan-Shan Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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7
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Wang Z, He J, Qi Q, Wang K, Tang H, Feng Y, Zhao X, Yi S, Zhao Y, Xu D. Chromosome-level genome assembly of Cnidium monnieri, a highly demanded traditional Chinese medicine. Sci Data 2024; 11:667. [PMID: 38909038 PMCID: PMC11193713 DOI: 10.1038/s41597-024-03523-6] [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: 01/23/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024] Open
Abstract
Cnidium monnieri, a medicinal herb of the Cnidium genus and the Apiaceae family, is among the most important traditional Chinese medicines and is widely distributed in China. However, to date, no C. monnieri-related genomic information has been described. In this study, we assembled the C. monnieri genome of approximately 1210.23 Mb with a contig N50 of 83.14 Mb. Using PacBio HiFi and Hi-C sequencing data, we successfully anchored 93.86% of the assembled sequences to 10 pseudochromosomes (2n = 20). We predicted a total of 37,460 protein-coding genes, with 97.02% of them being functionally annotated in Non-Redundant, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and other databases. In addition, we identified 2,778 tRNAs, 4,180 rRNAs, 258 miRNAs, and 1,700 snRNAs in the genome. This is the first reported C. monnieri genome. Hopefully, the availability of this chromosome-level reference genome provides a significant basis for upcoming natural product-related biosynthetic pathway assessment in C. monnieri.
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Affiliation(s)
- Zixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jiaxin He
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qi Qi
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Kaixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Huanying Tang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yimeng Feng
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xinyue Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yucheng Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
- Medical Botanical Garden, China Pharmaceutical University, Nanjing, 210009, China.
| | - Dingqiao Xu
- School of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, 712046, China.
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8
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Cheng S, Zhang Q, Geng X, Xie L, Chen M, Jiao S, Qi S, Yao P, Lu M, Zhang M, Zhai W, Yun Q, Feng S. Haplotype-resolved chromosome-level genome assembly of Ehretia macrophylla. Sci Data 2024; 11:589. [PMID: 38839803 PMCID: PMC11153487 DOI: 10.1038/s41597-024-03431-9] [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: 11/21/2023] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
Ehretia macrophylla Wall, known as wild loquat, is an ecologically, economically, and medicinally significant tree species widely grown in China, Japan, Vietnam, and Nepal. In this study, we have successfully generated a haplotype-resolved chromosome-scale genome assembly of E. macrophylla by integrating PacBio HiFi long-reads, Illumina short-reads, and Hi-C data. The genome assembly consists of two haplotypes, with sizes of 1.82 Gb and 1.58 Gb respectively, and contig N50 lengths of 28.11 Mb and 21.57 Mb correspondingly. Additionally, 99.41% of the assembly was successfully anchored into 40 pseudo-chromosomes. We predicted 58,886 protein-coding genes, of which 99.60% were functionally annotated from databases. We furthermore detected 2.65 Gb repeat sequences, 659,290 rRNAs, 4,931 tRNAs and 4,688 other ncRNAs. The high-quality assembly of the genome offers a solid basis for furthering the fields of molecular breeding and functional genomics of E. macrophylla.
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Affiliation(s)
- Shiping Cheng
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China.
| | | | - Xining Geng
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Lihua Xie
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Minghui Chen
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Siqian Jiao
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Shuaizheng Qi
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Pengqiang Yao
- Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China
| | - Mailin Lu
- Henan Forestry Vocational College, Luoyang, 471000, China
| | - Mengren Zhang
- Henan Forestry Vocational College, Luoyang, 471000, China
| | - Wenshan Zhai
- Henan Senzhuang Cukang Agriculture and Forestry Technology Co., Ltd, Luoyang, 471000, China
| | - Quanzheng Yun
- Kaitai Mingjing Genetech Corporation, Beijing, 100070, China
| | - Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, China.
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, 310036, China.
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9
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Song Y, Zhang Y, Wang X, Yu X, Liao Y, Zhang H, Li L, Wang Y, Liu B, Li W. Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis. HORTICULTURE RESEARCH 2024; 11:uhae107. [PMID: 38883331 PMCID: PMC11179851 DOI: 10.1093/hr/uhae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 03/31/2024] [Indexed: 06/18/2024]
Abstract
Ginseng (Panax ginseng) is a representative of Chinese traditional medicine, also used worldwide, while the triterpene saponin ginsenoside is the most important effective compound within it. Ginseng is an allotetraploid, with complex genetic background, making the study of its metabolic evolution challenging. In this study, we assembled a telomere-to-telomere ginseng reference genome, constructed of 3.45 Gb with 24 chromosomes and 77 266 protein-coding genes. Additionally, the reference genome was divided into two subgenomes, designated as subgenome A and B. Subgenome A contains a larger number of genes, whereas subgenome B has a general expression advantage, suggesting that ginseng subgenomes experienced asymmetric gene loss with biased gene expression. The two subgenomes separated approximately 6.07 million years ago, and subgenome B shows the closest relation to Panax vietnamensis var. fuscidiscus. Comparative genomics revealed an expansion of gene families associated with ginsenoside biosynthesis in both ginseng subgenomes. Furthermore, both tandem duplications and proximal duplications play crucial roles in ginsenoside biosynthesis. We also screened functional genes identified in previous research and found that some of these genes located in colinear regions between subgenomes have divergence functions, revealing an unbalanced evolution in both subgenomes and the saponin biosynthesis pathway in ginseng. Our work provides important resources for future genetic studies and breeding programs of ginseng, as well as the biosynthesis of ginsenosides.
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Affiliation(s)
- Yiting Song
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yating Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xu Wang
- National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xikai Yu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yi Liao
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Hao Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of Yangtze River Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Songhu Road 2005, Shanghai 200433, China
| | - Yingping Wang
- State-Local Joint Engineering Research Center of Ginseng Breeding and Application, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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10
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Wang ZH, Liu X, Cui Y, Wang YH, Lv ZL, Cheng L, Liu B, Liu H, Liu XY, Deyholos MK, Han ZM, Yang LM, Xiong AS, Zhang J. Genomic, transcriptomic, and metabolomic analyses provide insights into the evolution and development of a medicinal plant Saposhnikovia divaricata (Apiaceae). HORTICULTURE RESEARCH 2024; 11:uhae105. [PMID: 38883332 PMCID: PMC11179723 DOI: 10.1093/hr/uhae105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/31/2024] [Indexed: 06/18/2024]
Abstract
Saposhnikovia divaricata, 2n = 2x = 16, as a perennial species, is widely distributed in China, Mongolia, Russia, etc. It is a traditional Chinese herb used to treat tetanus, rubella pruritus, rheumatic arthralgia, and other diseases. Here, we assembled a 2.07 Gb and N50 scaffold length of 227.67 Mb high-quality chromosome-level genome of S. divaricata based on the PacBio Sequel II sequencing platform. The total number of genes identified was 42 948, and 42 456 of them were functionally annotated. A total of 85.07% of the genome was composed of repeat sequences, comprised mainly of long terminal repeats (LTRs) which represented 73.7% of the genome sequence. The genome size may have been affected by a recent whole-genome duplication event. Transcriptional and metabolic analyses revealed bolting and non-bolting S. divaricata differed in flavonoids, plant hormones, and some pharmacologically active components. The analysis of its genome, transcriptome, and metabolome helped to provide insights into the evolution of bolting and non-bolting phenotypes in wild and cultivated S. divaricata and lays the basis for genetic improvement of the species.
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Affiliation(s)
- Zhen-Hui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Xiao Liu
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Yi Cui
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Yun-He Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Ze-Liang Lv
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Lin Cheng
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xin-Yang Liu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Michael K Deyholos
- Department of Biology, University of British Columbia, Okanagan V1V1V7, Canada
| | - Zhong-Ming Han
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Li-Min Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Department of Biology, University of British Columbia, Okanagan V1V1V7, Canada
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11
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Oliveira JIN, Corradi N. Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis. G3 (BETHESDA, MD.) 2024; 14:jkae055. [PMID: 38507600 PMCID: PMC11075540 DOI: 10.1093/g3journal/jkae055] [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: 12/06/2023] [Revised: 12/06/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The genome of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises ∼50% repetitive sequences that include TEs. Despite their abundance, two-thirds of TEs remain unclassified, and their regulation among AMF life stages remains unknown. Here, we aimed to improve our understanding of TE diversity and regulation in this model species by curating repeat datasets obtained from chromosome-level assemblies and by investigating their expression across multiple conditions. Our analyses uncovered new TE superfamilies and families in this model symbiont and revealed significant differences in how these sequences evolve both within and between R. irregularis strains. With this curated TE annotation, we also found that the number of upregulated TE families in colonized roots is 4 times higher than in the extraradical mycelium, and their overall expression differs depending on the plant host. This work provides a fine-scale view of TE diversity and evolution in model plant symbionts and highlights their transcriptional dynamism and specificity during host-microbe interactions. We also provide Hidden Markov Model profiles of TE domains for future manual curation of uncharacterized sequences (https://github.com/jordana-olive/TE-manual-curation/tree/main).
