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Tsuda K. Evolution of the sporophyte shoot axis and functions of TALE HD transcription factors in stem development. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102594. [PMID: 38943830 DOI: 10.1016/j.pbi.2024.102594] [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: 02/13/2024] [Revised: 05/24/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
The stem is one of the major organs in seed plants and is important for plant survival as well as in agriculture. However, due to the lack of clear external landmarks in many species, its developmental and evolutionary processes are understudied compared to other organs. Recent approaches tackling these problems, especially those focused on KNOX1 and BLH transcription factors belonging to the TALE homeodomain superfamily have started unveiling the patterning process of nodes and internodes by connecting previously accumulated knowledge on lateral organ regulators. Fossil records played crucial roles in understanding the evolutionary process of the stem. The aim of this review is to introduce how the stem evolved from ancestorial sporophyte axes and to provide frameworks for future efforts in understanding the developmental process of this elusive but pivotal organ.
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Affiliation(s)
- Katsutoshi Tsuda
- Plant Cytogenetics Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540, Japan.
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2
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Xiao YL, Li GS. Differential expression and co-localization of transcriptional factors during callus transition to differentiation for shoot organogenesis in the water fern Ceratopteris richardii. ANNALS OF BOTANY 2024; 133:495-507. [PMID: 38206867 PMCID: PMC11006541 DOI: 10.1093/aob/mcae006] [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: 10/23/2023] [Accepted: 01/10/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND AND AIMS In flowering plants, regeneration can be achieved by a variety of approaches, and different sets of transcriptional factors are involved in these processes. However, regeneration in taxa other than flowering plants remains a mystery. Ceratopteris richardii is a representative fern capable of both direct and indirect organogenesis, and we aimed to investigate the genetics underlying the transition from callus proliferation to differentiation. METHODS Morphological and histological analyses were used to determine the type of regeneration involved. RNA sequencing and differential gene expression were used to investigate how the callus switches from proliferation to differentiation. Phylogenetic analysis and RNA in situ hybridization were used to understand whether transcriptional factors are involved in this transition. KEY RESULTS The callus formed on nascent leaves and subsequently developed the shoot pro-meristem and shoot meristem, thus completing indirect de novo shoot organogenesis in C. richardii. Genes were differentially expressed during the callus transition from proliferation to differentiation, indicating a role for photosynthesis, stimulus response and transmembrane signalling in this transition and the involvement of almost all cell layers that make up the callus. Transcriptional factors were either downregulated or upregulated, which were generally in many-to-many orthology with genes known to be involved in callus development in flowering plants, suggesting that the genetics of fern callus development are both conserved and divergent. Among them, an STM-like, a PLT-like and an ethylene- and salt-inducible ERF gene3-like gene were expressed simultaneously in the vasculature but not in the other parts of the callus, indicating that the vasculature played a role in the callus transition from proliferation to differentiation. CONCLUSIONS Indirect de novo shoot organogenesis could occur in ferns, and the callus transition from proliferation to differentiation required physiological changes, differential expression of transcriptional factors and involvement of the vasculature.
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Affiliation(s)
- Yuan-Le Xiao
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou 416000, China
| | - Gui-Sheng Li
- Laboratory of Plant Resource Conservation and Utilization, Jishou University, Jishou 416000, China
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3
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Arnoux-Courseaux M, Coudert Y. Re-examining meristems through the lens of evo-devo. TRENDS IN PLANT SCIENCE 2024; 29:413-427. [PMID: 38040554 DOI: 10.1016/j.tplants.2023.11.003] [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: 07/26/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023]
Abstract
The concept of the meristem was introduced in 1858 to characterize multicellular, formative, and proliferative tissues that give rise to the entire plant body, based on observations of vascular plants. Although its original definition did not encompass bryophytes, this concept has been used and continuously refined over the past 165 years to describe the diverse apices of all land plants. Here, we re-examine this matter in light of recent evo-devo research and show that, despite displaying high anatomical diversity, land plant meristems are unified by shared genetic control. We also propose a modular view of meristem function and highlight multiple evolutionary mechanisms that are likely to have contributed to the assembly and diversification of the varied meristems during the course of plant evolution.
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Affiliation(s)
- Moïra Arnoux-Courseaux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France; Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des Martyrs, F-38054, Grenoble, France
| | - Yoan Coudert
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, INRIA, Lyon 69007, France.
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4
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Jia P, Wang Y, Sharif R, Dong QL, Liu Y, Luan HA, Zhang XM, Guo SP, Qi GH. KNOTTED1-like homeobox (KNOX) transcription factors - Hubs in a plethora of networks: A review. Int J Biol Macromol 2023; 253:126878. [PMID: 37703987 DOI: 10.1016/j.ijbiomac.2023.126878] [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: 07/05/2023] [Revised: 09/09/2023] [Accepted: 09/10/2023] [Indexed: 09/15/2023]
Abstract
KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant development. Advancements in genetics and molecular biology research generate a large amount of information about KNOX genes in model and non-model plants, and their functions in different developmental backgrounds are gradually becoming clear. In this review, we summarize the known and presumed functions of the KNOX gene in plants, focusing on horticultural plants and crops. The classification and structural characteristics, expression characteristics and regulation, interacting protein factors, functions, and mechanisms of KNOX genes are systematically described. Further, the current research gaps and perspectives were discussed. These comprehensive data can provide a reference for the directional improvement of agronomic traits through KNOX gene regulation.
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Affiliation(s)
- Peng Jia
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
| | - Yuan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071000, China
| | - Rahat Sharif
- Department of Horticulture, School of Horticulture and Landscape, Yangzhou University, Yangzhou 225009, China
| | - Qing-Long Dong
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Yang Liu
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Hao-An Luan
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xue-Mei Zhang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Sup-Ping Guo
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Guo-Hui Qi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China.
