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Brown FD, Ishengoma E, Mayer G, Pabón-Mora N, Santos ME, Sears KE, de Sena Oliveira I. Uncovering developmental diversity in the field. Development 2024; 151:dev203084. [PMID: 39158021 DOI: 10.1242/dev.203084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Many developmental biologists seldom leave the lab for research, relying instead on establishing colonies of traditional and emerging model systems. However, to fully understand the mechanisms and principles of development and evolution, including the role of ecology and the environment, it is important to study a diverse range of organisms in context. In this Perspective, we hear from five research teams from around the world about the importance and challenges of going into the field to study their organisms of interest. We also invite you to share your own fieldwork stories on the Node.
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Affiliation(s)
- Federico D Brown
- Departamento de Zoologia - Instituto Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
- Prometeo-Senescyt Program, Escuela Superior Politécnica del Litoral, ESPOL, P.O. Box 09-01-5863, Guayaquil 090902, Ecuador
- Centro de Biologia Marinha (CEBIMar), Universidade de São Paulo, 11612-109, São Sebastião, Brazil
| | - Edson Ishengoma
- Department of Biological Sciences, Mkwawa University College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Georg Mayer
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
| | - Natalia Pabón-Mora
- Universidad de Antioquia, Instituto de Biología, Grupo Evo-Devo en Plantas, Medellín 050010, Colombia
| | - M Emília Santos
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology and Department of Molecular, Cellular, and Developmental Biology, University of California at Los Angeles, Los Angeles 90095, USA
| | - Ivo de Sena Oliveira
- Department of Zoology, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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Singh S, Pal L, Rajput R, Chhatwal H, Singh N, Chattopadhyay D, Pandey A. CaLAP1 and CaLAP2 orchestrate anthocyanin biosynthesis in the seed coat of Cicer arietinum. PLANTA 2024; 260:38. [PMID: 38951258 DOI: 10.1007/s00425-024-04470-7] [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: 12/22/2023] [Accepted: 06/17/2024] [Indexed: 07/03/2024]
Abstract
MAIN CONCLUSION Our findings shed light on the regulation of anthocyanin and proanthocyanidin biosynthesis in chickpea seed coats. Expression of R2R3-MYB transcription factors CaLAP1 and CaLAP2 enhanced the anthocyanins and proanthocyanidins content in chickpea. The seed coat color is a major economic trait in leguminous crop chickpea (Cicer arietinum). Anthocyanins and proanthocyanidins (PAs) are two classes of flavonoids that mainly contribute to the flower, seed coat and color of Desi chickpea cultivars. Throughout the land plant lineage, the accumulation of anthocyanins and PAs is regulated by MYB and bHLH transcription factors (TFs), which form an MBW (MYB, bHLH, and WD40) complex. Here, we report two R2R3-MYB TFs in chickpea belonging to the anthocyanin-specific subgroup-6, CaLAP1 (Legume Anthocyanin Production 1), and CaLAP2 (Legume Anthocyanin Production 2), which are mainly expressed in the flowers and developmental stages of the seeds. CaLAP1 and CaLAP2 interact with TT8-like CabHLH1 and WD40, forming the MBW complex, and bind to the promoter sequences of anthocyanin- and PA biosynthetic genes CaCHS6, CaDFR2, CaANS, and CaANR, leading to anthocyanins and PA accumulation in the seed coat of chickpea. Moreover, these CaLAPs partially complement the anthocyanin-deficient phenotype in the Arabidopsis thaliana sextuple mutant seedlings. Overexpression of CaLAPs in chickpea resulted in significantly higher expression of anthocyanin and PA biosynthetic genes leading to a darker seed coat color with higher accumulation of anthocyanin and PA. Our findings show that CaLAPs positively modulate anthocyanin and PA content in seed coats, which might influence plant development and resistance to various biotic and abiotic stresses.
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Affiliation(s)
- Samar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Lalita Pal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ruchika Rajput
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Himani Chhatwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nidhi Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Xie N, Guo Q, Li H, Yuan G, Gui Q, Xiao Y, Liao M, Yang L. Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis. BMC PLANT BIOLOGY 2024; 24:231. [PMID: 38561656 PMCID: PMC10985888 DOI: 10.1186/s12870-024-04949-1] [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: 09/21/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids-quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.
