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Zhou W, Liu J, Wang W, Li Y, Ma Z, He H, Wang X, Lian X, Dong X, Zhao X, Zhou Y. Molecular Mechanisms for Regulating Stomatal Formation across Diverse Plant Species. Int J Mol Sci 2024; 25:10403. [PMID: 39408731 PMCID: PMC11476680 DOI: 10.3390/ijms251910403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2024] [Revised: 09/20/2024] [Accepted: 09/24/2024] [Indexed: 10/20/2024] Open
Abstract
Plant stomata play a crucial role in photosynthesis by regulating transpiration and gas exchange. Meanwhile, environmental cues can also affect the formation of stomata. Stomatal formation, therefore, is optimized for the survival and growth of the plant despite variable environmental conditions. To adapt to environmental conditions, plants open and close stomatal pores and even regulate the number of stomata that develop on the epidermis. There are great differences in the leaf structure and developmental origin of the cell in the leaf between Arabidopsis and grass plants. These differences affect the fine regulation of stomatal formation due to different plant species. In this paper, a comprehensive overview of stomatal formation and the molecular networks and genetic mechanisms regulating the polar division and cell fate of stomatal progenitor cells in dicotyledonous plants such as Arabidopsis and Poaceae plants such as Oryza sativa and Zea mays is provided. The processes of stomatal formation mediated by plant hormones and environmental factors are summarized, and a model of stomatal formation in plants based on the regulation of multiple signaling pathways is outlined. These results contribute to a better understanding of the mechanisms of stomatal formation and epidermal morphogenesis in plants and provide a valuable theoretical basis and gene resources for improving crop resilience and yield traits.
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Affiliation(s)
- Wenqi Zhou
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
| | - Jieshan Liu
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenjin Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China;
| | - Yongsheng Li
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
| | - Zixu Ma
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Haijun He
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
| | - Xiaojuan Wang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
| | - Xiaorong Lian
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
| | - Xiaoyun Dong
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
| | - Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuqian Zhou
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China; (W.Z.); (J.L.); (Y.L.); (Z.M.); (H.H.); (X.W.); (X.L.); (X.D.)
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Xu C, Fan X, Shen G, Guo B. Genome-wide identification of the phenylalanine ammonia-lyase gene from Epimedium Pubescens Maxim. (Berberidaceae): novel insight into the evolution of the PAL gene family. BMC PLANT BIOLOGY 2024; 24:831. [PMID: 39232677 PMCID: PMC11373271 DOI: 10.1186/s12870-024-05480-z] [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: 01/09/2024] [Accepted: 08/01/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Phenylalanine ammonia-lyase (PAL) serves as a key gateway enzyme, bridging primary metabolism and the phenylpropanoid pathway, and thus playing an indispensable role in flavonoid, anthocyanin and lignin biosynthesis. PAL gene families have been extensively studied across species using public genomes. However, a comprehensive exploration of PAL genes in Epimedium species, especially those involved in prenylated flavonol glycoside, anthocyanin, or lignin biosynthesis, is still lacking. Moreover, an in-depth investigation into PAL gene family evolution is warranted. RESULTS Seven PAL genes (EpPAL1-EpPAL7) were identified. EpPAL2 and EpPAL3 exhibit low sequence identity to other EpPALs (ranging from 61.09 to 64.38%) and contain two unique introns, indicating distinct evolutionary origins. They evolve at a rate ~ 10 to ~ 54 times slower compared to EpPAL1 and EpPAL4-7, suggesting strong purifying selection. EpPAL1 evolved independently and is another ancestral gene. EpPAL1 formed EpPAL4 through segmental duplication, which lead to EpPAL5 and EpPAL6 through tandem duplications, and EpPAL7 through transposed duplication, shaping modern EpPALs. Correlation analysis suggests EpPAL1, EpPAL2 and EpPAL3 play important roles in prenylated flavonol glycosides biosynthesis, with EpPAL2 and EpPAL3 strongly correlated with both Epimedin C and total prenylated flavonol glycosides. EpPAL1, EpPAL2 and EpPAL3 may play a role in anthocyanin biosynthesis in leaves. EpPAL2, EpPAL3, EpPAL6, and EpPAL7 might be engaged in anthocyanin production in petals, and EpPAL2 and EpPAL3 might also contribute to anthocyanin synthesis in sepals. Further experiments are needed to confirm these hypotheses. Novel insights into the evolution of PAL gene family suggest that it might have evolved from a monophyletic group in bryophytes to large-scale sequence differentiation in gymnosperms, basal angiosperms, and Magnoliidae. Ancestral gene duplications and vertical inheritance from gymnosperms to angiosperms likely occurred during PAL evolution. Most early-diverging eudicotyledons and monocotyledons have distinct histories, while modern angiosperm PAL gene families share similar patterns and lack distant gene types. CONCLUSIONS EpPAL2 and EpPAL3 may play crucial roles in biosynthesis of prenylated flavonol glycosides and anthocyanins in leaves and flowers. This study provides novel insights into PAL gene family evolution. The findings on PAL genes in E. pubescens will aid in synthetic biology research on prenylated flavonol glycosides production.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China
| | - Xuelan Fan
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China
- College of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
| | - Guoan Shen
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China
| | - Baolin Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicines, Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, No.151 MaLianWa North Road, Haidian District, Beijing, 100193, China.