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5
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Sun R, Qin T, Wall SB, Wang Y, Guo X, Sun J, Liu Y, Wang Q, Zhang B. Genome-wide identification of KNOX transcription factors in cotton and the role of GhKNOX4-A and GhKNOX22-D in response to salt and drought stress. Int J Biol Macromol 2023; 226:1248-1260. [PMID: 36442570 DOI: 10.1016/j.ijbiomac.2022.11.238] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
Cotton is one of the most important economic and fiber crops in the world. KNOX is one class of universal transcription factors, which plays important roles in plant growth and development as well as response to different stresses. Although there are many researches on KNOXs in other plant species, there are few reports on cotton. In this study, we systematically and comprehensively identified all KNOX genes in upland cotton and its two ancestral species; we also studied their functions by employing RNA-seq analysis and virus-induced gene silence (VIGS). A total of 89 KNOX genes were identified from three cotton species. Among them, 44 were from upland cotton, 22 and 23 were found in its ancestral species G. raimondii and G. arboreum, respectively. Plant polyploidization and domestication play a selective force driving KNOX gene evolution. Phylogenetic analysis displayed that KNOX genes were evolved into three Classes. The intron length and exon number differed in each Class. Transcriptome data showed that KNOX genes of Class II were widely expressed in multiple tissues, including fiber. The majority of KNOX genes were induced by different abiotic stresses. Additionally, we found multiple cis-elements related to stress in the promoter region of KNOX genes. VIGS silence of GhKNOX4-A and GhKNOX22-D genes showed significant growth and development effect in cotton seedlings under salt and drought treatments. Both GhKNOX4-A and GhKNOX22-D regulated plant tolerance; silencing both genes induced oxidative stresses, evidenced by reduced SOD activity and induced leave cell death, and also enhanced stomatal open and water loss. Thus, GhKNOX4-A and GhKNOX22-D may contribute to drought response by regulating stomata opening and oxidative stresses.
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Affiliation(s)
- Runrun Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Tengfei Qin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Sarah Brooke Wall
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Yuanyuan Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xinlei Guo
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Jialiang Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Yongsheng Liu
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Qinglian Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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BREVIPEDICELLUS Positively Regulates Salt-Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24021054. [PMID: 36674568 PMCID: PMC9866879 DOI: 10.3390/ijms24021054] [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: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Salt stress is one of the major environmental threats to plant growth and development. However, the mechanisms of plants responding to salt stress are not fully understood. Through genetic screening, we identified and characterized a salt-sensitive mutant, ses5 (sensitive to salt 5), in Arabidopsis thaliana. Positional cloning revealed that the decreased salt-tolerance of ses5 was caused by a mutation in the transcription factor BP (BREVIPEDICELLUS). BP regulates various developmental processes in plants. However, the biological function of BP in abiotic stress-signaling and tolerance are still not clear. Compared with wild-type plants, the bp mutant exhibited a much shorter primary-root and lower survival rate under salt treatment, while the BP overexpressors were more tolerant. Further analysis showed that BP could directly bind to the promoter of XTH7 (xyloglucan endotransglucosylase/hydrolase 7) and activate its expression. Resembling the bp mutant, the disruption of XTH7 gave rise to salt sensitivity. These results uncovered novel roles of BP in positively modulating salt-stress tolerance, and illustrated a putative working mechanism.
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Sattler R, Rutishauser R. Fundamentals of Plant Morphology and Plant Evo-Devo (Evolutionary Developmental Morphology). PLANTS (BASEL, SWITZERLAND) 2022; 12:118. [PMID: 36616247 PMCID: PMC9823526 DOI: 10.3390/plants12010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Morphological concepts are used in plant evo-devo (evolutionary developmental biology) and other disciplines of plant biology, and therefore plant morphology is relevant to all of these disciplines. Many plant biologists still rely on classical morphology, according to which there are only three mutually exclusive organ categories in vascular plants such as flowering plants: root, stem (caulome), and leaf (phyllome). Continuum morphology recognizes a continuum between these organ categories. Instead of Aristotelian identity and either/or logic, it is based on fuzzy logic, according to which membership in a category is a matter of degree. Hence, an organ in flowering plants may be a root, stem, or leaf to some degree. Homology then also becomes a matter of degree. Process morphology supersedes structure/process dualism. Hence, structures do not have processes, they are processes, which means they are process combinations. These process combinations may change during ontogeny and phylogeny. Although classical morphology on the one hand and continuum and process morphology on the other use different kinds of logic, they can be considered complementary and thus together they present a more inclusive picture of the diversity of plant form than any one of the three alone. However, continuum and process morphology are more comprehensive than classical morphology. Insights gained from continuum and process morphology can inspire research in plant morphology and plant evo-devo, especially MorphoEvoDevo.
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Affiliation(s)
- Rolf Sattler
- Biology Department, McGill University, Montreal, QC H3G 0B1, Canada
| | - Rolf Rutishauser
- Department of Systematic and Evolutionary Botany, University of Zurich, CH-8008 Zurich, Switzerland
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8
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Ou X, Wang Y, Li J, Zhang J, Xie Z, He B, Jiang Z, Wang Y, Su W, Song S, Hao Y, Chen R. Genome-wide identification of the KNOTTED HOMEOBOX gene family and their involvement in stalk development in flowering Chinese cabbage. FRONTIERS IN PLANT SCIENCE 2022; 13:1019884. [PMID: 36438132 PMCID: PMC9686407 DOI: 10.3389/fpls.2022.1019884] [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: 09/20/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Gibberellin and cytokinin synergistically regulate the stalk development in flowering Chinese cabbage. KNOX proteins were reported to function as important regulators of the shoot apex to promote meristem activity by synchronously inducing CTK and suppressing GA biosynthesis, while their regulatory mechanism in the bolting and flowering is unknown. In this study, 9 BcKNOX genes were identified and mapped unevenly on 6 out of 10 flowering Chinese cabbage chromosomes. The BcKNOXs were divided into three subfamilies on the basis of sequences and gene structure. The proteins contain four conserved domains except for BcKNATM. Three BcKNOX TFs (BcKNOX1, BcKNOX3, and BcKNOX5) displayed high transcription levels on tested tissues at various stages. The major part of BcKNOX genes showed preferential expression patterns in response to low-temperature, zeatin (ZT), and GA3 treatment, indicating that they were involved in bud differentiation and bolting. BcKNOX1 and BcKNOX5 showed high correlation level with gibberellins synthetase, and CTK metabolic genes. BcKONX1 also showed high correlation coefficients within BcRGA1 and BcRGL1 which are negative regulators of GA signaling. In addition, BcKNOX1 interacted with BcRGA1 and BcRGL1, as confirmed by yeast two-hybrid (Y2H) and biomolecular fluorescence complementation assay (BiFC). This analysis has provided useful foundation for the future functional roles' analysis of flowering Chinese cabbage KNOX genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Yanwei Hao
- *Correspondence: Yanwei Hao, ; Riyuan Chen,
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9
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Fouracre JP, Harrison CJ. How was apical growth regulated in the ancestral land plant? Insights from the development of non-seed plants. PLANT PHYSIOLOGY 2022; 190:100-112. [PMID: 35771646 PMCID: PMC9434304 DOI: 10.1093/plphys/kiac313] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Land plant life cycles are separated into distinct haploid gametophyte and diploid sporophyte stages. Indeterminate apical growth evolved independently in bryophyte (moss, liverwort, and hornwort) and fern gametophytes, and tracheophyte (vascular plant) sporophytes. The extent to which apical growth in tracheophytes co-opted conserved gametophytic gene networks, or exploited ancestral sporophytic networks, is a long-standing question in plant evolution. The recent phylogenetic confirmation of bryophytes and tracheophytes as sister groups has led to a reassessment of the nature of the ancestral land plant. Here, we review developmental genetic studies of apical regulators and speculate on their likely evolutionary history.
