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Yu Y, Liufu Y, Ren Y, Zhang J, Li M, Tian S, Wang J, Liao S, Gong G, Zhang H, Guo S. Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon ( Citrullus lanatus). Int J Mol Sci 2023; 24:15333. [PMID: 37895011 PMCID: PMC10607834 DOI: 10.3390/ijms242015333] [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: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening.
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Affiliation(s)
- Yongtao Yu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Yuxiang Liufu
- College of Forestry, Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Ren
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Jie Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Maoying Li
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Shouwei Tian
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Jinfang Wang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Shengjin Liao
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Guoyi Gong
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Haiying Zhang
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China (J.W.)
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Liu XY, Huo YY, Yang J, Li TT, Xu FR, Wan HP, Li JN, Wu CH, Zhang YH, Dong X. Integrated physiological, metabolomic, and proteome analysis of Alpinia officinarum Hance essential oil inhibits the growth of Fusarium oxysporum of Panax notoginseng. Front Microbiol 2022; 13:1031474. [DOI: 10.3389/fmicb.2022.1031474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Fusarium oxysporum is the main pathogen of Panax notoginseng root rot, and chemical fungicides remain the primary measures to control the disease. Plant essential oil (EO) is a volatile plant secondary metabolic product that does not produce any residue to replace chemical pesticide. To comprehensively understand the antifungal mechanism of Alpinia officinarum Hance EO, the physiological indicators, proteome and metabolome were analyzed using F. oxysporum spores and hyphae treated with different EO concentrations. The cell membrane was damaged after both low and high concentrations of EO treatment, along with leakage of the cell contents. To resist the destruction of membrane structure, fungi can increase the function of steroid biosynthesis and expression of these catalytic enzymes, including squalene monooxygenase (SQLE), sterol 14alpha-demethylase (CYP51, CYP61A), delta14-sterol reductase (TM7SF2, ERG4), methylsterol monooxygenase (MESO1), and sterol 24-C-methyltransferase (SMT1). Furthermore, the tricarboxylic acid cycle (TCA) was influenced by inhibiting the expression of glutamate synthase (GLT1), 4-aminobutyrate aminotransferase (ABAT), and succinate-semialdehyde dehydrogenase (gabD); increasing malate and gamma-aminobutyric acid (GABA); and decreasing citrate content. The spore germination rate and mycelia growth were decreased because the expression of cohesin complex subunit SA-1/2 (IRR1) and cohesion complex subunit (YCS4, BRN1, YCG1) were inhibited. Particularly, under high EO concentrations, cyclin-dependent kinase (CDC28) and DNA replication licensing factor (MCM) were further inhibited to disrupt the cell cycle and meiosis, thus affecting cell division. The results of this study will enrich the understanding of the antifungal mechanism of EOs and provide an important basis to develop new plant-derived fungicides.
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