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Kean-Galeno T, Lopez-Arredondo D, Herrera-Estrella L. The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants. Int J Mol Sci 2024; 25:1519. [PMID: 38338798 PMCID: PMC10855264 DOI: 10.3390/ijms25031519] [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: 09/20/2023] [Revised: 11/27/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.
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Affiliation(s)
- Tania Kean-Galeno
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Damar Lopez-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
| | - Luis Herrera-Estrella
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Science Department, Texas Tech University, Lubbock, TX 79409, USA; (T.K.-G.); (D.L.-A.)
- Unidad de Genómica Avanzada/Langebio, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato 36821, Mexico
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Chen X, Yao C, Liu J, Liu J, Fang J, Deng H, Yao Q, Kang T, Guo X. Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC Genomics 2024; 25:67. [PMID: 38233751 PMCID: PMC10792839 DOI: 10.1186/s12864-023-09911-3] [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: 05/15/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.
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Affiliation(s)
- Xingyu Chen
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Caimei Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jiahao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jintao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jingmei Fang
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Hong Deng
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Qian Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Tairan Kang
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
| | - Xiaoqiang Guo
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China.
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Liang Y, Heyman J, Lu R, De Veylder L. Evolution of wound-activated regeneration pathways in the plant kingdom. Eur J Cell Biol 2023; 102:151291. [PMID: 36709604 DOI: 10.1016/j.ejcb.2023.151291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
Regeneration serves as a self-protective mechanism that allows a tissue or organ to recover its entire form and function after suffering damage. However, the regenerative capacity varies greatly within the plant kingdom. Primitive plants frequently display an amazing regenerative ability as they have developed a complex system and strategy for long-term survival under extreme stress conditions. The regenerative ability of dicot species is highly variable, but that of monocots often exhibits extreme recalcitrance to tissue replenishment. Recent studies have revealed key factors and signals that affect cell fate during plant regeneration, some of which are conserved among the plant lineage. Among these, several members of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors have been implicated in wound signaling, playing crucial roles in the regenerative mechanisms after different types of wounding. An understanding of plant regeneration may ultimately lead to an increased regenerative potential of recalcitrant species, producing more high-yielding, multi-resistant and environmentally friendly crops and ensuring the long-term development of global agriculture.
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Affiliation(s)
- Yuanke Liang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Jefri Heyman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Ran Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
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Suh DY, Ashton NW. A sporopollenin definition for the genomics age. THE NEW PHYTOLOGIST 2022; 236:2009-2013. [PMID: 36098674 DOI: 10.1111/nph.18484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Dae-Yeon Suh
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
| | - Neil W Ashton
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, S4S 0A2, Canada
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Chen S, Wang T, Shu J, Xiang Q, Yang T, Zhang X, Yan Y. Plastid Phylogenomics and Plastomic Diversity of the Extant Lycophytes. Genes (Basel) 2022; 13:genes13071280. [PMID: 35886063 PMCID: PMC9316050 DOI: 10.3390/genes13071280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Although extant lycophytes represent the most ancient surviving lineage of early vascular plants, their plastomic diversity has long been neglected. The ancient evolutionary history and distinct genetic diversity patterns of the three lycophyte families, each with its own characteristics, provide an ideal opportunity to investigate the interfamilial relationships of lycophytes and their associated patterns of evolution. To compensate for the lack of data on Lycopodiaceae, we sequenced and assembled 14 new plastid genomes (plastomes). Combined with other lycophyte plastomes available online, we reconstructed the phylogenetic relationships of the extant lycophytes based on 93 plastomes. We analyzed, traced, and compared the plastomic diversity and divergence of the three lycophyte families (Isoëtaceae, Lycopodiaceae, and Selaginellaceae) in terms of plastomic diversity by comparing their plastome sizes, GC contents, substitution rates, structural rearrangements, divergence times, ancestral states, RNA editings, and gene losses. Comparative analysis of plastid phylogenomics and plastomic diversity of three lycophyte families will set a foundation for further studies in biology and evolution in lycophytes and therefore in vascular plants.
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Affiliation(s)
- Sisi Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- College of Biodiversity Conservation, Southwest Forestry University, Kunming 650224, China
| | - Jiangping Shu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qiaoping Xiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
| | - Tuo Yang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
| | - Xianchun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China;
- Correspondence: (X.Z.); (Y.Y.)
| | - Yuehong Yan
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China; (S.C.); (T.W.); (J.S.); (T.Y.)
- Correspondence: (X.Z.); (Y.Y.)