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Affiliation(s)
| | - Nicolas Corradi
- Department of Biology, Faculty of Sciences, University of Ottawa, Ottawa, ON, Canada K1N 6N5
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12
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Liu H, Zhang JQ, Zhang RR, Zhao QZ, Su LY, Xu ZS, Cheng ZMM, Tan GF, Xiong AS. The high-quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:717-730. [PMID: 38213282 DOI: 10.1111/tpj.16628] [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: 02/03/2023] [Revised: 11/15/2023] [Accepted: 12/27/2023] [Indexed: 01/13/2024]
Abstract
Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well-known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high-quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single-cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species-specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high-quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jia-Qi Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rong-Rong Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qin-Zheng Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li-Yao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zong-Ming Max Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guo-Fei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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13
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Vega A, Brainard SH, Goldman IL. Linkage mapping of root shape traits in two carrot populations. G3 (BETHESDA, MD.) 2024; 14:jkae041. [PMID: 38412554 PMCID: PMC10989876 DOI: 10.1093/g3journal/jkae041] [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: 12/06/2023] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/29/2024]
Abstract
This study investigated the genetic basis of carrot root shape traits using composite interval mapping in two biparental populations (n = 119 and n = 128). The roots of carrot F2:3 progenies were grown over 2 years and analyzed using a digital imaging pipeline to extract root phenotypes that compose market class. Broad-sense heritability on an entry-mean basis ranged from 0.46 to 0.80 for root traits. Reproducible quantitative trait loci (QTL) were identified on chromosomes 2 and 6 on both populations. Colocalization of QTLs for phenotypically correlated root traits was also observed and coincided with previously identified QTLs in published association and linkage mapping studies. Individual QTLs explained between 14 and 27% of total phenotypic variance across traits, while four QTLs for length-to-width ratio collectively accounted for up to 73% of variation. Predicted genes associated with the OFP-TRM (OVATE Family Proteins-TONNEAU1 Recruiting Motif) and IQD (IQ67 domain) pathway were identified within QTL support intervals. This observation raises the possibility of extending the current regulon model of fruit shape to include carrot storage roots. Nevertheless, the precise molecular mechanisms through which this pathway operates in roots characterized by secondary growth originating from cambium layers remain unknown.
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Affiliation(s)
- Andrey Vega
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Scott H Brainard
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irwin L Goldman
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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14
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Jiang QP, Guo XL, Zhao AQ, Fan X, Li Q, Zhou SD, He XJ. Phylogeny and Taxonomic Revision of the Genus Melanosciadium (Apiaceae), Based on Plastid Genomes and Morphological Evidence. PLANTS (BASEL, SWITZERLAND) 2024; 13:907. [PMID: 38592923 PMCID: PMC10974901 DOI: 10.3390/plants13060907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/29/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Melanosciadium is considered a monotypic genus and is also endemic to the southwest of China. No detailed phylogenetic studies or plastid genomes have been identified in Melanosciadium. In this study, the plastid genome sequence and nrDNA sequence were used for the phylogenetic analysis of Melanosciadium and its related groups. Angelica tsinlingensis was previously considered a synonym of Hansenia forbesii. Similarly, Ligusticum angelicifolium was previously thought to be the genus Angelica or Ligusticopsis. Through field observations and morphological evidence, we believe that the two species are more similar to M. pimpinelloideum in leaves, umbel rays, and fruits. Meanwhile, we found a new species from Anhui Province (eastern China) that is similar to M. pimpinelloideum and have named it M. Jinzhaiensis. We sequenced and assembled the complete plastid genomes of these species and another three Angelica species. The genome comparison results show that M. pimpinelloideum, A. tsinlingensis, Ligusticum angelicifolium, and M. jinzhaiensis have similarities to each other in the plastid genome size, gene number, and length of the LSC and IR regions; the plastid genomes of these species are distinct from those of the Angelica species. In addition, we reconstruct the phylogenetic relationships using both plastid genome sequences and nrDNA sequences. The phylogenetic analysis revealed that A. tsinlingensis, M. pimpinelloideum, L. angelicifolium, and M. jinzhaiensis are closely related to each other and form a monophyletic group with strong support within the Selineae clade. Consequently, A. tsinlingensis and L. angelicifolium should be classified as members of the genus Melanosciadium, and suitable taxonomical treatments have been proposed. Meanwhile, a comprehensive description of the new species, M. jinzhaiensis, is presented, encompassing its habitat environment and detailed morphological traits.
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Affiliation(s)
- Qiu-Ping Jiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Q.-P.J.); (A.-Q.Z.); (S.-D.Z.)
| | - Xian-Lin Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610093, China;
| | - An-Qi Zhao
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Q.-P.J.); (A.-Q.Z.); (S.-D.Z.)
| | - Xing Fan
- Chengdu Branch of Giant Panda National Park, Chengdu 610083, China; (X.F.); (Q.L.)
| | - Qing Li
- Chengdu Branch of Giant Panda National Park, Chengdu 610083, China; (X.F.); (Q.L.)
| | - Song-Dong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Q.-P.J.); (A.-Q.Z.); (S.-D.Z.)
| | - Xing-Jin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China; (Q.-P.J.); (A.-Q.Z.); (S.-D.Z.)
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15
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Liu C, Jiang X, Liu S, Liu Y, Li H, Wang Z, Kan J, Yang Q, Li X. Comprehensive Evolutionary Analysis of the SMXL Gene Family in Rosaceae: Further Insights into Its Origin, Expansion, Diversification, and Role in Regulating Pear Branching. Int J Mol Sci 2024; 25:2971. [PMID: 38474218 DOI: 10.3390/ijms25052971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
SMXL genes constitute a conserved gene family that is ubiquitous in angiosperms and involved in regulating various plant processes, including branching, leaf elongation, and anthocyanin biosynthesis, but little is known about their molecular functions in pear branching. Here, we performed genome-wide identification and investigation of the SMXL genes in 16 angiosperms and analyzed their phylogenetics, structural features, conserved motifs, and expression patterns. In total, 121 SMXLs genes were identified and were classified into four groups. The number of non-redundant SMXL genes in each species varied from 3 (Amborella trichopoda Baill.) to 18 (Glycine max Merr.) and revealed clear gene expansion events over evolutionary history. All the SMXL genes showed conserved structures, containing no more than two introns. Three-dimensional protein structure prediction revealed distinct structures between but similar structures within groups. A quantitative real-time PCR analysis revealed different expressions of 10 SMXL genes from pear branching induced by fruit-thinning treatment. Overall, our study provides a comprehensive investigation of SMXL genes in the Rosaceae family, especially pear. The results offer a reference for understanding the evolutionary history of SMXL genes and provide excellent candidates for studying fruit tree branching regulation, and in facilitating pear pruning and planting strategies.
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Affiliation(s)
- Chunxiao Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianda Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Susha Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yilong Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Hui Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhonghua Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jialiang Kan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Qingsong Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xiaogang Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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16
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Han Y, Li F, Wu Y, Wang D, Luo G, Wang X, Wang X, Kuang H, Larkin RM. PSEUDO-ETIOLATION IN LIGHT proteins reduce greening by binding GLK transcription factors. PLANT PHYSIOLOGY 2024; 194:1722-1744. [PMID: 38051979 DOI: 10.1093/plphys/kiad641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 12/07/2023]
Abstract
Knocking out genes encoding proteins that downregulate the accumulation of pigments may lead to increases in crop quality and yield. PSEUDO-ETIOLATION IN LIGHT 1 (PEL1) downregulates the accumulation of carotenoids in carrot and chlorophyll in Arabidopsis and rice and may inhibit GOLDEN 2-LIKE (GLK) transcription factors. PEL1 belongs to a previously unstudied gene family found only in plants. We used CRISPR/Cas9 technology to knock out each member of the 4-member PEL gene family and both GLK genes in Arabidopsis. In pel mutants, chlorophyll levels were elevated in seedlings; after flowering, chloroplasts increased in size, and anthocyanin levels increased. Although the chlorophyll-deficient phenotype of glk1 glk2 was epistatic to pel1 pel2 pel3 pel4 in most of our experiments, glk1 glk2 was not epistatic to pel1 pel2 pel3 pel4 for the accumulation of anthocyanins in most of our experiments. The pel alleles attenuated growth, altered the accumulation of nutrients in seeds, disrupted an abscisic acid-inducible inhibition of seedling growth response that promotes drought tolerance, and affected the expression of genes associated with diverse biological functions, such as stress responses, cell wall metabolism hormone responses, signaling, growth, and the accumulation of phenylpropanoids and pigments. We found that PEL proteins specifically bind 6 transcription factors that influence the accumulation of anthocyanins, GLK2, and the carboxy termini of GLK1 and Arabidopsis thaliana myeloblastosis oncogene homolog 4 (AtMYB4). Our data indicate that the PEL proteins influence the accumulation of chlorophyll and many other processes, possibly by inhibiting GLK transcription factors and via other mechanisms, and that multiple mechanisms downregulate chlorophyll content.