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Affiliation(s)
- Na Xie
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Qiqaing Guo
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China.
| | - Huie Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Gangyi Yuan
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Qin Gui
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yang Xiao
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Mengyun Liao
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Lan Yang
- Institute for Forest Resources and Environment of Guizhou, College of Forestry, Guizhou University, Guiyang, 550025, China
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Chen BC, Wu XJ, Dong QJ, Xiao JP. Screening and functional analysis of StMYB transcription factors in pigmented potato under low-temperature treatment. BMC Genomics 2024; 25:283. [PMID: 38500027 PMCID: PMC10946176 DOI: 10.1186/s12864-024-10059-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: 05/28/2023] [Accepted: 01/29/2024] [Indexed: 03/20/2024] Open
Abstract
MYB transcription factors play an extremely important regulatory role in plant responses to stress and anthocyanin synthesis. Cloning of potato StMYB-related genes can provide a theoretical basis for the genetic improvement of pigmented potatoes. In this study, two MYB transcription factors, StMYB113 and StMYB308, possibly related to anthocyanin synthesis, were screened under low-temperature conditions based on the low-temperature-responsive potato StMYB genes family analysis obtained by transcriptome sequencing. By analyzed the protein properties and promoters of StMYB113 and StMYB308 and their relative expression levels at different low-temperature treatment periods, it is speculated that StMYB113 and StMYB308 can be expressed in response to low temperature and can promote anthocyanin synthesis. The overexpression vectors of StMYB113 and StMYB308 were constructed for transient transformation tobacco. Color changes were observed, and the expression levels of the structural genes of tobacco anthocyanin synthesis were determined. The results showed that StMYB113 lacking the complete MYB domain could not promote the accumulation of tobacco anthocyanins, while StMYB308 could significantly promote the accumulation involved in tobacco anthocyanins. This study provides a theoretical reference for further study of the mechanism of StMYB113 and StMYB308 transcription factors in potato anthocyanin synthesis.
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Affiliation(s)
- Bi-Cong Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China
| | - Xiao-Jie Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China
| | - Qiu-Ju Dong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China
| | - Ji-Ping Xiao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No.95 Jinhei Road, Panlong District, Kunming City, 650201, Yunnan, China.
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Ho WK, Tanzi AS, Sang F, Tsoutsoura N, Shah N, Moore C, Bhosale R, Wright V, Massawe F, Mayes S. A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat Commun 2024; 15:1901. [PMID: 38429275 PMCID: PMC10907731 DOI: 10.1038/s41467-024-45048-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: 02/13/2022] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.
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Affiliation(s)
- Wai Kuan Ho
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alberto Stefano Tanzi
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fei Sang
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Niki Tsoutsoura
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Niraj Shah
- Digital and Technology Services, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christopher Moore
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Rahul Bhosale
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Victoria Wright
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Festo Massawe
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean Mayes
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- International Centre for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India.
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Assis LCS. Pollination syndromes and the origins of floral traits. ANNALS OF BOTANY 2023; 132:1055-1072. [PMID: 37814841 PMCID: PMC10809047 DOI: 10.1093/aob/mcad147] [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: 06/29/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND A general view in the study of pollination syndromes is that floral traits usually represent convergent floral adaptations to specific functional pollinator groups. However, the definition of convergence is elusive and contradictory in the literature. Is convergence the independent evolution of either the same trait or similar traits with the same function? A review of the concept of convergence in developmental biology and phylogenetic systematics may shed new light in studies of pollination syndromes. SCOPE The aims of this article are (1) to explore the notion of convergence and other concepts (analogy, homoplasy and parallelism) within the theory and practice of developmental evolution and phylogenetic systematics; (2) to modify the definitions of syndromes in order to embrace the concepts of analogy and convergence; (3) to revisit the bat pollination syndrome in the context of angiosperm phylogeny, with focus on the showy 'petaloid' organs associated with the syndrome; (4) to revisit the genetic-developmental basis of flower colour; (5) to raise evolutionary hypotheses of floral evolution associated with the bat pollination syndrome; and (6) to highlight some of the current frontiers of research on the origin and evolution of flowers and its impact on pollination syndrome studies in the 21st century. CONCLUSIONS The inclusion of the concepts of analogy and convergence within the concept of syndromes will constitute a new agenda of inquiry that integrates floral biology, phylogenetic systematics and developmental biology. Phyllostomid and pteropodid bat pollination syndrome traits in eudicots and monocots represent cases of analogous and convergent evolution. Pollination syndromes are a multivariate concept intrinsically related to the understanding of flower organogenesis and evolution. The formulation of hypotheses of pollination syndromes must consider the phylogenetic levels of universality for both plant and animal taxa, flower development, genetics, homology and evolution, and a clear definition of evolutionary concepts, including analogy, convergence, homoplasy and parallelism.