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Naramoto S, Hata Y, Fujita T, Kyozuka J. The bryophytes Physcomitrium patens and Marchantia polymorpha as model systems for studying evolutionary cell and developmental biology in plants. THE PLANT CELL 2022; 34:228-246. [PMID: 34459922 PMCID: PMC8773975 DOI: 10.1093/plcell/koab218] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/25/2021] [Indexed: 05/03/2023]
Abstract
Bryophytes are nonvascular spore-forming plants. Unlike in flowering plants, the gametophyte (haploid) generation of bryophytes dominates the sporophyte (diploid) generation. A comparison of bryophytes with flowering plants allows us to answer some fundamental questions raised in evolutionary cell and developmental biology. The moss Physcomitrium patens was the first bryophyte with a sequenced genome. Many cell and developmental studies have been conducted in this species using gene targeting by homologous recombination. The liverwort Marchantia polymorpha has recently emerged as an excellent model system with low genomic redundancy in most of its regulatory pathways. With the development of molecular genetic tools such as efficient genome editing, both P. patens and M. polymorpha have provided many valuable insights. Here, we review these advances with a special focus on polarity formation at the cell and tissue levels. We examine current knowledge regarding the cellular mechanisms of polarized cell elongation and cell division, including symmetric and asymmetric cell division. We also examine the role of polar auxin transport in mosses and liverworts. Finally, we discuss the future of evolutionary cell and developmental biological studies in plants.
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Affiliation(s)
| | - Yuki Hata
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Tomomichi Fujita
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
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Hata Y, Kyozuka J. Fundamental mechanisms of the stem cell regulation in land plants: lesson from shoot apical cells in bryophytes. PLANT MOLECULAR BIOLOGY 2021; 107:213-225. [PMID: 33609252 PMCID: PMC8648652 DOI: 10.1007/s11103-021-01126-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/01/2021] [Indexed: 05/02/2023]
Abstract
This review compares the molecular mechanisms of stem cell control in the shoot apical meristems of mosses and angiosperms and reveals the conserved features and evolution of plant stem cells. The establishment and maintenance of pluripotent stem cells in the shoot apical meristem (SAM) are key developmental processes in land plants including the most basal, bryophytes. Bryophytes, such as Physcomitrium (Physcomitrella) patens and Marchantia polymorpha, are emerging as attractive model species to study the conserved features and evolutionary processes in the mechanisms controlling stem cells. Recent studies using these model bryophyte species have started to uncover the similarities and differences in stem cell regulation between bryophytes and angiosperms. In this review, we summarize findings on stem cell function and its regulation focusing on different aspects including hormonal, genetic, and epigenetic control. Stem cell regulation through auxin, cytokinin, CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) signaling and chromatin modification by Polycomb Repressive Complex 2 (PRC2) and PRC1 is well conserved. Several transcription factors crucial for SAM regulation in angiosperms are not involved in the regulation of the SAM in mosses, but similarities also exist. These findings provide insights into the evolutionary trajectory of the SAM and the fundamental mechanisms involved in stem cell regulation that are conserved across land plants.
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Affiliation(s)
- Yuki Hata
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan.
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10
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Phipps S, Delwiche CF, Bisson MA. Salinity-induced Changes in Gene Expression in the Streptophyte Alga Chara: The Critical Role of a Rare Na + -ATPase. JOURNAL OF PHYCOLOGY 2021; 57:1004-1013. [PMID: 33713364 DOI: 10.1111/jpy.13166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
The primarily freshwater genus Chara is comprised of many species that exhibit a wide range of salinity tolerance. The range of salt tolerance provides a good platform for investigating the role of transport mechanisms in response to salt stress, and the close evolutionary relationship between Charophytes and land plants can provide broader insights. We investigated the response to salt stress of previously identified transport mechanisms in two species of Chara, Chara longifolia (salt-tolerant), and Chara australis (salt-sensitive): a cation transporter (HKT), a Na+ /H+ antiport (NHX), H+ -ATPase (AHA), and a Na+ -ATPase (ENA). The presence of these candidate genes has been confirmed in both species of Chara, with the exception of the Na+ -ATPase, which is present only in salt-tolerant Chara longifolia. Time-course Illumina transcriptomes were created using RNA from multiple time points (0, 6, 12, 24 and 48 h) after freshwater cultures for each species were exposed to salt stress. These transcriptomes verified our hypotheses of these mechanisms conferring salt tolerance in the two species examined and also aided in identification of specific transcripts representing our genes of interest in both species. The expression of these transcripts was validated through use of qPCR, in a similar experimental set-up used for the RNAseq data described above. The RNAseq and qPCR data showed significant changes of expression mechanisms in C. longifolia (respectively), a down-regulation of HKT and a substantial up-regulation of ENA. Significant responses to salt stress in salt-sensitive C. australis show up-regulation of NHX and AHA.