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Affiliation(s)
- Yuting Han
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Fengfei Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Ying Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Dong Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Guangbao Luo
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xinning Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xin Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Hanhui Kuang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Robert M Larkin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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17
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Yokoyama R. How to make green and purple from gold. PLANT PHYSIOLOGY 2024; 194:1268-1270. [PMID: 38069683 PMCID: PMC10904317 DOI: 10.1093/plphys/kiad653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 03/02/2024]
Affiliation(s)
- Ryo Yokoyama
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
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18
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Feng X, Chen Q, Wu W, Wang J, Li G, Xu S, Shao S, Liu M, Zhong C, Wu CI, Shi S, He Z. Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication. Nat Commun 2024; 15:1635. [PMID: 38388712 PMCID: PMC10884412 DOI: 10.1038/s41467-024-46080-7] [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: 08/01/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization-rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Guohong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), 571100, Haikou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
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Duan AQ, Deng YJ, Tan SS, Liu SS, Liu H, Xu ZS, Shu S, Xiong AS. DcGST1, encoding a glutathione S-transferase activated by DcMYB7, is the main contributor to anthocyanin pigmentation in purple carrot. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1069-1083. [PMID: 37947285 DOI: 10.1111/tpj.16539] [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: 06/21/2023] [Revised: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/12/2023]
Abstract
The color of purple carrot taproots mainly depends on the anthocyanins sequestered in the vacuoles. Glutathione S-transferases (GSTs) are key enzymes involved in anthocyanin transport. However, the precise mechanism of anthocyanin transport from the cytosolic surface of the endoplasmic reticulum (ER) to the vacuoles in carrots remains unclear. In this study, we conducted a comprehensive analysis of the carrot genome, leading to the identification of a total of 41 DcGST genes. Among these, DcGST1 emerged as a prominent candidate, displaying a strong positive correlation with anthocyanin pigmentation in carrot taproots. It was highly expressed in the purple taproot tissues of purple carrot cultivars, while it was virtually inactive in the non-purple taproot tissues of purple and non-purple carrot cultivars. DcGST1, a homolog of Arabidopsis thaliana TRANSPARENT TESTA 19 (TT19), belongs to the GSTF clade and plays a crucial role in anthocyanin transport. Using the CRISPR/Cas9 system, we successfully knocked out DcGST1 in the solid purple carrot cultivar 'Deep Purple' ('DPP'), resulting in carrots with orange taproots. Additionally, DcMYB7, an anthocyanin activator, binds to the DcGST1 promoter, activating its expression. Compared with the expression DcMYB7 alone, co-expression of DcGST1 and DcMYB7 significantly increased anthocyanin accumulation in carrot calli. However, overexpression of DcGST1 in the two purple carrot cultivars did not change the anthocyanin accumulation pattern or significantly increase the anthocyanin content. These findings improve our understanding of anthocyanin transport mechanisms in plants, providing a molecular foundation for improving and enhancing carrot germplasm.
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Affiliation(s)
- Ao-Qi Duan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Jie Deng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan-Shan Tan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan-Shan Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sheng Shu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Facility Horticulture Research Institute of Suqian, Suqian Research Institute of Nanjing Agricultural University, Suqian, Jiangsu, 223800, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Facility Horticulture Research Institute of Suqian, Suqian Research Institute of Nanjing Agricultural University, Suqian, Jiangsu, 223800, China
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20
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Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
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Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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21
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Schelkunov MI, Shtratnikova VY, Klepikova AV, Makarenko MS, Omelchenko DO, Novikova LA, Obukhova EN, Bogdanov VP, Penin AA, Logacheva MD. The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite absence of recent whole-genome duplications. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:449-463. [PMID: 37846604 DOI: 10.1111/tpj.16500] [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: 08/16/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Heracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H. sosnowskyi to produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome-scale assembly of Sosnowsky's hogweed genome. Genomic analysis revealed an unusually high number of genes (55106) in the hogweed genome, in contrast to the 25-35 thousand found in most plants. However, we did not find any traces of recent whole-genome duplications not shared with its confamiliar, Daucus carota (carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates on tandem duplications as a main reason for this increase. We performed a genome-wide search of the genes of the FC biosynthesis pathway and surveyed their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.
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Affiliation(s)
- Mikhail I Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Viktoria Yu Shtratnikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Lyudmila A Novikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Viktor P Bogdanov
- Life Sciences Research Center, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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22
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Zhang H, Li Z, Wang M, Yang Y, Wang Y, Nie Q, Liang F, Qin H, Zhang Z. The chromosome-level genome assembly of Fraxinus americana provides insights into the evolution of Oleaceae plants. Int J Biol Macromol 2023; 253:127132. [PMID: 37778585 DOI: 10.1016/j.ijbiomac.2023.127132] [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: 07/17/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023]
Abstract
White ash (Fraxinus americana linn.) originates from the southeastern United States. It is a tall and fast-growing tree species with strong salt-alkali resistance and cold tolerance, making it an important reforestation species and widely planted worldwide. Here, we completed the chromosome-level reference genome assembly of F. americana based on Illumina, PacBio, and Hi-C reads, with a genome size of 878.98 Mb, an N50 of 3.27 Mb, and a heterozygosity rate of 0.3 %. Based on de novo prediction, transcriptome prediction, and homology-based protein prediction, we obtained 39,538 genes. Approximately 843.21 Mb of the assembly genome was composed of 37,928 annotated protein-coding genes, with a gene function annotation rate of 95.93 %. 99.94 % of the overlap clusters (877.44 Mb) were anchored to 23 chromosomes. Synteny analysis of F. americana and other Oleaceae plants showed that F. americana underwent frequent chromosome rearrangements. The amplification of the Ale transposons effectively promoted the genome size of F. americana. Compared with other Oleaceae plants, the Glutathione S-transferase (GST) gene family in the F. americana genome has undergone significant expansion, which may help F. americana cope with adverse natural environments. Furthermore, we found that key enzyme-coding gene families related to lignin biosynthesis were expanded and highly expressed in F. americana leaves. These key genes drive lignin synthesis and benefit F. americana in fast-growing, as well as resisting biotic and abiotic stress. Overall, the F. americana genome assembly provides insights into the evolution of Oleaceae plants and provides abundant resources for breeding and germplasm conservation of white ash.
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Affiliation(s)
- Hua Zhang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China.
| | - Zhiqi Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China
| | - Maoliang Wang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yipeng Yang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Yongge Wang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Qiufeng Nie
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Fang Liang
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Helan Qin
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Academy of Forestry and Landscape Architecture, Beijing 100102, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572024, China; Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou 570228, China.
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23
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Zhou J, Huang D, Liu C, Hu Z, Li H, Lou S. Research Progress in Heterologous Crocin Production. Mar Drugs 2023; 22:22. [PMID: 38248646 PMCID: PMC10820313 DOI: 10.3390/md22010022] [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: 11/24/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024] Open
Abstract
Crocin is one of the most valuable components of the Chinese medicinal plant Crocus sativus and is widely used in the food, cosmetics, and pharmaceutical industries. Traditional planting of C. sativus is unable to fulfill the increasing demand for crocin in the global market, however, such that researchers have turned their attention to the heterologous production of crocin in a variety of hosts. At present, there are reports of successful heterologous production of crocin in Escherichia coli, Saccharomyces cerevisiae, microalgae, and plants that do not naturally produce crocin. Of these, the microalga Dunaliella salina, which produces high levels of β-carotene, the substrate for crocin biosynthesis, is worthy of attention. This article describes the biosynthesis of crocin, compares the features of each heterologous host, and clarifies the requirements for efficient production of crocin in microalgae.
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Affiliation(s)
- Junjie Zhou
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (J.Z.); (D.H.); (C.L.); (Z.H.); (H.L.)
| | - Danqiong Huang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (J.Z.); (D.H.); (C.L.); (Z.H.); (H.L.)
| | - Chenglong Liu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (J.Z.); (D.H.); (C.L.); (Z.H.); (H.L.)
| | - Zhangli Hu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (J.Z.); (D.H.); (C.L.); (Z.H.); (H.L.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Hui Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (J.Z.); (D.H.); (C.L.); (Z.H.); (H.L.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
| | - Sulin Lou
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China; (J.Z.); (D.H.); (C.L.); (Z.H.); (H.L.)
- Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, Shenzhen University, Shenzhen 518060, China
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24
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Zhao X, Li Y, Zhang MM, He X, Ahmad S, Lan S, Liu ZJ. Research advances on the gene regulation of floral development and color in orchids. Gene 2023; 888:147751. [PMID: 37657689 DOI: 10.1016/j.gene.2023.147751] [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: 06/28/2023] [Revised: 08/08/2023] [Accepted: 08/30/2023] [Indexed: 09/03/2023]
Abstract
Orchidaceae is one of the largest monocotyledon families and contributes significantly to worldwide biodiversity, with value in the fields of landscaping, medicine, and ecology. The diverse phenotypes and vibrant colors of orchid floral organs make them excellent research objects for investigating flower development and pigmentation. In recent years, a number of orchid genomes have been published, laying the molecular foundation for revealing flower development and color presentation. In this article, we review transcription factors, the structural genes responsible for the floral pigment synthesis pathways, the molecular mechanisms of flower morphogenesis, and the potential relationship between flower type and flower color. This study provides a theoretical reference for the research on molecular mechanisms related to flower morphogenesis and color presentation, genetic improvement, and new variety creation in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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25
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Nothnagel T, Ulrich D, Dunemann F, Budahn H. Sensory Perception and Consumer Acceptance of Carrot Cultivars Are Influenced by Their Metabolic Profiles for Volatile and Non-Volatile Organic Compounds. Foods 2023; 12:4389. [PMID: 38137193 PMCID: PMC10742604 DOI: 10.3390/foods12244389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Sensory parameters as well as the volatile and non-volatile compound profiles of sixteen carrot cultivars were recorded to obtain insight into consumer preference decisions. The sensory test was carried out with a consumer panel of 88 untrained testers allowing a clear acceptance-based differentiation of the cultivars. Five individual sensory characters (sweetness, overall aroma, bitterness, astringency and off-flavor) supported this discrimination. Chemical analyses of volatile organic compounds, polyacetylenes, phenylpropanoids and sugars enabled us to correlate the influence of these ingredients on sensory perception. Higher concentrations of α-pinene, hexanal, styrene and acetophenone correlated with a better acceptance, as well as sweetness and overall aroma perception. In contrast, a low acceptance as well as a stronger perception of bitterness, astringency and off-flavor correlated with enhanced concentrations of camphene, bornylacetate, borneol, myristicine, falcarindiol, falcarindiol-3-acetate, laserin and epilaserin. The present study should support the development of new breeding strategies for carrot cultivars that better satisfy consumer demands.