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Affiliation(s)
- Jim P Fouracre
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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10
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Wang QH, Zhang J, Liu Y, Jia Y, Jiao YN, Xu B, Chen ZD. Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4306-4322. [PMID: 35437589 DOI: 10.1093/jxb/erac127] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.
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Affiliation(s)
- Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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11
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Zhang D, Lan S, Yin WL, Liu ZJ. Genome-Wide Identification and Expression Pattern Analysis of KNOX Gene Family in Orchidaceae. FRONTIERS IN PLANT SCIENCE 2022; 13:901089. [PMID: 35712569 PMCID: PMC9197187 DOI: 10.3389/fpls.2022.901089] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/19/2022] [Indexed: 05/13/2023]
Abstract
The establishment of lateral organs and subsequent plant architecture involves factors intrinsic to the stem apical meristem (SAM) from which they are derived. KNOTTED1-LIKE HOMEOBOX (KNOX) genes are a family of plant-specific homeobox transcription factors that especially act in determining stem cell fate in SAM. Although KNOXs have been studied in many land plants for decades, there is a dearth of knowledge on KNOX's role in Orchidaceae, the largest and most diverse lineage of flowering plants. In this study, a total of 32 putative KNOX genes were identified in the genomes of five orchid species and further designated into two classes (Class I and Class II) based on phylogenetic relationships. Sequence analysis showed that most orchid KNOX proteins retain four conserved domains (KNOX1, KNOX2, ELK, and Homeobox_KN). Comparative analysis of gene structure showed that the exon-intron structure is conserved in the same clade but most orchids exhibited longer intron, which may be a unique feature of Orchidaceae. Cis-elements identified in the promoter region of orchid KNOXs were found mostly enriched in a function of light responsiveness, followed by MeJA and ABA responsiveness, indicative of their roles in modulating light and phytohormones. Collinear analysis unraveled a one-to-one correspondence among KNOXs in orchids, and all KNOX genes experienced strong purifying selection, indicating the conservation of this gene family has been reinforced across the Orchidaceae lineage. Expression profiles based on transcriptomic data and real-time reverse transcription-quantitative PCR (RT-qPCR) revealed a stem-specific expression of KNOX Class I genes and a broader expression pattern of Class II genes. Taken together, our results provided a comprehensive analysis to uncover the underlying function of KNOX genes in Orchidaceae.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Lun Yin
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Wei-Lun Yin,
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Zhong-Jian Liu,
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12
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Abstract
There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.
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Affiliation(s)
- Philip C J Donoghue
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jordi Paps
- School of Biological Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Harald Schneider
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK; Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China
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13
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Hisanaga T, Fujimoto S, Cui Y, Sato K, Sano R, Yamaoka S, Kohchi T, Berger F, Nakajima K. Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants. eLife 2021; 10:57090. [PMID: 34579806 PMCID: PMC8478417 DOI: 10.7554/elife.57090] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/02/2021] [Indexed: 02/03/2023] Open
Abstract
KNOX and BELL transcription factors regulate distinct steps of diploid development in plants. In the green alga Chlamydomonas reinhardtii, KNOX and BELL proteins are inherited by gametes of the opposite mating types and heterodimerize in zygotes to activate diploid development. By contrast, in land plants such as Physcomitrium patens and Arabidopsis thaliana, KNOX and BELL proteins function in sporophyte and spore formation, meristem maintenance and organogenesis during the later stages of diploid development. However, whether the contrasting functions of KNOX and BELL were acquired independently in algae and land plants is currently unknown. Here, we show that in the basal land plant species Marchantia polymorpha, gamete-expressed KNOX and BELL are required to initiate zygotic development by promoting nuclear fusion in a manner strikingly similar to that in C. reinhardtii. Our results indicate that zygote activation is the ancestral role of KNOX/BELL transcription factors, which shifted toward meristem maintenance as land plants evolved.
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Affiliation(s)
- Tetsuya Hisanaga
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan.,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Shota Fujimoto
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Yihui Cui
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Katsutoshi Sato
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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Dierschke T, Flores-Sandoval E, Rast-Somssich MI, Althoff F, Zachgo S, Bowman JL. Gamete expression of TALE class HD genes activates the diploid sporophyte program in Marchantia polymorpha. eLife 2021; 10:57088. [PMID: 34533136 PMCID: PMC8476127 DOI: 10.7554/elife.57088] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/15/2021] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in gametes primes the haploid-to-diploid transition. In the unicellular chlorophyte alga Chlamydomonas, KNOX and BELL TALE-homeodomain genes mediate this transition. We demonstrate that in the liverwort Marchantia polymorpha, paternal (sperm) expression of three of five phylogenetically diverse BELL genes, MpBELL234, and maternal (egg) expression of both MpKNOX1 and MpBELL34 mediate the haploid-to-diploid transition. Loss-of-function alleles of MpKNOX1 result in zygotic arrest, whereas a loss of either maternal or paternal MpBELL234 results in variable zygotic and early embryonic arrest. Expression of MpKNOX1 and MpBELL34 during diploid sporophyte development is consistent with a later role for these genes in patterning the sporophyte. These results indicate that the ancestral mechanism to activate diploid gene expression was retained in early diverging land plants and subsequently co-opted during evolution of the diploid sporophyte body.