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Affiliation(s)
- Shaunna Phipps
- Department of Environment & Sustainability, State University at Buffalo, Buffalo, New York, USA
- Department of Biological Sciences, State University at Buffalo, Buffalo, New York, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Mary A Bisson
- Department of Environment & Sustainability, State University at Buffalo, Buffalo, New York, USA
- Department of Biological Sciences, State University at Buffalo, Buffalo, New York, USA
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Seguí-Simarro JM, Jacquier NMA, Widiez T. Overview of In Vitro and In Vivo Doubled Haploid Technologies. Methods Mol Biol 2021; 2287:3-22. [PMID: 34270023 DOI: 10.1007/978-1-0716-1315-3_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Doubled haploids (DH) have become a powerful tool to assist in different basic research studies, and also in applied research. The principal (but not the only) and routine use of DH by breeding companies is to produce pure lines for hybrid seed production in different crop species. Several decades after the discovery of haploid inducer lines in maize and of anther culture as a method to produce haploid plants from pollen precursors, the biotechnological revolution of the last decades allowed to the development of a variety of approaches to pursue the goal of doubled haploid production. Now, it is possible to produce haploids and DHs in many different species, because when a method does not work properly, there are several others to test. In this chapter, we overview the currently available approaches used to produce haploids and DHs by using methods based on in vitro culture, or involving the in vivo induction of haploid embryo development, or a combination of both.
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Affiliation(s)
- Jose M Seguí-Simarro
- Cell Biology Group, Ciudad Politécnica de la Innovación (CPI), COMAV Institute - Universitat Politècnica de València, Valencia, Spain.
| | - Nathanaël M A Jacquier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.,Limagrain, Limagrain Field Seeds, Research Center, Gerzat, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France
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Kumpeangkeaw A, Tan D, Fu L, Han B, Sun X, Hu X, Ding Z, Zhang J. Asymmetric birth and death of type I and type II MADS-box gene subfamilies in the rubber tree facilitating laticifer development. PLoS One 2019; 14:e0214335. [PMID: 30934009 PMCID: PMC6443149 DOI: 10.1371/journal.pone.0214335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 03/11/2019] [Indexed: 01/13/2023] Open
Abstract
The rubber tree (Hevea brasiliensis Muell. Arg.) is a rubber producing crop and contains specialized laticifers. MADS-box genes are a family of transcription factor genes that regulate plant development, especially floral organ and gametophyte development. 97 MADS-box genes were identified in the rubber tree through transcriptomes and genome mining. 93.8% of the genes were mapped onto the genome scaffolds in correspondence to the coverage (93.8%) of current version of sequenced genome. Phylogenetic analysis indicates that type II MADS-box genes have been more actively duplicated than their orthologous genes in Arabidopsis and rice, so that most (70, 72.2%) of the MADS-box genes in the rubber tree belong to type II subfamily. This is a high percentage compared to those in Arabidopsis (43.7%) and rice (56.8%). Moreover, 69 out of 70 type II genes in the rubber tree are transcribed, and they are mostly predominantly expressed in flowers, but some genes are predominantly expressed in laticifers, suggesting their roles in both flower and laticifer development. The number of type I genes in the rubber tree is only 27 (27.8%), a much smaller number compared to their orthologous genes in Arabidopsis (56.3%) and rice (43.2%). At the same time, most of the type I genes (55.6%, 15) in the rubber tree are silent and are probably pseudogenes. The high birth rate and low death rate of type II genes and low birth rate and high death rate of type I genes may corresponds to special developmental requirements in the rubber tree, e.g. the development of laticifer system for biosynthesis of cis-polyisoprene, the rubber. Moreover, atypical MIKC* factors (e.g. HbMADS1 in S-clade, and HbMADS20 in P-clade) are identified. These genes are diverged to typical MIKC* genes in sequences and facilitate functions required in laticifer development and rubber biosynthesis, which is not necessary in Arabidopsis and rice.
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Affiliation(s)
- Anuwat Kumpeangkeaw
- International College, Huazhong Agricultural University, Lion Mountain, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
- Song Khla Rubber Research Centre, Department of Agriculture, Ministry of Agriculture and Cooperatives, Had Yai, Song Khla, Thailand
| | - Deguan Tan
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Lili Fu
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Bingying Han
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Xuepiao Sun
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Xiaowen Hu
- Zhanjiang Experimental Station, CATAS, Zhanjiang, Guangdong Province, China
| | - Zehong Ding
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
| | - Jiaming Zhang
- Institute of Tropical Bioscience and Biotechnology, MOA Key Laboratory of Tropical Crops Biology and Genetic Resources, Hainan Bioenergy Center, CATAS, Haikou, Hainan Province, China
- * E-mail:
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Sigel EM, Schuettpelz E, Pryer KM, Der JP. Overlapping Patterns of Gene Expression Between Gametophyte and Sporophyte Phases in the Fern Polypodium amorphum (Polypodiales). FRONTIERS IN PLANT SCIENCE 2018; 9:1450. [PMID: 30356815 PMCID: PMC6190754 DOI: 10.3389/fpls.2018.01450] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
Ferns are unique among land plants in having sporophyte and gametophyte phases that are both free living and fully independent. Here, we examine patterns of sporophytic and gametophytic gene expression in the fern Polypodium amorphum, a member of the homosporous polypod lineage that comprises 80% of extant fern diversity, to assess how expression of a common genome is partitioned between two morphologically, ecologically, and nutritionally independent phases. Using RNA-sequencing, we generated transcriptome profiles for three replicates of paired samples of sporophyte leaf tissue and whole gametophytes to identify genes with significant differences in expression between the two phases. We found a nearly 90% overlap in the identity and expression levels of the genes expressed in both sporophytes and gametophytes, with less than 3% of genes uniquely expressed in either phase. We compare our results to those from similar studies to establish how phase-specific gene expression varies among major land plant lineages. Notably, despite having greater similarity in the identity of gene families shared between P. amorphum and angiosperms, P. amorphum has phase-specific gene expression profiles that are more like bryophytes and lycophytes than seed plants. Our findings suggest that shared patterns of phase-specific gene expression among seed-free plants likely reflect having relatively large, photosynthetic gametophytes (compared to the gametophytes of seed plants that are highly reduced). Phylogenetic analyses were used to further investigate the evolution of phase-specific expression for the phototropin, terpene synthase, and MADS-box gene families.