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Affiliation(s)
- Thomas Nothnagel
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural Crops, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany; (T.N.)
| | - Detlef Ulrich
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Königin-Luise-Str. 19, D-14195 Berlin, Germany
| | - Frank Dunemann
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural Crops, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany; (T.N.)
| | - Holger Budahn
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural Crops, Erwin-Baur-Str. 27, D-06484 Quedlinburg, Germany; (T.N.)
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26
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Wu X, Simpson SA, Youngblood RC, Liu XF, Scheffler BE, Rinehart TA, Alexander LW, Hulse-Kemp AM. Two haplotype-resolved genomes reveal important flower traits in bigleaf hydrangea ( Hydrangea macrophylla) and insights into Asterid evolution. HORTICULTURE RESEARCH 2023; 10:uhad217. [PMID: 38130599 PMCID: PMC10734616 DOI: 10.1093/hr/uhad217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 12/23/2023]
Abstract
The Hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants, which early diverged among the Asterids, and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable species in the nursery trade, yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype-resolved reference genomes of hydrangea cultivars 'Veitchii' and 'Endless Summer' [highest quality at 2.22 gigabase pairs (Gb), 396 contigs, N50 22.8 megabase pairs (Mb)] were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data were found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contribute to understanding the largest group of flowering plants, the Asterids.
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Affiliation(s)
- Xingbo Wu
- Department of Environmental Horticulture, Tropical Research and Education Center, University of Florida, Homestead, FL 33031, United States
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
| | - Sheron A Simpson
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, MS 39762, United States
| | - Xiaofen F Liu
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, USDA-ARS, Stoneville, MS 38776, United States
| | - Timothy A Rinehart
- Crop Production and Protection, USDA-ARS, Beltsville, MD 20705, United States
| | - Lisa W Alexander
- Floral and Nursery Plants Research Unit, U.S. National Arboretum, USDA-ARS, McMinnville, TN 37110, United States
| | - Amanda M Hulse-Kemp
- Genomics and Bioinformatics Research Unit, USDA-ARS, Raleigh, NC 27695, United States
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, United States
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Keller-Pearson M, Bortolazzo A, Willems L, Smith B, Peterson A, Ané JM, Silva EM. A Dual Transcriptomic Approach Reveals Contrasting Patterns of Differential Gene Expression During Drought in Arbuscular Mycorrhizal Fungus and Carrot. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:821-832. [PMID: 37698455 DOI: 10.1094/mpmi-04-23-0038-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
While arbuscular mycorrhizal (AM) fungi are known for providing host plants with improved drought tolerance, we know very little about the fungal response to drought in the context of the fungal-plant relationship. In this study, we evaluated the drought responses of the host and symbiont, using the fungus Rhizophagus irregularis with carrot (Daucus carota) as a plant model. Carrots inoculated with spores of R. irregularis DAOM 197198 were grown in a greenhouse. During taproot development, carrots were exposed to a 10-day water restriction. Compared with well-watered conditions, drought caused diminished photosynthetic activity and reduced plant growth in carrot with and without AM fungi. Droughted carrots had lower root colonization. For R. irregularis, 93% of 826 differentially expressed genes (DEGs) were upregulated during drought, including phosphate transporters, several predicted transport proteins of potassium, and the aquaporin RiAQPF2. In contrast, 78% of 2,486 DEGs in AM carrot were downregulated during drought, including the symbiosis-specific genes FatM, RAM2, and STR, which are implicated in lipid transfer from the host to the fungus and were upregulated exclusively in AM carrot during well-watered conditions. Overall, this study provides insight into the drought response of an AM fungus in relation to its host; the expression of genes related to symbiosis and nutrient exchange were downregulated in carrot but upregulated in the fungus. This study reveals that carrot and R. irregularis exhibit contrast in their regulation of gene expression during drought, with carrot reducing its apparent investment in symbiosis and the fungus increasing its apparent symbiotic efforts. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Anthony Bortolazzo
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Luke Willems
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Brendan Smith
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Annika Peterson
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Erin M Silva
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, U.S.A
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28
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Rempel A, Choudhary N, Pucker B. KIPEs3: Automatic annotation of biosynthesis pathways. PLoS One 2023; 18:e0294342. [PMID: 37972102 PMCID: PMC10653506 DOI: 10.1371/journal.pone.0294342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/28/2023] [Indexed: 11/19/2023] Open
Abstract
Flavonoids and carotenoids are pigments involved in stress mitigation and numerous other processes. Both pigment classes can contribute to flower and fruit coloration. Flavonoid aglycones and carotenoids are produced by a pathway that is largely conserved across land plants. Glycosylations, acylations, and methylations of the flavonoid aglycones can be species-specific and lead to a plethora of biochemically diverse flavonoids. We previously developed KIPEs for the automatic annotation of biosynthesis pathways and presented an application on the flavonoid aglycone biosynthesis. KIPEs3 is an improved version with additional features and the potential to identify not just the core biosynthesis players, but also candidates involved in the decoration steps and in the transport of flavonoids. Functionality of KIPEs3 is demonstrated through the analysis of the flavonoid biosynthesis in Arabidopsis thaliana Nd-1, Capsella grandiflora, and Dioscorea dumetorum. We demonstrate the applicability of KIPEs to other pathways by adding the carotenoid biosynthesis to the repertoire. As a technical proof of concept, the carotenoid biosynthesis was analyzed in the same species and Daucus carota. KIPEs3 is available as an online service to enable access without prior bioinformatics experience. KIPEs3 facilitates the automatic annotation and analysis of biosynthesis pathways with a consistent and high quality in a large number of plant species. Numerous genome sequencing projects are generating a huge amount of data sets that can be analyzed to identify evolutionary patterns and promising candidate genes for biotechnological and breeding applications.
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Affiliation(s)
- Andreas Rempel
- Genome Informatics, Faculty of Technology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
- Graduate School “Digital Infrastructure for the Life Sciences” (DILS), Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, Bielefeld, Germany
| | - Nancy Choudhary
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & BRICS, TU Braunschweig, Braunschweig, Germany
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29
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Meyer CM, Goldman IL, Krysan PJ. Chromosome-level changes and genome elimination by manipulation of CENH3 in carrot ( Daucus carota). FRONTIERS IN PLANT SCIENCE 2023; 14:1294551. [PMID: 38034555 PMCID: PMC10684906 DOI: 10.3389/fpls.2023.1294551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 12/02/2023]
Abstract
Hybrid cultivars are valuable in many crop species due to their high yield, uniformity, and other desirable traits. Doubled haploids, which have two identical sets of chromosomes, are valuable for hybrid breeding because they can be produced in one generation, in comparison to the multigenerational process typically used to produce inbred parents for hybrid production. One method to produce haploid plants is manipulation of centromeric histone H3 (CENH3). This method of producing haploids has so far been successful in Arabidopsis, maize (Zea mays), and wheat (Triticum aestivum). Here we describe modification of CENH3 in carrot (Daucus carota) to test for the ability of these modifications to induce uniparental genome elimination, which is the basis for haploid induction. Base editing was used to make cenh3 mutant plants with amino acid substitutions in the region of CENH3 encoding the histone fold domain. These cenh3 mutant plants were then outcrossed with CENH3 wild-type plants. Using PCR-based genotyping assays, we identified two candidates for genome elimination. One candidate was classified as a putative aneuploid plant in which chromosome 7 is in a single copy state. The other candidate was characterized as a putative tetraploid that was likely haploid during its genesis. Our results suggest that this putative tetraploid inherited all of its chromosomes from the CENH3 wild-type parent and that the genome of the cenh3 mutant plant was lost. This study provides evidence that modification of CENH3 in carrot has the potential to induce genome elimination and ploidy changes in carrot.
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Affiliation(s)
| | | | - Patrick J. Krysan
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
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30
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Hernández F, Palmieri L, Brunet J. Introgression and persistence of cultivar alleles in wild carrot (Daucus carota) populations in the United States. AMERICAN JOURNAL OF BOTANY 2023; 110:e16242. [PMID: 37681637 DOI: 10.1002/ajb2.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
PREMISE Cultivated species and their wild relatives often hybridize in the wild, and the hybrids can survive and reproduce in some environments. However, it is unclear whether cultivar alleles are permanently incorporated into the wild genomes or whether they are purged by natural selection. This question is key to accurately assessing the risk of escape and spread of cultivar genes into wild populations. METHODS We used genomic data and population genomic methods to study hybridization and introgression between cultivated and wild carrot (Daucus carota) in the United States. We used single nucleotide polymorphisms (SNPs) obtained via genotyping by sequencing for 450 wild individuals from 29 wild georeferenced populations in seven states and 144 cultivars from the United States, Europe, and Asia. RESULTS Cultivated and wild carrot formed two genetically differentiated groups, and evidence of crop-wild admixture was detected in several but not all wild carrot populations in the United States. Two regions were identified where cultivar alleles were present in wild carrots: California and Nantucket Island (Massachusetts). Surprisingly, there was no evidence of introgression in some populations with a long-known history of sympatry with the crop, suggesting that post-hybridization barriers might prevent introgression in some areas. CONCLUSIONS Our results provide support for the introgression and long-term persistence of cultivar alleles in wild carrots populations. We thus anticipate that the release of genetically engineered (GE) cultivars would lead to the introduction and spread of GE alleles in wild carrot populations.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina
- CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Luciano Palmieri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Madison, WI, USA
| | - Johanne Brunet
- Vegetable Crops Research Unit, USDA-ARS, Madison, WI, USA
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31
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He Z, Chao H, Zhou X, Ni Q, Hu Y, Yu R, Wang M, Li C, Chen J, Chen Y, Chen Y, Cui C, Zhang L, Chen M, Chen D. A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development. HORTICULTURE RESEARCH 2023; 10:uhad196. [PMID: 38023476 PMCID: PMC10673659 DOI: 10.1093/hr/uhad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.