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Affiliation(s)
- Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, Australia.,Botany Department, University of Osnabrück, Osnabrück, Germany
| | | | | | - Felix Althoff
- Botany Department, University of Osnabrück, Osnabrück, Germany
| | - Sabine Zachgo
- Botany Department, University of Osnabrück, Osnabrück, Germany
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Australia
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15
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Li X, Shen F, Xu X, Zheng Q, Wang Y, Wu T, Li W, Qiu C, Xu X, Han Z, Zhang X. An HD-ZIP transcription factor, MxHB13, integrates auxin-regulated and juvenility-determined control of adventitious rooting in Malus xiaojinensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1663-1680. [PMID: 34218490 DOI: 10.1111/tpj.15406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Adventitious root (AR) formation is a critical factor in the vegetative propagation of forestry and horticultural plants. Competence for AR formation declines in many species during the miR156/SPL-mediated vegetative phase change. Auxin also plays a regulatory role in AR formation. In apple rootstock, both high miR156 expression and exogenous auxin application are prerequisites for AR formation. However, the mechanism by which the miR156/SPL module interacts with auxin in controlling AR formation is unclear. In this paper, leafy cuttings of juvenile (Mx-J) and adult (Mx-A) phase Malus xiaojinensis were used in an RNA-sequencing experiment. The results revealed that numerous genes involved in phytohormone signaling, carbohydrate metabolism, cell dedifferentiation, and reactivation were downregulated in Mx-A cuttings in response to indole butyric acid treatment. Among the differentially expressed genes, an HD-ZIP transcription factor gene, MxHB13, was found to be under negative regulation of MdSPL26 by directly binding to MxHB13 promoter. MxTIFY9 interacts with MxSPL26 and may play a role in co-repressing the expression of MxHB13. The expression of MxTIFY9 was induced by exogenous indole butyric acid. MxHB13 binds to the promoter of MxABCB19-2 and positively affects the expression. A model is proposed in which MxHB13 links juvenility-limited and auxin-limited AR recalcitrance mechanisms in Mx-A.
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Affiliation(s)
- Xu Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaozhao Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Qingbo Zheng
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Wei Li
- College of Horticulture, China Agricultural University, Beijing, China
| | - Changpeng Qiu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
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16
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Romani F, Moreno JE. Molecular mechanisms involved in functional macroevolution of plant transcription factors. THE NEW PHYTOLOGIST 2021; 230:1345-1353. [PMID: 33368298 DOI: 10.1111/nph.17161] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/17/2020] [Indexed: 05/04/2023]
Abstract
Transcription factors (TFs) are key components of the transcriptional regulation machinery. In plants, they accompanied the evolution from unicellular aquatic algae to complex flowering plants that dominate the land environment. The adaptations of the body plan and physiological responses required changes in the biological functions of TFs. Some ancestral gene regulatory networks are highly conserved, while others evolved more recently and only exist in particular lineages. The recent emergence of novel model organisms provided the opportunity for comparative studies, producing new insights to infer these evolutionary trajectories. In this review, we comprehensively revisit the recent literature on TFs of nonseed plants and algae, focusing on the molecular mechanisms driving their functional evolution. We discuss the particular contribution of changes in DNA-binding specificity, protein-protein interactions and cis-regulatory elements to gene regulatory networks. Current advances have shown that these evolutionary processes were shaped by changes in TF expression pattern, not through great innovation in TF protein sequences. We propose that the role of TFs associated with environmental and developmental regulation was unevenly conserved during land plant evolution.
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Affiliation(s)
- Facundo Romani
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral - CONICET, Colectora RN 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Javier E Moreno
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral, Centro Científico Tecnológico CONICET Santa Fe, Universidad Nacional del Litoral - CONICET, Colectora RN 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
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17
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Geng Y, Guo L, Han H, Liu X, Banks JA, Wisecaver JH, Zhou Y. Conservation and diversification of HAIRY MERISTEM gene family in land plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:366-378. [PMID: 33484592 DOI: 10.1111/tpj.15169] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 01/07/2021] [Accepted: 01/18/2021] [Indexed: 05/27/2023]
Abstract
The shoot apical meristems (SAMs) of land plants are crucial for plant growth and organ formation. In several angiosperms, the HAIRY MERISTEM (HAM) genes function as key regulators that control meristem development and stem cell homeostasis. To date, the origin and evolutionary history of the HAM family in land plants remains unclear. Potentially shared and divergent functions of HAM family members from angiosperms and non-angiosperms are also not known. In constructing a comprehensive phylogeny of the HAM family, we show that HAM proteins are widely present in land plants and that HAM proteins originated prior to the divergence of bryophytes. The HAM family was duplicated in a common ancestor of angiosperms, leading to two distinct groups: type I and type II. Type-II HAM members are widely present in angiosperms, whereas type-I HAM members were independently lost in different orders of monocots. Furthermore, HAM members from angiosperms and non-angiosperms (including bryophytes, lycophytes, ferns and gymnosperms) are able to replace the role of the type-II HAM genes in Arabidopsis, maintaining established SAMs and promoting the initiation of new stem cell niches. Our results uncover the conserved functions of HAM family members and reveal the conserved regulatory mechanisms underlying HAM expression patterning in meristems, providing insight into the evolution of key stem cell regulators in land plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Lei Guo
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Han Han
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Xing Liu
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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18
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Frangedakis E, Shimamura M, Villarreal JC, Li FW, Tomaselli M, Waller M, Sakakibara K, Renzaglia KS, Szövényi P. The hornworts: morphology, evolution and development. THE NEW PHYTOLOGIST 2021; 229:735-754. [PMID: 32790880 PMCID: PMC7881058 DOI: 10.1111/nph.16874] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 05/12/2023]
Abstract
Extant land plants consist of two deeply divergent groups, tracheophytes and bryophytes, which shared a common ancestor some 500 million years ago. While information about vascular plants and the two of the three lineages of bryophytes, the mosses and liverworts, is steadily accumulating, the biology of hornworts remains poorly explored. Yet, as the sister group to liverworts and mosses, hornworts are critical in understanding the evolution of key land plant traits. Until recently, there was no hornwort model species amenable to systematic experimental investigation, which hampered detailed insight into the molecular biology and genetics of this unique group of land plants. The emerging hornwort model species, Anthoceros agrestis, is instrumental in our efforts to better understand not only hornwort biology but also fundamental questions of land plant evolution. To this end, here we provide an overview of hornwort biology and current research on the model plant A. agrestis to highlight its potential in answering key questions of land plant biology and evolution.