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Affiliation(s)
- Erin M. Sigel
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | | | - Joshua P. Der
- Department of Biological Science, California State University Fullerton, Fullerton, CA, United States
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Liu W, Xu L. Recruitment of IC-WOX Genes in Root Evolution. TRENDS IN PLANT SCIENCE 2018; 23:490-496. [PMID: 29680635 DOI: 10.1016/j.tplants.2018.03.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/09/2018] [Accepted: 03/20/2018] [Indexed: 05/25/2023]
Abstract
Root evolution has resulted in the extant bifurcating roots in lycophytes, adventitious/lateral roots in euphyllophytes (ferns and seed plants), and primary roots in seed plants. Here, we hypothesize a role for intermediate-clade-WUSCHEL-RELATED HOMEOBOX (IC-WOX) genes in root evolution. IC-WOX might not be specifically involved in lycophyte bifurcation rooting. In the fern Ceratopteris richardii, IC-WOX is expressed in adventitious/lateral root founder cells. In the seed plant Arabidopsis thaliana, there are two IC-WOX subclades, AtWOX11/12 and AtWOX8/9, in adventitious and primary root founder cells, respectively. Thus, IC-WOX was recruited in the common ancestor of ferns and seed plants for adventitious/lateral root organogenesis and evolved into two subclades in seed plants: one was retained in adventitious root organogenesis, while the other was recruited for primary root organogenesis.
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Affiliation(s)
- Wu Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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The calmodulin fused kinase novel gene family is the major system in plants converting Ca 2+ signals to protein phosphorylation responses. Sci Rep 2017. [PMID: 28646145 PMCID: PMC5482843 DOI: 10.1038/s41598-017-03367-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Eukaryotes utilize Ca2+ as a universal second messenger to convert and multiply environmental and developmental signals to downstream protein phosphorylation responses. However, the phylogenetic relationships of the genes that convert Ca2+ signal (CS) to protein phosphorylation responses (PPRs) remain highly controversial, and their origin and evolutionary trajectory are unclear, which greatly hinders functional studies. Here we examined the deep phylogeny of eukaryotic CS converter gene families and identified a phylogenetically and structurally distinctive monophyly in Archaeplastida. This monophyly can be divided into four subfamilies, and each can be traced to ancestral members that contain a kinase domain and a calmodulin-like domain. This strongly indicates that the ancestor of this monophyly originated by a de novo fusion of a kinase gene and a calmodulin gene. This gene family, with a proposed new name, Calmodulin Fused Kinase (CFK), had expanded and diverged significantly both in sizes and in structures for efficient and accurate Ca2+ signalling, and was shown to play pivotal roles in all the six major plant adaptation events in evolution. Our findings elucidated the common origin of all CS-PPR converter genes except CBL-CIPK converter genes, and revealed that CFKs act as the main CS conversion system in plants.
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Jill Harrison C. Development and genetics in the evolution of land plant body plans. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150490. [PMID: 27994131 PMCID: PMC5182422 DOI: 10.1098/rstb.2015.0490] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2016] [Indexed: 12/22/2022] Open
Abstract
The colonization of land by plants shaped the terrestrial biosphere, the geosphere and global climates. The nature of morphological and molecular innovation driving land plant evolution has been an enigma for over 200 years. Recent phylogenetic and palaeobotanical advances jointly demonstrate that land plants evolved from freshwater algae and pinpoint key morphological innovations in plant evolution. In the haploid gametophyte phase of the plant life cycle, these include the innovation of mulitcellular forms with apical growth and multiple growth axes. In the diploid phase of the life cycle, multicellular axial sporophytes were an early innovation priming subsequent diversification of indeterminate branched forms with leaves and roots. Reverse and forward genetic approaches in newly emerging model systems are starting to identify the genetic basis of such innovations. The data place plant evo-devo research at the cusp of discovering the developmental and genetic changes driving the radiation of land plant body plans.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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17
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Ishizaki K. Evolution of land plants: insights from molecular studies on basal lineages. Biosci Biotechnol Biochem 2017; 81:73-80. [DOI: 10.1080/09168451.2016.1224641] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Abstract
The invasion of the land by plants, or terrestrialization, was one of the most critical events in the history of the Earth. The evolution of land plants included significant transformations in body plans: the emergence of a multicellular diploid sporophyte, transition from gametophyte-dominant to sporophyte-dominant life histories, and development of many specialized tissues and organs, such as stomata, vascular tissues, roots, leaves, seeds, and flowers. Recent advances in molecular genetics in two model basal plants, bryophytes Physcomitrella patens and Marchantia polymorpha, have begun to provide answers to several key questions regarding land plant evolution. This paper discusses the evolution of the genes and regulatory mechanisms that helped drive such significant morphological innovations among land-based plants.