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Affiliation(s)
- Zhenxiang He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoyu Chao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Minghuai Wang
- Forest Protection Department, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Jingzhen Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yunzhu Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yong Chen
- Xishan Forest Farm, Dazu District, Chongqing 402360, China
| | - Chunyi Cui
- Longshan Forest Farm, Lechang 512221, China
| | - Liangbo Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
- Hunan Horticultural Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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32
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Baczyński J, Claßen-Bockhoff R. Pseudanthia in angiosperms: a review. ANNALS OF BOTANY 2023; 132:179-202. [PMID: 37478306 PMCID: PMC10583202 DOI: 10.1093/aob/mcad103] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/19/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Pseudanthia or 'false flowers' are multiflowered units that resemble solitary flowers in form and function. Over the last century the term 'pseudanthium' has been applied to a wide array of morphologically divergent blossoms, ranging from those with easily noticeable florets to derived, reduced units in which individual flowers become almost indistinguishable. Although initially admired mostly by botanists, the diversity and widespread distribution of pseudanthia across angiosperms has already made them a fascinating topic for evolutionary and developmental comparative studies. SCOPE This review synthesizes historical and current concepts on the biology of pseudanthia. Our first aim is to establish a clear, operational definition of pseudanthium and disentangle common terminological misconceptions surrounding that term. Our second aim is to summarize knowledge of the morphological and developmental diversity of pseudanthia and embed it within a modern phylogenetic framework. Lastly, we want to provide a comprehensive overview on the evolution and ecological importance of pseudanthia and outline perspectives for future studies. CONCLUSIONS The understanding of pseudanthia has changed multiple times and reflects three different interpretations of their 'flower-like' qualities: developmental (similarity in structure), figural (similarity in form and function) and phylogenetic (homology between angiosperm flowers and monoecious reproductive shoots in gymnosperms). Here, we propose to narrow the term pseudanthium to multiflowered blossoms resembling zoophilous flowers in form, i.e. in being structurally subdivided in a showy periphery and a reproductive centre. According to this definition, pseudanthia sensu stricto evolved independently in at least 41 angiosperm families. The recurrent acquisition of pseudanthia sensu stricto in all major lineages of flowering plants indicates repeated interactions between developmental constraints (smallness of flowers, meristematic conditions) and selective pressures, such as demands of pollinators and/or environmental conditions.
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Affiliation(s)
- Jakub Baczyński
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia, USA
| | - Regine Claßen-Bockhoff
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Mainz, Germany
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33
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Schulz K, Machaj G, Knox P, Hancock RD, Verrall SR, Korpinen R, Saranpää P, Kärkönen A, Karpinska B, Foyer CH. Restraining Quiescence Release-Related Ageing in Plant Cells: A Case Study in Carrot. Cells 2023; 12:2465. [PMID: 37887309 PMCID: PMC10605352 DOI: 10.3390/cells12202465] [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: 09/13/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/28/2023] Open
Abstract
The blackening of cut carrots causes substantial economic losses to the food industry. Blackening was not observed in carrots that had been stored underground for less than a year, but the susceptibility to blackening increased with the age of the carrots that were stored underground for longer periods. Samples of black, border, and orange tissues from processed carrot batons and slices, prepared under industry standard conditions, were analyzed to identify the molecular and metabolic mechanisms underpinning processing-induced blackening. The black tissues showed substantial molecular and metabolic rewiring and large changes in the cell wall structure, with a decreased abundance of xyloglucan, pectins (homogalacturonan, rhamnogalacturonan-I, galactan and arabinan), and higher levels of lignin and other phenolic compounds when compared to orange tissues. Metabolite profiling analysis showed that there was a major shift from primary to secondary metabolism in the black tissues, which were depleted in sugars, amino acids, and tricarboxylic acid (TCA) cycle intermediates but were rich in phenolic compounds. These findings suggest that processing triggers a release from quiescence. Transcripts encoding proteins associated with secondary metabolism were less abundant in the black tissues, but there were no increases in transcripts associated with oxidative stress responses, programmed cell death, or senescence. We conclude that restraining quiescence release alters cell wall metabolism and composition, particularly regarding pectin composition, in a manner that increases susceptibility to blackening upon processing.
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Affiliation(s)
- Katie Schulz
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (K.S.); (P.K.)
| | - Gabriela Machaj
- Department of Plant Biology and Biotechnology, University of Agriculture in Krakow, 31-120 Krakow, Poland;
| | - Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (K.S.); (P.K.)
| | - Robert D. Hancock
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Susan R. Verrall
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 1BE, UK;
| | - Risto Korpinen
- Natural Resources Institute Finland, Production Systems, Latokartanonkaari 9, 00790 Helsinki, Finland; (R.K.); (P.S.); (A.K.)
| | - Pekka Saranpää
- Natural Resources Institute Finland, Production Systems, Latokartanonkaari 9, 00790 Helsinki, Finland; (R.K.); (P.S.); (A.K.)
| | - Anna Kärkönen
- Natural Resources Institute Finland, Production Systems, Latokartanonkaari 9, 00790 Helsinki, Finland; (R.K.); (P.S.); (A.K.)
| | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
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Coe K, Bostan H, Rolling W, Turner-Hissong S, Macko-Podgórni A, Senalik D, Liu S, Seth R, Curaba J, Mengist MF, Grzebelus D, Van Deynze A, Dawson J, Ellison S, Simon P, Iorizzo M. Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots. NATURE PLANTS 2023; 9:1643-1658. [PMID: 37770615 PMCID: PMC10581907 DOI: 10.1038/s41477-023-01526-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023]
Abstract
Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and β-carotene orange phenotype. All three genes control high α- and β-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.
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Affiliation(s)
- Kevin Coe
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Hamed Bostan
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - William Rolling
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA
| | | | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Douglas Senalik
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA
| | - Su Liu
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Romit Seth
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Julien Curaba
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Molla Fentie Mengist
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, CA, USA
| | - Julie Dawson
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Shelby Ellison
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Philipp Simon
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Agricultural Research Service, Vegetable Crops Research Unit, US Department of Agriculture, Madison, WI, USA.
| | - Massimo Iorizzo
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, USA.
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, USA.
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35
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Guo Y, Lu F. The changing colour of carrot. NATURE PLANTS 2023; 9:1583-1584. [PMID: 37770614 DOI: 10.1038/s41477-023-01523-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Affiliation(s)
- Yafei Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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36
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Kulkarni CC, Cholin SS, Bajpai AK, Ondrasek G, Mesta RK, Rathod S, Patil HB. Comparative Root Transcriptome Profiling and Gene Regulatory Network Analysis between Eastern and Western Carrot ( Daucus carota L.) Cultivars Reveals Candidate Genes for Vascular Tissue Patterning. PLANTS (BASEL, SWITZERLAND) 2023; 12:3449. [PMID: 37836190 PMCID: PMC10575051 DOI: 10.3390/plants12193449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023]
Abstract
Carrot (Daucus carota L.) is a highly consumed vegetable rich in carotenoids, known for their potent antioxidant, anti-inflammatory, and immune-protecting properties. While genetic and molecular studies have largely focused on wild and Western carrot cultivars (cvs), little is known about the evolutionary interactions between closely related Eastern and Western cvs. In this study, we conducted comparative transcriptome profiling of root tissues from Eastern (UHSBC-23-1) and Western (UHSBC-100) carrot cv. to better understand differentially expressed genes (DEGs) associated with storage root development and vascular cambium (VC) tissue patterning. Through reference-guided TopHat mapping, we achieved an average mapping rate of 73.87% and identified a total of 3544 DEGs (p < 0.05). Functional annotation and gene ontology classification revealed 97 functional categories, including 33 biological processes, 19 cellular components, 45 metabolic processes, and 26 KEGG pathways. Notably, Eastern cv. exhibited enrichment in cell wall, plant-pathogen interaction, and signal transduction terms, while Western cv. showed dominance in photosynthesis, metabolic process, and carbon metabolism terms. Moreover, constructed gene regulatory network (GRN) for both cvs. obtained orthologs with 1222 VC-responsive genes of Arabidopsis thaliana. In Western cv, GRN revealed VC-responsive gene clusters primarily associated with photosynthetic processes and carbon metabolism. In contrast, Eastern cv. exhibited a higher number of stress-responsive genes, and transcription factors (e.g., MYB15, WRKY46, AP2/ERF TF connected via signaling pathways with NAC036) were identified as master regulators of xylem vessel differentiation and secondary cell wall thickening. By elucidating the comparative transcriptome profiles of Eastern and Western cvs. for the first time, our study provides valuable insights into the differentially expressed genes involved in root development and VC tissue patterning. The identification of key regulatory genes and their roles in these processes represents a significant advancement in our understanding of the evolutionary relations and molecular mechanisms underlying secondary growth of carrot and regulation by vascular cambium.