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Affiliation(s)
| | - Masaki Shimamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 739-8528, Japan
| | - Juan Carlos Villarreal
- Department of Biology, Laval University, Quebec City, Quebec, G1V 0A6, Canada
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panamá
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, 14853-1801, USA
- Plant Biology Section, Cornell University, Ithaca, New York, 14853-1801, USA
| | - Marta Tomaselli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB3 EA, UK
| | - Manuel Waller
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
| | - Keiko Sakakibara
- Department of Life Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Karen S. Renzaglia
- Department of Plant Biology, Southern Illinois University, Illinois, 62901, USA
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Switzerland
- Zurich-Basel Plant Science Center, Zurich, 8092, Switzerland
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19
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Bueno N, Alvarez JM, Ordás RJ. Characterization of the KNOTTED1-LIKE HOMEOBOX (KNOX) gene family in Pinus pinaster Ait. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110691. [PMID: 33218649 DOI: 10.1016/j.plantsci.2020.110691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 05/27/2023]
Abstract
KNOTTED1-LIKE HOMEOBOX (KNOX) genes are a family of plant-specific homeobox transcription factors with important roles in plant development that have been classified into two subfamilies with differential expression domains and functions. Studies in angiosperms have shown that class I members are related to the maintenance of meristem homeostasis and leaf development, whereas class II members promote differentiation of tissues and organs. However, little is known about its diversification and function in gymnosperms. By combining PCR-based detection and transcriptome data analysis, we identified four class I and two class II KNOX genes in Pinus pinaster. Expression analyses showed that class I members were mainly expressed in meristematic regions and differentiating tissues, with practically no expression in lateral organs, whereas expression of class II members was restricted to lateral organs. Furthermore, overexpression of P. pinaster KNOX genes in Arabidopsis thaliana caused similar phenotypic effects to those described for their angiosperms counterparts. This is the first time to our knowledge that functional analyses of class II members are reported in a conifer species. These results suggest a high conservation of the KNOX gene family throughout seed plants, as the functional differentiation of both subfamilies observed in angiosperms might be partially conserved in gymnosperms.
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Affiliation(s)
- Natalia Bueno
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Spain
| | - José Manuel Alvarez
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Spain.
| | - Ricardo J Ordás
- Instituto Universitario de Biotecnología de Asturias (IUBA), Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Spain
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20
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Abstract
Plants and animals are both important for studies in evolutionary developmental biology (EvoDevo). Plant morphology as a valuable discipline of EvoDevo is set for a paradigm shift. Process thinking and the continuum approach in plant morphology allow us to perceive and interpret growing plants as combinations of developmental processes rather than as assemblages of structural units (“organs”) such as roots, stems, leaves, and flowers. These dynamic philosophical perspectives were already favored by botanists and philosophers such as Agnes Arber (1879–1960) and Rolf Sattler (*1936). The acceptance of growing plants as dynamic continua inspires EvoDevo scientists such as developmental geneticists and evolutionary biologists to move towards a more holistic understanding of plants in time and space. This review will appeal to many young scientists in the plant development research fields. It covers a wide range of relevant publications from the past to present.
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21
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Spencer V, Nemec Venza Z, Harrison CJ. What can lycophytes teach us about plant evolution and development? Modern perspectives on an ancient lineage. Evol Dev 2020; 23:174-196. [PMID: 32906211 DOI: 10.1111/ede.12350] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023]
Abstract
All Evo-Devo studies rely on representative sampling across the tree of interest to elucidate evolutionary trajectories through time. In land plants, genetic resources are well established in model species representing lineages including bryophytes (mosses, liverworts, and hornworts), monilophytes (ferns and allies), and seed plants (gymnosperms and flowering plants), but few resources are available for lycophytes (club mosses, spike mosses, and quillworts). Living lycophytes are a sister group to the euphyllophytes (the fern and seed plant clade), and have retained several ancestral morphological traits despite divergence from a common ancestor of vascular plants around 420 million years ago. This sister relationship offers a unique opportunity to study the conservation of traits such as sporophyte branching, vasculature, and indeterminacy, as well as the convergent evolution of traits such as leaves and roots which have evolved independently in each vascular plant lineage. To elucidate the evolution of vascular development and leaf formation, molecular studies using RNA Seq, quantitative reverse transcription polymerase chain reaction, in situ hybridisation and phylogenetics have revealed the diversification and expression patterns of KNOX, ARP, HD-ZIP, KANADI, and WOX gene families in lycophytes. However, the molecular basis of further trait evolution is not known. Here we describe morphological traits of living lycophytes and their extinct relatives, consider the molecular underpinnings of trait evolution and discuss future research required in lycophytes to understand the key evolutionary innovations enabling the growth and development of all vascular plants.
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Affiliation(s)
- Victoria Spencer
- School of Biological Sciences, The University of Bristol, Bristol, UK
| | - Zoe Nemec Venza
- School of Biological Sciences, The University of Bristol, Bristol, UK
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22
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Vasco A, Ambrose BA. Simple and Divided Leaves in Ferns: Exploring the Genetic Basis for Leaf Morphology Differences in the Genus Elaphoglossum (Dryopteridaceae). Int J Mol Sci 2020; 21:E5180. [PMID: 32707812 PMCID: PMC7432805 DOI: 10.3390/ijms21155180] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/01/2020] [Accepted: 07/18/2020] [Indexed: 12/29/2022] Open
Abstract
Despite the implications leaves have for life, their origin and development remain debated. Analyses across ferns and seed plants are fundamental to address the conservation or independent origins of megaphyllous leaf developmental mechanisms. Class I KNOX expression studies have been used to understand leaf development and, in ferns, have only been conducted in species with divided leaves. We performed expression analyses of the Class I KNOX and Histone H4 genes throughout the development of leaf primordia in two simple-leaved and one divided-leaved fern taxa. We found Class I KNOX are expressed (1) throughout young and early developing leaves of simple and divided-leaved ferns, (2) later into leaf development of divided-leaved species compared to simple-leaved species, and (3) at the leaf primordium apex and margins. H4 expression is similar in young leaf primordia of simple and divided leaves. Persistent Class I KNOX expression at the margins of divided leaf primordia compared with simple leaf primordia indicates that temporal and spatial patterns of Class I KNOX expression correlate with different fern leaf morphologies. However, our results also indicate that Class I KNOX expression alone is not sufficient to promote divided leaf development in ferns. Class I KNOX patterns of expression in fern leaves support the conservation of an independently recruited developmental mechanism for leaf dissection in megaphylls, the shoot-like nature of fern leaves compared with seed plant leaves, and the critical role marginal meristems play in fern leaf development.