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Affiliation(s)
- Leandro C S Assis
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
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Ai P, Xue J, Shi Z, Liu Y, Li Z, Li T, Zhao W, Khan MA, Kang D, Wang K, Wang Z. Genome-wide characterization and expression analysis of MYB transcription factors in Chrysanthemum nankingense. BMC PLANT BIOLOGY 2023; 23:140. [PMID: 36915063 PMCID: PMC10012607 DOI: 10.1186/s12870-023-04137-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Chrysanthemum is a popular ornamental plant worldwide. MYB (v-myb avian myeloblastosis viral oncogene homolog) transcription factors play an important role in everything from stress resistance to plant growth and development. However, the MYB family of chrysanthemums has not been the subject of a detailed bioinformatics and expression investigation. RESULTS In this study, we examined 324 CnMYB transcription factors from Chrysanthemum nankingense genome data, which contained 122 Cn1R-MYB, 183 CnR2R3-MYB, 12 Cn3R-MYB, 2 Cn4R-MYB, and 5 atypical CnMYB. The protein motifs and classification of CnMYB transcription factors were analyzed. Among them, motifs 1, 2, 3, and 4 were found to encode the MYB DNA-binding domain in R2R3-MYB proteins, while in other-MYB proteins, the motifs 1, 2, 3, 4, 5, 6, 7, and 8 encode the MYB DNA-binding domain. Among all CnMYBs, 44 genes were selected due to the presence of CpG islands, while methylation is detected in three genes, including CnMYB9, CnMYB152, and CnMYB219. We analyzed the expression levels of each CnMYB gene in ray floret, disc floret, flower bud, leaf, stem, and root tissues. Based on phylogenetic analysis and gene expression analysis, three genes appeared likely to control cellulose and lignin synthesis in stem tissue, and 16 genes appeared likely to regulate flowering time, anther, pollen development, and flower color. Fifty-one candidate genes that may be involved in stress response were identified through phylogenetic, stress-responseve motif of promoter, and qRT-PCR analyses. According to genes expression levels under stress conditions, six CnMYB genes (CnMYB9, CnMYB172, CnMYB186, CnMYB199, CnMYB219, and CnMYB152) were identified as key stress-responsive genes. CONCLUSIONS This research provides useful information for further functional analysis of the CnMYB gene family in chrysanthemums, as well as offers candidate genes for further study of cellulose and lignin synthesis, flowering traits, salt and drought stress mechanism.
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Affiliation(s)
- Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Jundong Xue
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Zhongya Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Yuru Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Tong Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Dongru Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Kangxiang Wang
- Technology&Media University of Henan Kaifeng, Jinming Road, Kaifeng, 475004, Henan, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China.