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Affiliation(s)
- Chaitra C. Kulkarni
- Plant Molecular Biology Lab (DBT-BIOCARe), Department of Biotechnology & Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot 587103, Karnataka, India;
- Kittur Rani Chennamma College of Horticulture, Arabhavi, Gokak 591218, Belgaum Dt., Karnataka, India
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
| | - Sarvamangala S. Cholin
- Plant Molecular Biology Lab (DBT-BIOCARe), Department of Biotechnology & Crop Improvement, College of Horticulture, University of Horticultural Sciences, Bagalkot 587103, Karnataka, India;
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
| | - Akhilesh K. Bajpai
- Shodhaka Life Sciences Pvt. Ltd., Electronic City, Phase-I, Bengaluru 560100, Karnataka, India
| | - Gabrijel Ondrasek
- Department of Soil Amelioration, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
| | - R. K. Mesta
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
| | - Santosha Rathod
- Indian Institute of Rice Research, Hyderabad 500030, Telangana, India
| | - H. B. Patil
- University of Horticultural Sciences, Bagalkot 587103, Karnataka, India
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Wolters SM, Benninghaus VA, Roelfs KU, van Deenen N, Twyman RM, Prüfer D, Schulze Gronover C. Overexpression of a pseudo-etiolated-in-light-like protein in Taraxacum koksaghyz leads to a pale green phenotype and enables transcriptome-based network analysis of photomorphogenesis and isoprenoid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1228961. [PMID: 37841614 PMCID: PMC10569127 DOI: 10.3389/fpls.2023.1228961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/21/2023] [Indexed: 10/17/2023]
Abstract
Introduction Plant growth and greening in response to light require the synthesis of photosynthetic pigments such as chlorophylls and carotenoids, which are derived from isoprenoid precursors. In Arabidopsis, the pseudo-etiolated-in-light phenotype is caused by the overexpression of repressor of photosynthetic genes 2 (RPGE2), which regulates chlorophyll synthesis and photosynthetic genes. Methods We investigated a homologous protein in the Russian dandelion (Taraxacum koksaghyz) to determine its influence on the rich isoprenoid network in this species, using a combination of in silico analysis, gene overexpression, transcriptomics and metabolic profiling. Results Homology-based screening revealed a gene designated pseudo-etiolated-in-light-like (TkPEL-like), and in silico analysis identified a light-responsive G-box element in its promoter. TkPEL-like overexpression in dandelion plants and other systems reduced the levels of chlorophylls and carotenoids, but this was ameliorated by the mutation of one or both conserved cysteine residues. Comparative transcriptomics in dandelions overexpressing TkPEL-like showed that genes responsible for the synthesis of isoprenoid precursors and chlorophyll were downregulated, probably explaining the observed pale green leaf phenotype. In contrast, genes responsible for carotenoid synthesis were upregulated, possibly in response to feedback signaling. The evaluation of additional differentially expressed genes revealed interactions between pathways. Discussion We propose that TkPEL-like negatively regulates chlorophyll- and photosynthesis-related genes in a light-dependent manner, which appears to be conserved across species. Our data will inform future studies addressing the regulation of leaf isoprenoid biosynthesis and photomorphogenesis and could be used in future breeding strategies to optimize selected plant isoprenoid profiles and generate suitable plant-based production platforms.
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Affiliation(s)
- Silva Melissa Wolters
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | | | - Kai-Uwe Roelfs
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
| | - Nicole van Deenen
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | | | - Dirk Prüfer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
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Rosas-Saavedra C, Quiroz LF, Parra S, Gonzalez-Calquin C, Arias D, Ocarez N, Lopez F, Stange C. Putative Daucus carota Capsanthin-Capsorubin Synthase (DcCCS) Possesses Lycopene β-Cyclase Activity, Boosts Carotenoid Levels, and Increases Salt Tolerance in Heterologous Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2788. [PMID: 37570943 PMCID: PMC10421225 DOI: 10.3390/plants12152788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 08/13/2023]
Abstract
Plant carotenoids are synthesized and accumulated in plastids through a highly regulated pathway. Lycopene β-cyclase (LCYB) is a key enzyme involved directly in the synthesis of α-carotene and β-carotene through the cyclization of trans-lycopene. Daucus carota harbors two LCYB genes, of which DcLCYB2 (annotated as CCS-Like) is mostly expressed in mature storage roots, an organ that accumulates high α-carotene and β-carotene content. In this work, we determined that DcLCYB2 of the orange Nantes variety presents plastid localization and encodes for a functional LCYB enzyme determined by means of heterologous complementation in Escherichia coli. Also, ectopic expression of DcLCYB2 in tobacco (Nicotiana tabacum) and kiwi (Actinidia deliciosa) plants increases total carotenoid content showing its functional role in plants. In addition, transgenic tobacco T2 homozygous plants showed better performance under chronic salt treatment, while kiwi transgenic calli also presented a higher survival rate under salt treatments than control calli. Our results allow us to propose DcLCYB2 as a prime candidate to engineer carotenoid biofortified crops as well as crops resilient to saline environments.
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Affiliation(s)
- Carolina Rosas-Saavedra
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Luis Felipe Quiroz
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
- Genetics & Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Samuel Parra
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Christian Gonzalez-Calquin
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Daniela Arias
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Nallat Ocarez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
- Instituto de Investigaciones Agropecuarias (INIA), La Platina, Research Centre, Av. Santa Rosa 11610, Santiago 8820000, Chile
| | - Franco Lopez
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
| | - Claudia Stange
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7750000, Chile; (C.R.-S.); (L.F.Q.); (S.P.); (C.G.-C.); (D.A.); (N.O.); (F.L.)
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D'Amelia V, Curaba J, Abid MA, Esposito S, Cavagnaro P, Carputo D, Iorizzo M. Functional characterization of DcMYB11, an R2R3 MYB associated with the purple pigmentation of carrot petiole. PLANTA 2023; 258:50. [PMID: 37488440 DOI: 10.1007/s00425-023-04200-5] [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: 05/29/2023] [Accepted: 07/04/2023] [Indexed: 07/26/2023]
Abstract
MAIN CONCLUSION DcMYB11, an R2R3 MYB gene associated with petiole anthocyanin pigmentation in carrot, was functionally characterized. A putative enhancer sequence is able to increase DcMYB11 activity. The accumulation of anthocyanin pigments can exhibit different patterns across plant tissues and crop varieties. This variability allowed the investigation of the molecular mechanisms behind the biosynthesis of these pigments in several plant species. Among crops, carrots have a well-defined anthocyanin pigmentation pattern depending on the genic background. In this work, we report on the discovery of DNA structural differences affecting the activity of an R2R3 MYB (encoded by DcMYB11) involved in anthocyanin regulation in carrot petiole. To this end, we first verified the function of DcMYB11 using heterologous systems and identified three different alleles which may explain differences in petiole pigmentation. Characterization of the DcMYB11 alleles at the 5' upstream sequence unveiled a sequence that functions as a putative enhancer. In conclusion, this study provides novel insight into the molecular mechanisms controlling anthocyanin accumulation in carrot. By these outcomes, we expanded our knowledge on the cis-regulatory sequences in plants.
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Affiliation(s)
- Vincenzo D'Amelia
- Institute of Bioscience and BioResources, National Research Council, Via Università 100, 80055, Portici, Italy
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Julien Curaba
- Horticulture Science Department, Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Muhammad Ali Abid
- Horticulture Science Department, Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, USA
| | - Salvatore Esposito
- CREA Research Centre for Cereal and Industrial Crops (CREA-CI), 71122, Foggia, Italy
| | - Pablo Cavagnaro
- National Scientific and Technical Research Council (CONICET), National Institute of Agricultural Technology (INTA) E.E.A. La Consulta, La Consulta CC8, San Carlos, 5567, Mendoza, Argentina
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Massimo Iorizzo
- Horticulture Science Department, Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, USA.
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Xiong W, Berke L, Michelmore R, van Workum DJM, Becker FFM, Schijlen E, Bakker LV, Peters S, van Treuren R, Jeuken M, Bouwmeester K, Schranz ME. The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:108-126. [PMID: 36987839 DOI: 10.1111/tpj.16212] [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: 10/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibility (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad-spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non-host species. This phenomenon of resistance in L. saligna is called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant-pathogen interaction triggered by pathogen recognition receptors, including nucleotide-binding leucine-rich repeat (NLR) proteins and receptor-like kinases (RLKs). We report a chromosome-level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis of Bremia-infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidates for determinants of the NHR phenotype of L. saligna.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Frank F M Becker
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Elio Schijlen
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Linda V Bakker
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Sander Peters
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rob van Treuren
- Centre for Genetic Resources, The Netherlands (CGN), Wageningen University and Research, Wageningen, The Netherlands
| | - Marieke Jeuken
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
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Wang YH, Liu PZ, Liu H, Zhang RR, Liang Y, Xu ZS, Li XJ, Luo Q, Tan GF, Wang GL, Xiong AS. Telomere-to-telomere carrot ( Daucus carota) genome assembly reveals carotenoid characteristics. HORTICULTURE RESEARCH 2023; 10:uhad103. [PMID: 37786729 PMCID: PMC10541555 DOI: 10.1093/hr/uhad103] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/08/2023] [Indexed: 10/04/2023]
Abstract
Carrot (Daucus carota) is an Apiaceae plant with multi-colored fleshy roots that provides a model system for carotenoid research. In this study, we assembled a 430.40 Mb high-quality gapless genome to the telomere-to-telomere (T2T) level of "Kurodagosun" carrot. In total, 36 268 genes were identified and 34 961 of them were functionally annotated. The proportion of repeat sequences in the genome was 55.3%, mainly long terminal repeats. Depending on the coverage of the repeats, 14 telomeres and 9 centromeric regions on the chromosomes were predicted. A phylogenetic analysis showed that carrots evolved early in the family Apiaceae. Based on the T2T genome, we reconstructed the carotenoid metabolic pathway and identified the structural genes that regulate carotenoid biosynthesis. Among the 65 genes that were screened, 9 were newly identified. Additionally, some gene sequences overlapped with transposons, suggesting replication and functional differentiation of carotenoid-related genes during carrot evolution. Given that some gene copies were barely expressed during development, they might be functionally redundant. Comparison of 24 cytochrome P450 genes associated with carotenoid biosynthesis revealed the tandem or proximal duplication resulting in expansion of CYP gene family. These results provided molecular information for carrot carotenoid accumulation and contributed to a new genetic resource.