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Affiliation(s)
- Alejandra Vasco
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107-3400, USA
| | - Barbara A. Ambrose
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458-5126, USA
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23
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Cesarino I, Dello Ioio R, Kirschner GK, Ogden MS, Picard KL, Rast-Somssich MI, Somssich M. Plant science's next top models. ANNALS OF BOTANY 2020; 126:1-23. [PMID: 32271862 PMCID: PMC7304477 DOI: 10.1093/aob/mcaa063] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Model organisms are at the core of life science research. Notable examples include the mouse as a model for humans, baker's yeast for eukaryotic unicellular life and simple genetics, or the enterobacteria phage λ in virology. Plant research was an exception to this rule, with researchers relying on a variety of non-model plants until the eventual adoption of Arabidopsis thaliana as primary plant model in the 1980s. This proved to be an unprecedented success, and several secondary plant models have since been established. Currently, we are experiencing another wave of expansion in the set of plant models. SCOPE Since the 2000s, new model plants have been established to study numerous aspects of plant biology, such as the evolution of land plants, grasses, invasive and parasitic plant life, adaptation to environmental challenges, and the development of morphological diversity. Concurrent with the establishment of new plant models, the advent of the 'omics' era in biology has led to a resurgence of the more complex non-model plants. With this review, we introduce some of the new and fascinating plant models, outline why they are interesting subjects to study, the questions they will help to answer, and the molecular tools that have been established and are available to researchers. CONCLUSIONS Understanding the molecular mechanisms underlying all aspects of plant biology can only be achieved with the adoption of a comprehensive set of models, each of which allows the assessment of at least one aspect of plant life. The model plants described here represent a step forward towards our goal to explore and comprehend the diversity of plant form and function. Still, several questions remain unanswered, but the constant development of novel technologies in molecular biology and bioinformatics is already paving the way for the next generation of plant models.
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Affiliation(s)
- Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, Rua do Matão 277, Butantã, São Paulo, Brazil
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Università di Roma La Sapienza, Rome, Italy
| | - Gwendolyn K Kirschner
- University of Bonn, Institute of Crop Science and Resource Conservation (INRES), Division of Crop Functional Genomics, Bonn, Germany
| | - Michael S Ogden
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Kelsey L Picard
- School of Natural Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Madlen I Rast-Somssich
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, VIC, Australia
| | - Marc Somssich
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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24
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Cruz R, Melo-de-Pinna GFA, Vasco A, Prado J, Ambrose BA. Class I KNOX Is Related to Determinacy during the Leaf Development of the Fern Mickelia scandens (Dryopteridaceae). Int J Mol Sci 2020; 21:ijms21124295. [PMID: 32560264 PMCID: PMC7352642 DOI: 10.3390/ijms21124295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 12/19/2022] Open
Abstract
Unlike seed plants, ferns leaves are considered to be structures with delayed determinacy, with a leaf apical meristem similar to the shoot apical meristems. To better understand the meristematic organization during leaf development and determinacy control, we analyzed the cell divisions and expression of Class I KNOX genes in Mickelia scandens, a fern that produces larger leaves with more pinnae in its climbing form than in its terrestrial form. We performed anatomical, in situ hybridization, and qRT-PCR experiments with histone H4 (cell division marker) and Class I KNOX genes. We found that Class I KNOX genes are expressed in shoot apical meristems, leaf apical meristems, and pinnae primordia. During early development, cell divisions occur in the most distal regions of the analyzed structures, including pinnae, and are not restricted to apical cells. Fern leaves and pinnae bear apical meristems that may partially act as indeterminate shoots, supporting the hypothesis of homology between shoots and leaves. Class I KNOX expression is correlated with indeterminacy in the apex and leaf of ferns, suggesting a conserved function for these genes in euphyllophytes with compound leaves.
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Affiliation(s)
- Rafael Cruz
- Instituto de Botânica, Av. Miguel Estéfano 3687, São Paulo (SP) CEP 04301-902, Brazil;
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo (SP) CEP 05422-971, Brazil;
- Correspondence:
| | - Gladys F. A. Melo-de-Pinna
- Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo (SP) CEP 05422-971, Brazil;
| | - Alejandra Vasco
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107-3400, USA;
| | - Jefferson Prado
- Instituto de Botânica, Av. Miguel Estéfano 3687, São Paulo (SP) CEP 04301-902, Brazil;
- UNESP, IBILCE, Depto. de Zoologia e Botânica, Rua Cristóvão Colombo, 2265, São José do Rio Preto (SP) CEP 15054-000, Brazil
| | - Barbara A. Ambrose
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY 10458-5126, USA;
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25
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Meng L, Liu X, He C, Xu B, Li Y, Hu Y. Functional divergence and adaptive selection of KNOX gene family in plants. Open Life Sci 2020; 15:346-363. [PMID: 33817223 PMCID: PMC7874613 DOI: 10.1515/biol-2020-0036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/09/2020] [Accepted: 04/23/2020] [Indexed: 12/16/2022] Open
Abstract
KNOTTED-like homeodomain (KNOX) genes are transcriptional regulators that play an important role in morphogenesis. In the present study, a comparative analysis was performed to investigate the molecular evolution of the characteristics of the KNOX gene family in 10 different plant species. We identified 129 KNOX gene family members, which were categorized into two subfamilies based on multiple sequence alignment and phylogenetic tree reconstruction. Several segmental duplication pairs were found, indicating that different species share a common expansion model. Functional divergence analysis identified the 15 and 52 amino acid sites with significant changes in evolutionary rates and amino acid physicochemical properties as functional divergence sites. Additional selection analysis showed that 14 amino acid sites underwent positive selection during evolution, and two groups of co-evolutionary amino acid sites were identified by Coevolution Analysis using Protein Sequences software. These sites could play critical roles in the molecular evolution of the KNOX gene family in these species. In addition, the expression profiles of KNOX duplicated genes demonstrated functional divergence. Taken together, these results provide novel insights into the structural and functional evolution of the KNOX gene family.
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Affiliation(s)
- Lingyan Meng
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiaomei Liu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Congfen He
- Beijing Key Lab of Plant Resource Research and Development, Beijing Technology and Business University, Beijing, 100048, China
| | - Biyao Xu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yaxuan Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yingkao Hu
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
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Zhao Y, Song X, Zhou H, Wei K, Jiang C, Wang J, Cao Y, Tang F, Zhao S, Lu MZ. KNAT2/6b, a class I KNOX gene, impedes xylem differentiation by regulating NAC domain transcription factors in poplar. THE NEW PHYTOLOGIST 2020; 225:1531-1544. [PMID: 31257603 DOI: 10.1111/nph.16036] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/22/2019] [Indexed: 05/21/2023]
Abstract
Wood formation is the terminal differentiation of xylem mother cells derived from cambial initials, and negative regulators play important roles in xylem differentiation. The molecular mechanism of the negative regulator of xylem differentiation PagKNAT2/6b was investigated. PagKNAT2/6b is an ortholog of Arabidopsis KNAT2 and KNAT6 that is highly expressed in phloem and xylem. Compared to nontransgenic control plants, transgenic poplar plants overexpressing PagKNAT2/6b present with altered vascular patterns, characterized by decreased secondary xylem with thin cell walls containing less cellulose, xylose and lignin. RNA sequencing analyses revealed that differentially expressed genes are enriched in xylem differentiation and secondary wall synthesis functions. Expression of NAM/ATAF/CUC (NAC) domain genes including PagSND1-A1, PagSND1-A2, PagSND1-B2 and PagVND6-C1 is downregulated by PagKNAT2/6b, while PagXND1a is directly upregulated. Accordingly, the dominant repression form of PagKNAT2/6b leads to increased xylem width per stem diameter through downregulation of PagXND1a. PagKNAT2/6b can inhibit cell differentiation and secondary wall deposition during wood formation in poplar by modulating the expression of NAC domain transcription factors. Direct activation of PagXND1a by PagKNAT2/6b is a key node in the negative regulatory network of xylem differentiation by KNOXs.