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Feng X, Abubakar AS, Chen K, Yu C, Zhu A, Chen J, Gao G, Wang X, Mou P, Chen P. Genome-wide analysis of R2R3-MYB transcription factors in Boehmeria nivea (L.) gaudich revealed potential cadmium tolerance and anthocyanin biosynthesis genes. Front Genet 2023; 14:1080909. [PMID: 36896232 PMCID: PMC9989182 DOI: 10.3389/fgene.2023.1080909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Gene family, especially MYB as one of the largest transcription factor family in plants, the study of its subfunctional characteristics is a key step in the study of plant gene function. The sequencing of ramie genome provides a good opportunity to study the organization and evolutionary characters of the ramie MYB gene at the whole genome level. In this study, a total of 105 BnGR2R3-MYB genes were identified from ramie genome and subsequently grouped into 35 subfamilies according to phylogeny divergence and sequences similarity. Chromosomal localization, gene structure, synteny analysis, gene duplication, promoter analysis, molecular characteristics and subcellular localization were accomplished using several bioinformatics tools. Collinearity analysis showed that the segmental and tandem duplication events is the dominant form of the gene family expansion, and duplications prominent in distal telomeric regions. Highest syntenic relationship was obtained between BnGR2R3-MYB genes and that of Apocynum venetum (88). Furthermore, transcriptomic data and phylogenetic analysis revealed that BnGMYB60, BnGMYB79/80 and BnGMYB70 might inhibit the biosynthesis of anthocyanins, and UPLC-QTOF-MS data further supported the results. qPCR and phylogenetic analysis revealed that the six genes (BnGMYB9, BnGMYB10, BnGMYB12, BnGMYB28, BnGMYB41, and BnGMYB78) were cadmium stress responsive genes. Especially, the expression of BnGMYB10/12/41 in roots, stems and leaves all increased more than 10-fold after cadmium stress, and in addition they may interact with key genes regulating flavonoid biosynthesis. Thus, a potential link between cadmium stress response and flavonoid synthesis was identified through protein interaction network analysis. The study thus provided significant information into MYB regulatory genes in ramie and may serve as a foundation for genetic enhancement and increased productivity.
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Affiliation(s)
- Xinkang Feng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aminu Shehu Abubakar
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Department of Agronomy, Bayero University, Kano, Nigeria
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Pan Mou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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Huang D, Xu S, Qin Y, Li Y, Ming R, Huang R, Wang J, Tan Y. Comparative transcriptomic analysis identifies KcMYB1 as a R2R3-MYB anthocyanin activator in Kadsura coccinea. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111458. [PMID: 36084765 DOI: 10.1016/j.plantsci.2022.111458] [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: 07/14/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Fruit color, as an important appearance attribute, is crucial for attracting consumers. However, the underlying mechanism regulating mature fruit color formation in Kadsura coccinea remains unclear. Here, a comprehensive metabolomics and transcriptomics analysis was performed to investigate the molecular mechanisms of anthocyanin accumulation between two K. coccinea cultivars with different mature fruit colors-'Dahong No. 1' (red) and 'Jinhu' (yellow). Targeted metabolomic analysis revealed high anthocyanin levels, most of which were cyanidin and delphinidin derivatives, in 'Dahong No. 1' mature fruit peel. The SNP analysis indicated that the two different cultivars had similar genetic background. Moreover, comparative transcriptomic analysis demonstrated that differentially expressed genes (DEGs) were related to flavonoid biosynthesis and metabolic process in the two K. coccinea cultivars. Gene expression profiling data showed that the structural and regulatory genes associated with anthocyanin biosynthesis were significantly upregulated in 'Dahong No. 1' mature fruit peel, which was verified by quantitative real-time polymerase chain reaction (qRT-PCR). Notably, the key anthocyanin activator KcMYB1 was identified, which was significantly upregulated in 'Dahong No. 1' compared with 'Jinhu'. We further confirmed that KcMYB1 actively regulated the accumulation of anthocyanin by ectopic expression in vivo. Furthermore, allelic constitution of KcMYB1 in K. coccinea were investigated. The present study can provide insights for understanding the regulatory mechanisms of anthocyanin differential accumulation in the mature fruits of K. coccinea.
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Affiliation(s)
- Ding Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.
| | - Shiqiang Xu
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yanhong Qin
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Yingjie Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Ruhong Ming
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Rongshao Huang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yong Tan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China.