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Affiliation(s)
- Ya-Hui Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Pei-Zhuo Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Rong-Rong Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yi Liang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in North China, Beijing 100097, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiao-Jie Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in North China, Beijing 100097, China
| | - Qing Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550025, China
| | - Guo-Fei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550025, China
| | - Guang-Long Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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Selvakumar R, Jat GS, Manjunathagowda DC. Allele mining through TILLING and EcoTILLING approaches in vegetable crops. PLANTA 2023; 258:15. [PMID: 37311932 DOI: 10.1007/s00425-023-04176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023]
Abstract
MAIN CONCLUSION The present review illustrates a comprehensive overview of the allele mining for genetic improvement in vegetable crops, and allele exploration methods and their utilization in various applications related to pre-breeding of economically important traits in vegetable crops. Vegetable crops have numerous wild descendants, ancestors and terrestrial races that could be exploited to develop high-yielding and climate-resilient varieties resistant/tolerant to biotic and abiotic stresses. To further boost the genetic potential of economic traits, the available genomic tools must be targeted and re-opened for exploitation of novel alleles from genetic stocks by the discovery of beneficial alleles from wild relatives and their introgression to cultivated types. This capability would be useful for giving plant breeders direct access to critical alleles that confer higher production, improve bioactive compounds, increase water and nutrient productivity as well as biotic and abiotic stress resilience. Allele mining is a new sophisticated technique for dissecting naturally occurring allelic variants in candidate genes that influence important traits which could be used for genetic improvement of vegetable crops. Target-induced local lesions in genomes (TILLINGs) is a sensitive mutation detection avenue in functional genomics, particularly wherein genome sequence information is limited or not available. Population exposure to chemical mutagens and the absence of selectivity lead to TILLING and EcoTILLING. EcoTILLING may lead to natural induction of SNPs and InDels. It is anticipated that as TILLING is used for vegetable crops improvement in the near future, indirect benefits will become apparent. Therefore, in this review we have highlighted the up-to-date information on allele mining for genetic enhancement in vegetable crops and methods of allele exploration and their use in pre-breeding for improvement of economic traits.
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Affiliation(s)
- Raman Selvakumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India
| | - Gograj Singh Jat
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi, 110 012, India.
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He G, Zhang R, Jiang S, Wang H, Ming F. The MYB transcription factor RcMYB1 plays a central role in rose anthocyanin biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad080. [PMID: 37323234 PMCID: PMC10261888 DOI: 10.1093/hr/uhad080] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Rose (Rosa hybrida) is one of most famous ornamental plants in the world, and its commodity value largely depends on its flower color. However, the regulatory mechanism underlying rose flower color is still unclear. In this study, we found that a key R2R3-MYB transcription factor, RcMYB1, plays a central role in rose anthocyanin biosynthesis. Overexpression of RcMYB1 significantly promoted anthocyanin accumulation in both white rose petals and tobacco leaves. In 35S:RcMYB1 transgenic lines, a significant accumulation of anthocyanins occurred in leaves and petioles. We further identified two MBW complexes (RcMYB1-RcBHLH42-RcTTG1; RcMYB1-RcEGL1-RcTTG1) associated with anthocyanin accumulation. Yeast one-hybrid and luciferase assays showed that RcMYB1 could active its own gene promoter and those of other EBGs (early anthocyanin biosynthesis genes) and LBGs (late anthocyanin biosynthesis genes). In addition, both of the MBW complexes enhanced the transcriptional activity of RcMYB1 and LBGs. Interestingly, our results also indicate that RcMYB1 is involved in the metabolic regulation of carotenoids and volatile aroma. In summary, we found that RcMYB1 widely participates in the transcriptional regulation of ABGs (anthocyanin biosynthesis genes), indicative of its central role in the regulation of anthocyanin accumulation in rose. Our results provide a theoretical basis for the further improvement of the flower color trait in rose by breeding or genetic modification.
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Affiliation(s)
| | | | - Shenghang Jiang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Huanhuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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El-Batal AI, Ismail MA, Amin MA, El-Sayyad GS, Osman MS. Selenium nanoparticles induce growth and physiological tolerance of wastewater‑stressed carrot plants. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01401-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
AbstractClimate changes have a direct impact on agricultural lands through their impact on the rate of water levels in the oceans and seas, which leads to a decrease in the amount of water used in agriculture, and therefore the use of alternative sources of irrigation such as wastewater and overcoming its harmful effect on plants was one of the solutions to face this problem. In the present study, the impacts of the synthesized selenium nanoparticles (Se NPs) alone or in combination with glycine betaine and proline treatments on the growth, physiological, and yield attributes of wastewater irrigated carrot plants are investigated. Furthermore, to evaluate heavy metals uptake and accumulation in edible plant parts. The usage of wastewater to carrot plants significantly increased free proline contents, total phenols, superoxide dismutase, catalase, peroxidase, polyphenol oxidase, Malondialdehyde (MDA), and hydrogen peroxide (H2O2) throughout the two growth stages. While total soluble carbohydrate and soluble protein content in carrot shoots and roots were significantly reduced. Moreover, the concentrations of nickel (Ni), cadmium (Cd), lead (Pb), and cobalt (Co) in carrot plants were considerably higher than the recommended limits set by international organizations. Application of selenium nanoparticles alone or in combination with glycine betaine and proline reduced the contents of Ni, Cd, Pb, and Co; free proline; total phenols; superoxide dismutase; catalase; peroxidase; polyphenol oxidase; Malondialdehyde (MDA) and Hydrogen peroxide (H2O2) in carrot plants. However, morphological aspects, photosynthetic pigments, soluble carbohydrates, soluble protein, total phenol, and β-Carotene were enhanced in response to Se NPs application. As an outcome, this research revealed that Se NPs combined with glycine betaine and proline can be used as a strategy to minimize heavy metal stress caused by wastewater irrigation in carrot plants, consequently enhancing crop productivity and growth.
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Deng YJ, Duan AQ, Liu H, Wang YH, Zhang RR, Xu ZS, Xiong AS. Generating colorful carrot germplasm through metabolic engineering of betalains pigments. HORTICULTURE RESEARCH 2023; 10:uhad024. [PMID: 37786858 PMCID: PMC10541523 DOI: 10.1093/hr/uhad024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/05/2023] [Indexed: 10/04/2023]
Abstract
Betalains are tyrosine-derived plant pigments exclusively found in the Caryophyllales order and some higher fungi and generally classified into two groups: red-violet betacyanins and yellow-orange betaxanthins. Betalains attract great scientific and economic interest because of their relatively simple biosynthesis pathway, attractive colors and health-promoting properties. Co-expressing two core genes BvCYP76AD1 and BvDODA1 with or without a glycosyltransferase gene MjcDOPA5GT allowed the engineering of carrot (an important taproot vegetable) to produce a palette of unique colors. The highest total betalains content, 943.2 μg·g-1 DW, was obtained in carrot taproot transformed with p35S:RUBY which produces all of the necessary enzymes for betalains synthesis. Root-specific production of betalains slightly relieved tyrosine consumption revealing the possible bottleneck in betalains production. Furthermore, a unique volcano-like phenotype in carrot taproot cross-section was created by vascular cambium-specific production of betalains. The betalains-fortified carrot in this study is thus anticipated to be used as functional vegetable and colorful carrot germplasm in breeding to promote health.
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Affiliation(s)
- Yuan-Jie Deng
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ao-Qi Duan
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Hui Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ya-Hui Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Rong-Rong Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Zhi-Sheng Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Ai-Sheng Xiong
- National Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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Mangal V, Lal MK, Tiwari RK, Altaf MA, Sood S, Gahlaut V, Bhatt A, Thakur AK, Kumar R, Bhardwaj V, Kumar V, Singh B, Singh R, Kumar D. A comprehensive and conceptual overview of omics-based approaches for enhancing the resilience of vegetable crops against abiotic stresses. PLANTA 2023; 257:80. [PMID: 36913037 DOI: 10.1007/s00425-023-04111-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Abiotic stresses adversely affect the productivity and production of vegetable crops. The increasing number of crop genomes that have been sequenced or re-sequenced provides a set of computationally anticipated abiotic stress-related responsive genes on which further research may be focused. Knowledge of omics approaches and other advanced molecular tools have all been employed to understand the complex biology of these abiotic stresses. A vegetable can be defined as any component of a plant that is eaten for food. These plant parts may be celery stems, spinach leaves, radish roots, potato tubers, garlic bulbs, immature cauliflower flowers, cucumber fruits, and pea seeds. Abiotic stresses, such as deficient or excessive water, high temperature, cold, salinity, oxidative, heavy metals, and osmotic stress, are responsible for the adverse activity in plants and, ultimately major concern for decreasing yield in many vegetable crops. At the morphological level, altered leaf, shoot and root growth, altered life cycle duration and fewer or smaller organs can be observed. Likewise different physiological and biochemical/molecular processes are also affected in response to these abiotic stresses. In order to adapt and survive in a variety of stressful situations, plants have evolved physiological, biochemical, and molecular response mechanisms. A comprehensive understanding of the vegetable's response to different abiotic stresses and the identification of tolerant genotypes are essential to strengthening each vegetable's breeding program. The advances in genomics and next-generation sequencing have enabled the sequencing of many plant genomes over the last twenty years. A combination of modern genomics (MAS, GWAS, genomic selection, transgenic breeding, and gene editing), transcriptomics, and proteomics along with next-generation sequencing provides an array of new powerful approaches to the study of vegetable crops. This review examines the overall impact of major abiotic stresses on vegetables, adaptive mechanisms and functional genomic, transcriptomic, and proteomic processes used by researchers to minimize these challenges. The current status of genomics technologies for developing adaptable vegetable cultivars that will perform better in future climates is also examined.