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Affiliation(s)
- Kimitsune Ishizaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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18
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Stem cell lineage in body layer specialization and vascular patterning of rice root and leaf. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-015-0849-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Rose JP, Kriebel R, Sytsma KJ. Shape analysis of moss (Bryophyta) sporophytes: Insights into land plant evolution. AMERICAN JOURNAL OF BOTANY 2016; 103:652-62. [PMID: 26944353 DOI: 10.3732/ajb.1500394] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/08/2016] [Indexed: 05/05/2023]
Abstract
PREMISE OF THE STUDY The alternation of generations life cycle represents a key feature of land-plant evolution and has resulted in a diverse array of sporophyte forms and modifications in all groups of land plants. We test the hypothesis that evolution of sporangium (capsule) shape of the mosses-the second most diverse land-plant lineage-has been driven by differing physiological demands of life in diverse habitats. This study provides an important conceptual framework for analyzing the evolution of a single, homologous character in a continuous framework across a deep expanse of time, across all branches of the tree of life. METHODS We reconstruct ancestral sporangium shape and ancestral habitat on the largest phylogeny of mosses to date, and use phylogenetic generalized least squares regression to test the association between habitat and sporangium shape. In addition, we examine the association between shifts in sporangium shape and species diversification. RESULTS We demonstrate that sporangium shape is convergent, under natural selection, and associated with habitat type, and that many shifts in speciation rate are associated with shifts in sporangium shape. CONCLUSIONS Our results suggest that natural selection in different microhabitats results in the diversity of sporangium shape found in mosses, and that many increasing shifts in speciation rate result in changes in sporangium shape across their 480 million year history. Our framework provides a way to examine if diversification shifts in other land plants are also associated with massive changes in sporophyte form, among other morphological traits.
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Affiliation(s)
- Jeffrey P Rose
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706.
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin 53706
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Harholt J, Moestrup Ø, Ulvskov P. Why Plants Were Terrestrial from the Beginning. TRENDS IN PLANT SCIENCE 2016; 21:96-101. [PMID: 26706443 DOI: 10.1016/j.tplants.2015.11.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 09/27/2015] [Accepted: 11/13/2015] [Indexed: 05/21/2023]
Abstract
The current hypothesis is that land plants originated from a charophycean green alga and that a prominent feature for adaptation to land was their development of alternating life cycles. Our work on cell wall evolution and morphological and physiological observations in the charophycean green algae challenged us to reassess how land plants became terrestrial. Our hypothesis is simple in that the charophycean green algae ancestors were already living on land and had been doing so for some time before the emergence of land plants. The evolution of alternate life cycles merely made the ancestral land plants evolutionary successful and had nothing to do with terrestrialization per se.
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Affiliation(s)
| | - Øjvind Moestrup
- Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark.
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Ge Y, Liu J, Zeng M, He J, Qin P, Huang H, Xu L. Identification of WOX Family Genes in Selaginella kraussiana for Studies on Stem Cells and Regeneration in Lycophytes. FRONTIERS IN PLANT SCIENCE 2016; 7:93. [PMID: 26904063 PMCID: PMC4742569 DOI: 10.3389/fpls.2016.00093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/18/2016] [Indexed: 05/02/2023]
Abstract
Plant stem cells give rise to all tissues and organs and also serve as the source for plant regeneration. The organization of plant stem cells has undergone a progressive change from simple to complex during the evolution of vascular plants. Most studies on plant stem cells have focused on model angiosperms, the most recently diverged branch of vascular plants. However, our knowledge of stem cell function in other vascular plants is limited. Lycophytes and euphyllophytes (ferns, gymnosperms, and angiosperms) are two existing branches of vascular plants that separated more than 400 million years ago. Lycophytes retain many of the features of early vascular plants. Based on genome and transcriptome data, we identified WUSCHEL-RELATED HOMEOBOX (WOX) genes in Selaginella kraussiana, a model lycophyte that is convenient for in vitro culture and observations of organ formation and regeneration. WOX genes are key players controlling stem cells in plants. Our results showed that the S. kraussiana genome encodes at least eight members of the WOX family, which represent an early stage of WOX family evolution. Identification of WOX genes in S. kraussiana could be a useful tool for molecular studies on the function of stem cells in lycophytes.
