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Fleck SJ, Tomlin C, da Silva Coelho FA, Richter M, Danielson ES, Backenstose N, Krabbenhoft T, Lindqvist C, Albert VA. High quality genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered Fraxinus (ash) species. Commun Biol 2024; 7:54. [PMID: 38184717 PMCID: PMC10771460 DOI: 10.1038/s42003-023-05748-4] [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: 12/06/2022] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
With populations of threatened and endangered species declining worldwide, efforts are being made to generate high quality genomic records of these species before they are lost forever. Here, we demonstrate that data from single Oxford Nanopore Technologies (ONT) MinION flow cells can, even in the absence of highly accurate short DNA-read polishing, produce high quality de novo plant genome assemblies adequate for downstream analyses, such as synteny and ploidy evaluations, paleodemographic analyses, and phylogenomics. This study focuses on three North American ash tree species in the genus Fraxinus (Oleaceae) that were recently added to the International Union for Conservation of Nature (IUCN) Red List as critically endangered. Our results support a hexaploidy event at the base of the Oleaceae as well as a subsequent whole genome duplication shared by Syringa, Osmanthus, Olea, and Fraxinus. Finally, we demonstrate the use of ONT long-read sequencing data to reveal patterns in demographic history.
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Affiliation(s)
- Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
| | - Crystal Tomlin
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Michaela Richter
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | | | - Nathan Backenstose
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Trevor Krabbenhoft
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
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Lu Z, Wang X, Mostafa S, Noor I, Lin X, Ren S, Cui J, Jin B. WRKY Transcription Factors in Jasminum sambac: An Insight into the Regulation of Aroma Synthesis. Biomolecules 2023; 13:1679. [PMID: 38136552 PMCID: PMC10742223 DOI: 10.3390/biom13121679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
WRKY transcription factors are one of the largest families of transcription regulators that play essential roles in regulating the synthesis of secondary metabolites in plants. Jasmine (Jasminum sambac), renowned for its aromatic nature and fragrant blossoms, possesses a significant abundance of volatile terpene compounds. However, the role of the WRKY family in terpene synthesis in jasmine remains undetermined. In this study, 72 WRKY family genes of J. sambac were identified with their conserved WRKY domains and were categorized into three main groups based on their structural and phylogenetic characteristics. The extensive segmental duplications contributed to the expansion of the WRKY gene family. Expression profiles derived from the transcriptome data and qRT-PCR analysis showed that the majority of JsWRKY genes were significantly upregulated in fully bloomed flowers compared to buds. Furthermore, multiple correlation analyses revealed that the expression patterns of JsWRKYs (JsWRKY27/33/45/51/55/57) were correlated with both distinct terpene compounds (monoterpenes and sesquiterpenes). Notably, the majority of jasmine terpene synthase (JsTPS) genes related to terpene synthesis and containing W-box elements exhibited a significant correlation with JsWRKYs, particularly with JsWRKY51, displaying a strong positive correlation. A subcellular localization analysis showed that JsWRKY51 was localized in the nucleus. Moreover, transgenic tobacco leaves and jasmine calli experiments demonstrated that overexpression of JsWRKY51 was a key factor in enhancing the accumulation of β-ocimene, which is an important aromatic terpene component. Collectively, our findings suggest the roles of JsWRKY51 and other JsWRKYs in regulating the synthesis of aromatic compounds in J. sambac, providing a foundation for the potential utilization of JsWRKYs to facilitate the breeding of fragrant plant varieties with an improved aroma.
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Affiliation(s)
- Zhaogeng Lu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
| | - Xinwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
| | - Salma Mostafa
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Iqra Noor
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
| | - Xinyi Lin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
| | - Shixiong Ren
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
| | - Jiawen Cui
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
| | - Biao Jin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.); (X.W.)
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