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Affiliation(s)
- Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kaili Wei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuan Cao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
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Cheng X, Li M, Abdullah M, Li G, Zhang J, Manzoor MA, Wang H, Jin Q, Jiang T, Cai Y, Li D, Lin Y. In Silico Genome-Wide Analysis of the Pear ( Pyrus bretschneideri) KNOX Family and the Functional Characterization of PbKNOX1, an Arabidopsis BREVIPEDICELLUS Orthologue Gene, Involved in Cell Wall and Lignin Biosynthesis. Front Genet 2019; 10:632. [PMID: 31333718 PMCID: PMC6624237 DOI: 10.3389/fgene.2019.00632] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/17/2019] [Indexed: 12/18/2022] Open
Abstract
Stone cells are a characteristic trait of pear fruit, but the contents and sizes of stone cells negatively correlate with fruit texture and flavor. Secondary cell wall thickening and lignification have been established as key steps of stone cell development. KNOTTED-LIKE HOMEOBOX (KNOX) proteins play important roles in plant cell growth and development, including cell wall formation and lignification. Although the characteristics and biological functions of KNOX proteins have been investigated in other plants, this gene family has not been functionally characterized in pear. Eighteen PbKNOX genes were identified in the present study, and all of the identified family members contained the KNOX I and/or KNOX II domains. Based on the phylogenetic tree and chromosomal localization, the 18 PbKNOX genes were divided into five subfamilies [SHOOT MERISTEMLESS (STM)-like, BREVIPEDICELLUS (BP)-like, KNOTTED ARABIDOPSIS THALIANA 2/6 (KNAT2/6)-like, KNAT7-like, and KNAT3-5-like] and were distributed among 10 chromosomes. In addition, we identified 9, 11, and 11 KNOX genes in the genomes of grape, mei, and strawberry, respectively, and the greatest number of collinear KNOX gene pairs formed between pears and peaches. Analyses of the spatiotemporal expression patterns showed that the tissue specificity of PbKNOX gene expression was not very significant and that the level of the PbKNOX1 transcript showed an opposite trend to the levels of stone cells and lignin accumulation. Furthermore, PbKNOX1 has high sequence identity and similarity with Arabidopsis BP. Compared with wild-type Arabidopsis, plants overexpressing PbKNOX1 not only showed an approximately 19% decrease in the secondary cell wall thickness of vessel cells but also exhibited an approximately 13% reduction in the lignin content of inflorescence stems. Moreover, the expression of several genes involved in lignin biosynthesis was downregulated in transgenic lines. Based on our results, PbKNOX1/BP participates in cell wall-thickening and lignin biosynthesis and represses the transcription of key structural genes involved in lignin synthesis, providing genetic evidence for the roles of KNOX in cell wall thickening and lignin biosynthesis in pear.
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Affiliation(s)
- Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Manli Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Jingyun Zhang
- School of Life Science, Anhui Agricultural University, Hefei, China.,Horticultural Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | | | - Han Wang
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Taoshan Jiang
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Dahui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
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Moody LA, Kelly S, Rabbinowitsch E, Langdale JA. Genetic Regulation of the 2D to 3D Growth Transition in the Moss Physcomitrella patens. Curr Biol 2019; 28:473-478.e5. [PMID: 29395927 PMCID: PMC5807088 DOI: 10.1016/j.cub.2017.12.052] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/20/2017] [Accepted: 12/22/2017] [Indexed: 01/16/2023]
Abstract
One of the most important events in the history of life on earth was the colonization of land by plants; this transition coincided with and was most likely enabled by the evolution of 3-dimensional (3D) growth. Today, the diverse morphologies exhibited across the terrestrial biosphere arise from the differential regulation of 3D growth processes during development. In many plants, 3D growth is initiated during the first few divisions of the zygote, and therefore, the genetic basis cannot be dissected because mutants do not survive. However, in mosses, which are representatives of the earliest land plants, 3D shoot growth is preceded by a 2D filamentous phase that can be maintained indefinitely. Here, we used the moss Physcomitrella patens to identify genetic regulators of the 2D to 3D transition. Mutant screens yielded individuals that could only grow in 2D, and through an innovative strategy that combined somatic hybridization with bulk segregant analysis and genome sequencing, the causative mutation was identified in one of them. The NO GAMETOPHORES 1 (NOG1) gene, which encodes a ubiquitin-associated protein, is present only in land plant genomes. In mutants that lack PpNOG1 function, transcripts encoding 3D-promoting PpAPB transcription factors [1] are significantly reduced, and apical initial cells specified for 3D growth are not formed. PpNOG1 acts at the earliest identified stage of the 2D to 3D transition, possibly through degradation of proteins that suppress 3D growth. The acquisition of NOG1 function in land plants could thus have enabled the evolution and development of 3D morphology. NO GAMETOPHORES 1 (PpNOG1) regulates the 2D to 3D growth transition in P. patens PpNOG1 acts upstream of 3D-promoting PpAPB transcription factors PpNOG1 is required for the formation of apical initial cells specified for 3D growth NOG1 genes are found only in land plants and thus evolved coincident with 3D growth
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK
| | - Ester Rabbinowitsch
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Rd., Oxford OX1 3RB, UK.