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Affiliation(s)
- Yachao Ge
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Jie Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Minhuan Zeng
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Jianfeng He
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Peng Qin
- Department of Instrumentation Science and Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Hai Huang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Lin Xu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Lin Xu,
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Singh H, Rai KM, Upadhyay SK, Pant P, Verma PC, Singh AP, Singh PK. Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery. Sci Rep 2015; 5:15350. [PMID: 26481431 PMCID: PMC4611483 DOI: 10.1038/srep15350] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/22/2015] [Indexed: 12/26/2022] Open
Abstract
Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using 454 pyrosequencer. De novo assembly of reads yielded 85,240 unigenes (12,439 contigs and 72,801 singletons). BlastX search at NCBI-NR database showed similarity of 33,662 unigenes with 10-(10) e-value. A total of 23,685 unigenes were annotated at TAIR10 protein database. The annotated unigenes were further classified using the Gene Ontology. Analysis at Kyoto Encyclopedia of Genes and Genomes pathway database identified 95 pathways with significant scores, among which metabolic and biosynthesis of secondary metabolite were the major ones. Phenylpropanoid pathway was elucidated and selected genes were characterized by real time qPCR. We identified 447 transcription factors belonging to 41 families and 1594 eSSRs in 1479 unigenes. D. hirsuta unigenes showed homology across the taxa from algae to angiosperm indicating their role as the connecting link between aquatic and terrestrial plants. This could be a valuable genomic resource for molecular and evolutionary studies. Further, it sheds light for the isolation and characterization of new genes with unique functions.
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Affiliation(s)
- Harpal Singh
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, UP, India
| | - Krishan Mohan Rai
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, UP, India
| | | | - Poonam Pant
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, UP, India
| | - Praveen Chandra Verma
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, UP, India
| | - Ajit Pratap Singh
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, UP, India
| | - Pradhyumna Kumar Singh
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research, Rana Pratap Marg, Lucknow 226001, UP, India
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Domozych DS, Domozych CE. Multicellularity in green algae: upsizing in a walled complex. FRONTIERS IN PLANT SCIENCE 2014; 5:649. [PMID: 25477895 PMCID: PMC4235416 DOI: 10.3389/fpls.2014.00649] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 09/03/2014] [Indexed: 05/09/2023]
Abstract
Modern green algae constitute a large and diverse taxonomic assemblage that encompasses many multicellular phenotypes including colonial, filamentous, and parenchymatous forms. In all multicellular green algae, each cell is surrounded by an extracellular matrix (ECM), most often in the form of a cell wall. Volvocalean taxa like Volvox have an elaborate, gel-like, hydroxyproline rich glycoprotein covering that contains the cells of the colony. In "ulvophytes," uronic acid-rich and sulfated polysaccharides are the likely adhesion agents that maintain the multicellular habit. Charophytes also produce polysaccharide-rich cell walls and in late divergent taxa, pectin plays a critical role in cell adhesion in the multicellular complex. Cell walls are products of coordinated interaction of membrane trafficking, cytoskeletal dynamics and the cell's signal transduction machinery responding both to precise internal clocks and external environmental cues. Most often, these activities must be synchronized with the secretion, deposition and remodeling of the polymers of the ECM. Rapid advances in molecular genetics, cell biology and cell wall biochemistry of green algae will soon provide new insights into the evolution and subcellular processes leading to multicellularity.
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Affiliation(s)
- David S. Domozych
- Skidmore Microscopy Imaging Center, Department of Biology, Skidmore College, Saratoga SpringsNY, USA
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García AN, Ayub ND, Fox AR, Gómez MC, Diéguez MJ, Pagano EM, Berini CA, Muschietti JP, Soto G. Alfalfa snakin-1 prevents fungal colonization and probably coevolved with rhizobia. BMC PLANT BIOLOGY 2014; 14:248. [PMID: 25227589 PMCID: PMC4177055 DOI: 10.1186/s12870-014-0248-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/11/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND The production of antimicrobial peptides is a common defense strategy of living cells against a wide range of pathogens. Plant snakin peptides inhibit bacterial and fungal growth at extremely low concentrations. However, little is known of their molecular and ecological characteristics, including origin, evolutionary equivalence, specific functions and activity against beneficial microbes. The aim of this study was to identify and characterize snakin-1 from alfalfa (MsSN1). RESULTS Phylogenetic analysis showed complete congruence between snakin-1 and plant trees. The antimicrobial activity of MsSN1 against bacterial and fungal pathogens of alfalfa was demonstrated in vitro and in vivo. Transgenic alfalfa overexpressing MsSN1 showed increased antimicrobial activity against virulent fungal strains. However, MsSN1 did not affect nitrogen-fixing bacterial strains only when these had an alfalfa origin. CONCLUSIONS The results reported here suggest that snakin peptides have important and ancestral roles in land plant innate immunity. Our data indicate a coevolutionary process, in which alfalfa exerts a selection pressure for resistance to MsSN1 on rhizobial bacteria. The increased antimicrobial activity against virulent fungal strains without altering the nitrogen-fixing symbiosis observed in MsSN1-overexpressing alfalfa transgenic plants opens the way to the production of effective legume transgenic cultivars for biotic stress resistance.