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Affiliation(s)
- Vikas Mangal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Milan Kumar Lal
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | - Rahul Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
| | | | - Salej Sood
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vijay Gahlaut
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
- Department of Biotechnology and University Center for Research and Development, Chandigarh University, Mohali, Punjab, India
| | | | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ravinder Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinay Bhardwaj
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajender Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Devendra Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
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Valerga L, González RE, Pérez MB, Concellón A, Cavagnaro PF. Differential and Cultivar-Dependent Antioxidant Response of Whole and Fresh-Cut Carrots of Different Root Colors to Postharvest UV-C Radiation. PLANTS (BASEL, SWITZERLAND) 2023; 12:1297. [PMID: 36986985 PMCID: PMC10053824 DOI: 10.3390/plants12061297] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/03/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Fresh-cut produce have become widely popular, increasing vegetable consumption in many parts of the word. However, they are more perishable than unprocessed fresh vegetables, requiring cold storage to preserve their quality and palatability. In addition to cold storage, UV radiation has been used experimentally to try to increase nutritional quality and postharvest shelf life, revealing increased antioxidant levels in some fruits and vegetables, including orange carrots. Carrot is one of the main whole and fresh-cut vegetables worldwide. In addition to orange carrots, other root color phenotypes (e.g., purple, yellow, red) are becoming increasingly popular in some markets. The effect of the UV radiation and cold storage has not been explored in these root phenotypes. This study investigated the effect of postharvest UV-C radiation in whole and fresh-cut (sliced and shredded) roots of two purple, one yellow, and one orange-rooted cultivar, with regard to changes in concentration of total phenolics (TP) and hydroxycinnamic acids (HA), chlorogenic acid (CGA), total and individual anthocyanins, antioxidant capacity (by DPPH and ABTS), and superficial color appearance, monitoring such changes during cold storage. Results revealed that the UV-C radiation, the fresh-cut processing, and the cold storage influenced the content of antioxidant compounds and activities to varying extents, depending on the carrot cultivar, the degree of processing, and the phytochemical compound analyzed. UV-C radiation increased antioxidant capacity up to 2.1, 3.8, 2.5-folds; TP up to 2.0, 2.2, and 2.1-folds; and CGA up to 3.2, 6.6, and 2.5-folds, relative to UV-C untreated controls, for orange, yellow, and purple carrots, respectively. Anthocyanin levels were not significantly modified by the UV-C in both purple carrots evaluated. A moderate increase in tissue browning was found in some fresh-cut processed UV-C treated samples of yellow and purple but not orange roots. These data suggest variable potential for increasing functional value by UV-C radiation in different carrot root colors.
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Affiliation(s)
- Lucia Valerga
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires CP1425, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria La Consulta, La Consulta, San Carlos, Mendoza M5567, Argentina
| | - Roxana E. González
- Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria La Consulta, La Consulta, San Carlos, Mendoza M5567, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza M5502, Argentina
| | - María B. Pérez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires CP1425, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria La Consulta, La Consulta, San Carlos, Mendoza M5567, Argentina
| | - Analía Concellón
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires CP1425, Argentina
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos (CIDCA), La Plata B1900, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata B1900, Argentina
| | - Pablo F. Cavagnaro
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires CP1425, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) Estación Experimental Agropecuaria La Consulta, La Consulta, San Carlos, Mendoza M5567, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria M5528, Argentina
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Wu W, Luo X, Wang Y, Xie X, Lan Y, Li L, Zhu T, Ren M. Combined metabolomics and transcriptomics analysis reveals the mechanism underlying blue light-mediated promotion of flavones and flavonols accumulation in Ligusticum chuanxiong Hort. microgreens. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 242:112692. [PMID: 36958087 DOI: 10.1016/j.jphotobiol.2023.112692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Ligusticum chuanxiong Hort. (Chuanxiong) is an important Chinese medicinal herb, whose rhizomes are widely used as raw materials for treating various diseases caused by blood stasis. The fresh tender stems and leaves of Chuanxiong are also consumed and have the potential as microgreens. Here, we investigated the effect of light spectra on yield and total flavonoid content of Chuanxiong microgreens by treatment with LED-based white light (WL), red light (RL), blue light (BL), and continuous darkness (DD). The results showed that WL and BL reduced biomass accumulation but significantly increased total flavonoid content compared to RL or DD treatments. Widely targeted metabolomics analysis confirmed that BL promoted the accumulation of flavones and flavonols in Chuanxiong microgreens. Further integration of transcriptomics and metabolomics analysis revealed the mechanism by which BL induces the up-regulation of transcription factors such as HY5 and MYBs, promotes the expression of key genes targeted for flavonoid biosynthesis, and ultimately leads to the accumulation of flavones and flavonols. This study suggests that blue light is a proper light spectra to improve the quality of Chuanxiong microgreens, and the research results lay a foundation for guiding the de-etiolation of Chuanxiong microgreens to obtain both yield and quality in production practice.
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Affiliation(s)
- Wenxian Wu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China
| | - Xiumei Luo
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China
| | - Ying Wang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China
| | - Xiulan Xie
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China
| | - Yizhou Lan
- School of Foreign Languages, Shenzhen University, Shenzhen 518000, Guangdong Province, China
| | - Linxuan Li
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China
| | - Tingting Zhu
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences; Chengdu Agricultural Science and Technology Center, Chengdu 610000, Sichuan Province, China.
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Cheng L, Li M, Wang Y, Han Q, Hao Y, Qiao Z, Zhang W, Qiu L, Gong A, Zhang Z, Li T, Luo S, Tang L, Liu D, Yin H, Lu S, Balbuena TS, Zhao Y. Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population. FRONTIERS IN PLANT SCIENCE 2023; 14:1114284. [PMID: 36890899 PMCID: PMC9986275 DOI: 10.3389/fpls.2023.1114284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yachao Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Qiu
- Institute of Forestry Science, Xinyang Forestry Bureau, Xinyang, Henan, China
| | - Andong Gong
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhihan Zhang
- College of Engineering and Technology, Northeast Forestry University, Harbin, China
| | - Tao Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Shanshan Luo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Linshuang Tang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Daliang Liu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Hao Yin
- College of Agriculture, Guizhou University, Guiyang, China
| | - Song Lu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal, Brazil
| | - Yiyong Zhao
- College of Agriculture, Guizhou University, Guiyang, China
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Jang W, Kang JN, Jo IH, Lee SM, Park GH, Kim CK. The chromosome-level genome assembly of lance asiabell ( Codonopsis lanceolata), a medicinal and vegetable plant of the Campanulaceae family. Front Genet 2023; 14:1100819. [PMID: 36816041 PMCID: PMC9929348 DOI: 10.3389/fgene.2023.1100819] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Codonopsis lanceolata (2n = 2x = 16) belongs to the Campanulaceae family and is a valuable medicinal and vegetable plant primarily found in East Asia. Several studies have demonstrated its excellent pharmacological effects, for example in bronchial treatment. However, genomic information of C. lanceolata is scarce, hindering studies on crop improvement of the species. Here, we report a high-quality chromosome-level genome assembly of C. lanceolata based on a hybrid method using Nanopore long-read, Illumina short-read, and Hi-C data. The assembled genome was completed as 1,273 Mb (84.5% of the estimated genome size), containing eight pseudo-chromosomes, ranging from 101.3 to 184.3 Mb. The genome comprised of 71.3% repeat sequences and 46,005 protein-coding genes, of which 85.7% genes were functionally annotated. Completeness of the assembled genome and genes was assessed to be 97.5% and 90.4%, respectively, by Benchmarking Universal Single-Copy Orthologs analysis. Phylogenetic and synteny analysis revealed that C. lanceolata was closely related to Platycodon grandiflorus in the Campanulaceae family. Gene family evolution revealed significant expansion of related genes involved in saponin biosynthesis in the C. lanceolata genome. This is the first reference genome reported for C. lanceolata. The genomic data produced in this study will provide essential information for further research to improve this medicinal plant and will broaden the understanding of the Campanulaceae family.
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Affiliation(s)
- Woojong Jang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, South Korea
| | - Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea
| | - Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Eumseong, South Korea
| | - Si-Myung Lee
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea
| | - Gyu-Hwang Park
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences (NAS), Rural Development Administration, Jeonju, South Korea,*Correspondence: Chang-Kug Kim,
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