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Xia M, Tu L, Liu Y, Jiang Z, Wu X, Gao W, Huang L. Genome-wide analysis of MYB family genes in Tripterygium wilfordii and their potential roles in terpenoid biosynthesis. PLANT DIRECT 2022; 6:e424. [PMID: 35898558 PMCID: PMC9307386 DOI: 10.1002/pld3.424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/04/2022] [Accepted: 06/22/2022] [Indexed: 06/13/2023]
Abstract
Terpenoids are a class of significant bioactive components in the woody vine of Tripterygium wilfordii. Previous studies have shown that MYB transcription factors play important roles in plant secondary metabolism, growth, and developmental processes. However, the MYB involved in terpenoid biosynthesis in Tripterygium wilfordii are unknown. To identify Tripterygium wilfordii MYB (TwMYB) genes that are involved in terpenoid biosynthesis, we conducted the genome-wide analysis of the TwMYB gene family. A total of 207 TwMYBs were identified including 84 1R-TwMYB, 117 R2R3-TwMYB, four 3R-TwMYB, and two 4R-TwMYB genes. The most abundant R2R3-TwMYBs together with their Arabidopsis homologs were categorized into 26 subgroups. Intraspecific collinearity analysis found that the 74.9% of the TwMYBs may be generated by segmental duplication events, and 36.7% of duplicated gene pairs were derived from the specific whole genome duplication (WGD) event in Tripterygium wilfordii. In addition, interspecies collinearity analysis found that 16 TwMYB genes formed homologous gene pairs with MYB genes in seven representative species, which indicated they may have a key role in evolution. Notably, we found that the TwMYB genes were differentially expressed in various tissues by expression pattern analysis. In order to further select the candidate genes related to terpenoid biosynthesis, the assay of Methyl jasmonate (MeJA) induction and analysis of phylogenetic tree was conducted. It was speculated that six candidate TwMYB genes (TwMYB33, TwMYB34, TwMYB45, TwMYB67, TwMYB102, and TwMYB103) are involved in regulating terpenoid biosynthesis. This study is the first systematic analysis of the TwMYB gene family and will lay a foundation for the functional characterization of TwMYB genes in the regulation of terpenoid biosynthesis.
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Affiliation(s)
- Meng Xia
- School of Traditional Chinese MedicineCapital Medical UniversityBeijingChina
| | - Lichan Tu
- School of Traditional Chinese MedicineCapital Medical UniversityBeijingChina
- Department of Pharmacy, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuan Liu
- School of Traditional Chinese MedicineCapital Medical UniversityBeijingChina
| | - Zhouqian Jiang
- School of Traditional Chinese MedicineCapital Medical UniversityBeijingChina
| | - Xiaoyi Wu
- School of Traditional Chinese MedicineCapital Medical UniversityBeijingChina
| | - Wei Gao
- School of Traditional Chinese MedicineCapital Medical UniversityBeijingChina
- Beijing Shijitan HospitalCapital Medical UniversityBeijingChina
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao‐di Herbs, National Resource Center for Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijingChina
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11
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Powell AF, Feder A, Li J, Schmidt MHW, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B. A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1791-1810. [PMID: 35411592 DOI: 10.1111/tpj.15770] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/10/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.