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30
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Histology versus phylogeny: Viewing plant embryogenesis from an evo-devo perspective. Curr Top Dev Biol 2019; 131:545-564. [DOI: 10.1016/bs.ctdb.2018.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Joo S, Wang MH, Lui G, Lee J, Barnas A, Kim E, Sudek S, Worden AZ, Lee JH. Common ancestry of heterodimerizing TALE homeobox transcription factors across Metazoa and Archaeplastida. BMC Biol 2018; 16:136. [PMID: 30396330 PMCID: PMC6219170 DOI: 10.1186/s12915-018-0605-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/25/2018] [Indexed: 12/22/2022] Open
Abstract
Background Complex multicellularity requires elaborate developmental mechanisms, often based on the versatility of heterodimeric transcription factor (TF) interactions. Homeobox TFs in the TALE superclass are deeply embedded in the gene regulatory networks that orchestrate embryogenesis. Knotted-like homeobox (KNOX) TFs, homologous to animal MEIS, have been found to drive the haploid-to-diploid transition in both unicellular green algae and land plants via heterodimerization with other TALE superclass TFs, demonstrating remarkable functional conservation of a developmental TF across lineages that diverged one billion years ago. Here, we sought to delineate whether TALE-TALE heterodimerization is ancestral to eukaryotes. Results We analyzed TALE endowment in the algal radiations of Archaeplastida, ancestral to land plants. Homeodomain phylogeny and bioinformatics analysis partitioned TALEs into two broad groups, KNOX and non-KNOX. Each group shares previously defined heterodimerization domains, plant KNOX-homology in the KNOX group and animal PBC-homology in the non-KNOX group, indicating their deep ancestry. Protein-protein interaction experiments showed that the TALEs in the two groups all participated in heterodimerization. Conclusions Our study indicates that the TF dyads consisting of KNOX/MEIS and PBC-containing TALEs must have evolved early in eukaryotic evolution. Based on our results, we hypothesize that in early eukaryotes, the TALE heterodimeric configuration provided transcription-on switches via dimerization-dependent subcellular localization, ensuring execution of the haploid-to-diploid transition only when the gamete fusion is correctly executed between appropriate partner gametes. The TALE switch then diversified in the several lineages that engage in a complex multicellular organization. Electronic supplementary material The online version of this article (10.1186/s12915-018-0605-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sunjoo Joo
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Ming Hsiu Wang
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Gary Lui
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Jenny Lee
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Andrew Barnas
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
| | - Eunsoo Kim
- Division of Invertebrate Zoology and Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY, 10024, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Rd, Moss Landing, CA, 95039, USA
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.
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32
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Kenrick P. Changing expressions: a hypothesis for the origin of the vascular plant life cycle. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170149. [PMID: 29254970 PMCID: PMC5745341 DOI: 10.1098/rstb.2017.0149] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 02/06/2023] Open
Abstract
Plant life cycles underwent fundamental changes during the initial colonization of the land in the Early Palaeozoic, shaping the direction of evolution. Fossils reveal unanticipated diversity, including new variants of meiotic cell division and leafless gametophytes with mycorrhizal-like symbioses, rhizoids, vascular tissues and stomata. Exceptional fossils from the 407-Ma Rhynie chert (Scotland) play a key role in unlocking this diversity. These fossils are reviewed against progress in our understanding of the plant tree of life and recent advances in developmental genetics. Combining data from different sources sheds light on a switch in life cycle that gave rise to the vascular plants. One crucial step was the establishment of a free-living sporophyte from one that was an obligate matrotroph borne on the gametophyte. It is proposed that this difficult evolutionary transition was achieved through expansion of gene expression primarily from the gametophyte to the sporophyte, establishing a now extinct life cycle variant that was more isomorphic than heteromorphic. These changes also linked for the first time in one developmental system rhizoids, vascular tissues and stomata, putting in place the critical components that regulate transpiration and forming a physiological platform of primary importance to the diversification of vascular plants.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- Paul Kenrick
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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Kramer EM, Kong H, Rausher MD. Plant evolutionary developmental biology. Introduction to a special issue. THE NEW PHYTOLOGIST 2017; 216:335-336. [PMID: 28921559 DOI: 10.1111/nph.14808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Affiliation(s)
- Elena M Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, NC, 27708-0338, USA
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Joo S, Nishimura Y, Cronmiller E, Hong RH, Kariyawasam T, Wang MH, Shao NC, El Akkad SED, Suzuki T, Higashiyama T, Jin E, Lee JH. Gene Regulatory Networks for the Haploid-to-Diploid Transition of Chlamydomonas reinhardtii. PLANT PHYSIOLOGY 2017; 175:314-332. [PMID: 28710131 PMCID: PMC5580766 DOI: 10.1104/pp.17.00731] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/12/2017] [Indexed: 05/20/2023]
Abstract
The sexual cycle of the unicellular Chlamydomonas reinhardtii culminates in the formation of diploid zygotes that differentiate into dormant spores that eventually undergo meiosis. Mating between gametes induces rapid cell wall shedding via the enzyme g-lysin; cell fusion is followed by heterodimerization of sex-specific homeobox transcription factors, GSM1 and GSP1, and initiation of zygote-specific gene expression. To investigate the genetic underpinnings of the zygote developmental pathway, we performed comparative transcriptome analysis of both pre- and post-fertilization samples. We identified 253 transcripts specifically enriched in early zygotes, 82% of which were not up-regulated in gsp1 null zygotes. We also found that the GSM1/GSP1 heterodimer negatively regulates the vegetative wall program at the posttranscriptional level, enabling prompt transition from vegetative wall to zygotic wall assembly. Annotation of the g-lysin-induced and early zygote genes reveals distinct vegetative and zygotic wall programs, supported by concerted up-regulation of genes encoding cell wall-modifying enzymes and proteins involved in nucleotide-sugar metabolism. The haploid-to-diploid transition in Chlamydomonas is masterfully controlled by the GSM1/GSP1 heterodimer, translating fertilization and gamete coalescence into a bona fide differentiation program. The fertilization-triggered integration of genes required to make related, but structurally and functionally distinct organelles-the vegetative versus zygote cell wall-presents a likely scenario for the evolution of complex developmental gene regulatory networks.
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Affiliation(s)
- Sunjoo Joo
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Yoshiki Nishimura
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-Shirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Evan Cronmiller
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Ran Ha Hong
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Thamali Kariyawasam
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Ming Hsiu Wang
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Nai Chun Shao
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Saif-El-Din El Akkad
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
| | - Takamasa Suzuki
- ERATO, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tetsuya Higashiyama
- ERATO, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Eonseon Jin
- Department Life Sciences, Research Institute for Natural Sciences, Hanyang University, 222 Wangsipri-ro, Sungdong-gu, Seoul 133-791, Republic of Korea
| | - Jae-Hyeok Lee
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T1Z4, Canada
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