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Luo Y, Li Y, Yin X, Deng W, Liao J, Pan Y, Jiang B, Yang H, Ding K, Jia Y. Transcriptomics analyses reveal the key genes involved in stamen petaloid formation in Alcea rosea L. BMC PLANT BIOLOGY 2024; 24:551. [PMID: 38877392 PMCID: PMC11177533 DOI: 10.1186/s12870-024-05263-6] [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: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
Alcea rosea L. is a traditional flower with a long cultivation history. It is extensively cultivated in China and is widely planted in green belt parks or used as cut flowers and potted ornamental because of its rich colors and flower shapes. Double-petal A. rosea flowers have a higher aesthetic value compared to single-petal flowers, a phenomenon determined by stamen petaloid. However, the underlying molecular mechanism of this phenomenon is still very unclear. In this study, an RNA-based comparative transcriptomic analysis was performed between the normal petal and stamen petaloid petal of A. rosea. A total of 3,212 differential expressed genes (DEGs), including 2,620 up-regulated DEGs and 592 down-regulated DEGs, were identified from 206,188 unigenes. Numerous DEGs associated with stamen petaloid were identified through GO and KEGG enrichment analysis. Notably, there were 63 DEGs involved in the plant hormone synthesis and signal transduction, including auxin, cytokinin, gibberellin, abscisic acid, ethylene, brassinosteroid, jasmonic acid, and salicylic acid signaling pathway and 56 key transcription factors (TFs), such as MADS-box, bHLH, GRAS, and HSF. The identification of these DEGs provides an important clue for studying the regulation pathway and mechanism of stamen petaloid formation in A. rosea and provides valuable information for molecular plant breeding.
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Affiliation(s)
- Yuanzhi Luo
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yifeng Li
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiancai Yin
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wanqing Deng
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianwei Liao
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanzhi Pan
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Beibei Jiang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hongchen Yang
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Keying Ding
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yin Jia
- College of Landscape Architecture, Sichuan Agricultural University, Chengdu, 611130, China.
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Chow CN, Yang CW, Wu NY, Wang HT, Tseng KC, Chiu YH, Lee TY, Chang WC. PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. Nucleic Acids Res 2024; 52:D1569-D1578. [PMID: 37897338 PMCID: PMC10767843 DOI: 10.1093/nar/gkad945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
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Affiliation(s)
- Chi-Nga Chow
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- School of Molecular Sciences, Arizona State University, Tempe 85281, USA
| | - Chien-Wen Yang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Nai-Yun Wu
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Hung-Teng Wang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Kuan-Chieh Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Hsuan Chiu
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan 701, Taiwan
| | - Tzong-Yi Lee
- Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan 701, Taiwan
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Li G, Cheng L, Li Z, Zhao Y, Wang Y. Over-expression of CcMYB24, encoding a R2R3-MYB transcription factor from a high-leaf-number mutant of Cymbidium, increases the number of leaves in Arabidopsis. PeerJ 2023; 11:e15490. [PMID: 37273531 PMCID: PMC10239231 DOI: 10.7717/peerj.15490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
Ornamental foliage plants have long been cultivated for their attractive leaves. Variation in leaf traits of ornamental foliage plants is one of the goals in breeding. MYB transcription factors regulate many aspects of leaf development, and thus influence morphological traits of leaves. However, little is known about the function of MYB transcription factors in leaf development of Cymbidium, one of the most economically important ornamental plants in the world. In the present study, a MYB transcription factor, CcMYB24, was identified and the corresponding gene cloned from a new orchid mutant, TRIR-2, which produces more leaves than control plants. The CcMYB24 showed a higher expression level in 'TRIR-2' than in control plants, and the protein was located in the nucleus. The sequence of CcMYB24 showed a high similarity with RAX2-like genes which belong to the R2R3-MYB gene family in other Cymbidium plants. Overexpression of CcMYB24 resulted in a phenotype with an increased number of leaves, elevated chlorophyll content, and decreased contents of carotenoids and flavonoids in Arabidopsis. These results provide functional evidence for the role of CcMYB24 in promoting the production of leaves in 'TRIR-2'. Understanding the role of CcMYB24 in Cymbidium will be beneficial for the molecular breeding of ornamental foliage plants.
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Álvarez-Urdiola R, Matus JT, Riechmann JL. Multi-Omics Methods Applied to Flower Development. Methods Mol Biol 2023; 2686:495-508. [PMID: 37540374 DOI: 10.1007/978-1-0716-3299-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Developmental processes in multicellular organisms depend on the proficiency of cells to orchestrate different gene expression programs. Over the past years, several studies of reproductive organ development have considered genomic analyses of transcription factors and global gene expression changes, modeling complex gene regulatory networks. Nevertheless, the dynamic view of developmental processes requires, as well, the study of the proteome in its expression, complexity, and relationship with the transcriptome. In this chapter, we describe a dual extraction method-for protein and RNA-for the characterization of genome expression at proteome level and its correlation to transcript expression data. We also present a shotgun proteomic procedure (LC-MS/MS) followed by a pipeline for the imputation of missing values in mass spectrometry results.
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Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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