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Affiliation(s)
| | - Ari Feder
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Jie Li
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Lance Courtney
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Emma M Jobson
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Alexander Vogel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Yimin Xu
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - David Lyon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Kathryn Dumschott
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Marcus McHale
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Ronan Sulpice
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Kan Bao
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Rohit Lal
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asha Duhan
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisandra K Denton
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Sarah R Hind
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA, and
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Cathie Martin
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - James J Giovannoni
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | | | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
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12
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Tang Q, Chi FM, Liu HD, Zhang HJ, Song Y. Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry. FRONTIERS IN PLANT SCIENCE 2021; 12:754325. [PMID: 34659323 PMCID: PMC8514788 DOI: 10.3389/fpls.2021.754325] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/08/2021] [Indexed: 05/24/2023]
Abstract
Blueberries (Vaccinium corymbosum) contain large amounts of flavonoids, which play important roles in the plant's ability to resist stress and can also have beneficial effects on human health when the fruits are eaten. However, the molecular mechanisms that regulate flavonoid synthesis in blueberries are still unclear. In this study, we combined two different transcriptome sequencing platforms, single-molecule real-time (SMRT) and Illumina sequencing, to elucidate the flavonoid synthetic pathways in blueberries. We analyzed transcript quantity, length, and the number of annotated genes. We mined genes associated with flavonoid synthesis (such as anthocyanins, flavonols, and proanthocyanidins) and employed fluorescence quantitative PCR to analyze the expression of these genes and their correlation with flavonoid synthesis. We discovered one R2R3 MYB transcription factor from the sequencing library, VcMYB1, that can positively regulate anthocyanin synthesis in blueberries. VcMYB1 is mainly expressed in colored (mature) fruits. Experiments showed that overexpression and transient expression of VcMYB1 promoted anthocyanin synthesis in Arabidopsis, tobacco (Nicotiana benthamiana) plants and green blueberry fruits. Yeast one-hybrid (Y1H) assay, electrophoretic mobility shift assay, and transient expression experiments showed that VcMYB1 binds to the MYB binding site on the promoter of the structural gene for anthocyanin synthesis, VcMYB1 to positively regulate the transcription of VcDFR, thereby promoting anthocyanin synthesis. We also performed an in-depth investigation of transcriptional regulation of anthocyanin synthesis. This study provides background information and data for studying the synthetic pathways of flavonoids and other secondary metabolites in blueberries.
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Yin X, Zhang Y, Zhang L, Wang B, Zhao Y, Irfan M, Chen L, Feng Y. Regulation of MYB Transcription Factors of Anthocyanin Synthesis in Lily Flowers. FRONTIERS IN PLANT SCIENCE 2021; 12:761668. [PMID: 34925411 PMCID: PMC8672200 DOI: 10.3389/fpls.2021.761668] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/28/2021] [Indexed: 05/13/2023]
Abstract
Flower color is the decisive factor that affects the commercial value of ornamental flowers. Therefore, it is important to study the regulation of flower color formation in lily to discover the positive and negative factors that regulate this important trait. In this study, MYB transcription factors (TFs) were characterized to understand the regulatory mechanism of anthocyanin biosynthesis in lily. Two R2R3-MYB TFs, LvMYB5, and LvMYB1, were found to regulate anthocyanin biosynthesis in lily flowers. LvMYB5, which has an activation motif, belongs to the SG6 MYB protein subgroup of Arabidopsis thaliana. Transient expression of LvMYB5 indicated that LvMYB5 can promote coloration in Nicotiana benthamiana leaves, and that expression of LvMYB5 increases the expression levels of NbCHS, NbDFR, and NbANS. VIGS experiments in lily petals showed that the accumulation of anthocyanins was reduced when LvMYB5 was silenced. Luciferase assays showed that LvMYB5 can promote anthocyanin synthesis by activating the ANS gene promoter. Therefore, LvMYB5 plays an important role in flower coloration in lily. In addition, the transient expression experiment provided preliminary evidence that LvMYB1 (an R2R3-MYB TF) inhibits anthocyanin synthesis in lily flowers. The discovery of activating and inhibitory factors related to anthocyanin biosynthesis in lily provides a theoretical basis for improving flower color through genetic engineering. The results of our study provide a new direction for the further study of the mechanisms of flower color formation in lilies.
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Affiliation(s)
- Xiaojuan Yin
- Plant Protection College, Shenyang Agricultural University, Shenyang, China
| | - Yibing Zhang
- Key Laboratory of Agriculture Biotechnology, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Li Zhang
- Key Laboratory of Agriculture Biotechnology, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Baohua Wang
- Key Laboratory of Agriculture Biotechnology, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yidi Zhao
- Key Laboratory of Agriculture Biotechnology, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Muhammad Irfan
- Department of Biotechnology, Faculty of Science, University of Sargodha, Sargodha, Pakistan
| | - Lijing Chen
- Key Laboratory of Agriculture Biotechnology, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Protected Horticulture (Ministry of Education), College of Horticulture, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Lijing Chen, ;
| | - Yulong Feng
- Plant Protection College, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agriculture Biotechnology, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Yulong Feng, ;
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