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Affiliation(s)
- Araceli Nora García
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
| | - Nicolás Daniel Ayub
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
| | - Ana Romina Fox
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
| | - María Cristina Gómez
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
| | - María José Diéguez
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
| | - Elba María Pagano
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
| | - Carolina Andrea Berini
- />Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), UBA-CONICET, Paraguay 2155, C1121ABG Ciudad Autónoma de Buenos Aires, Argentina
| | - Jorge Prometeo Muschietti
- />Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Pabellón II, C1428EGA Ciudad Autónoma de Buenos Aires, Argentina
- />Instituto de Investigaciones en Ingeniería Genética y Biología Molecular, “Dr. Hector Torres”, (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriela Soto
- />Instituto de Genética Ewald A. Favret (CICVyA-INTA), De los Reseros S/N, Castelar, C25 (1712) Buenos Aires Argentina
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Golokhvast KS, Seryodkin IV, Chaika VV, Zakharenko AM, Pamirsky IE. Phytoliths in taxonomy of phylogenetic domains of plants. BIOMED RESEARCH INTERNATIONAL 2014; 2014:648326. [PMID: 25243171 PMCID: PMC4163427 DOI: 10.1155/2014/648326] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/03/2014] [Indexed: 11/25/2022]
Abstract
We discuss, from the aspect of phylogeny, the interrelationships of the phytolith types in plants from the main taxonomical groups (algae, lichens, horsetails, gymnosperms, and floral plants) with homologues of known proteins of biomineralization. Phytolith morphotypes in various phylogenetic plant domains have different shapes. We found that, in ancient types of plants (algae, horsetails, and gymnosperms), there are fewer different phytolith morphotypes compared to more modern plants (floral plants). The phytolith morphotypes in primitive plants are generally larger than the morphotypes in more highly organized plants. We found that the irregular ruminate and irregular smooth morphotypes are the two most frequently encountered phytolith morphotypes in the tested plants (from algae to floral plants). These two morphotypes probably have a universal role. Silacidins, silicon transporters, silicateins, silaffins, and silicase homologues are often found in the major taxonomic groups of plants. Red algae had the smallest number of homologues of the biomineralization proteins (70-80), Monocotyledonous: 142, Coniferous: 166, Mosses: 227, and Dicotyledones: 336.
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Affiliation(s)
- Kirill S. Golokhvast
- Scientific Educational Center of Nanotechnology, Far Eastern Federal University, 10 Pushkinskaya Street, Vladivostok 690990, Russia
| | - Ivan V. Seryodkin
- Laboratory of Ecology and Protection Animals, Pacific Institute of Geography FEB RAS, 7 Radio Street, Vladivostok 690041, Russia
| | - Vladimir V. Chaika
- Scientific Educational Center of Nanotechnology, Far Eastern Federal University, 10 Pushkinskaya Street, Vladivostok 690990, Russia
| | - Alexander M. Zakharenko
- Laboratory of Enzyme Chemistry, Pacific Institute of Bioorganic Chemistry FEB RAS, 159 Prospect 100 Let Vladivostoku, Vladivostok 690022, Russia
| | - Igor E. Pamirsky
- Laboratory of Molecular Biology, Blagoveshchensk State Pedagogical University, 104 Lenina Street, Blagoveshchensk 675000, Russia
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O’Donoghue MT, Chater C, Wallace S, Gray JE, Beerling DJ, Fleming AJ. Genome-wide transcriptomic analysis of the sporophyte of the moss Physcomitrella patens. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:3567-81. [PMID: 23888066 PMCID: PMC3745722 DOI: 10.1093/jxb/ert190] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Bryophytes, the most basal of the extant land plants, diverged at least 450 million years ago. A major feature of these plants is the biphasic alternation of generations between a dominant haploid gametophyte and a minor diploid sporophyte phase. These dramatic differences in form and function occur in a constant genetic background, raising the question of whether the switch from gametophyte-to-sporophyte development reflects major changes in the spectrum of genes being expressed or alternatively whether only limited changes in gene expression occur and the differences in plant form are due to differences in how the gene products are put together. This study performed replicated microarray analyses of RNA from several thousand dissected and developmentally staged sporophytes of the moss Physcomitrella patens, allowing analysis of the transcriptomes of the sporophyte and early gametophyte, as well as the early stages of moss sporophyte development. The data indicate that more significant changes in transcript profile occur during the switch from gametophyte to sporophyte than recently reported, with over 12% of the entire transcriptome of P. patens being altered during this major developmental transition. Analysis of the types of genes contributing to these differences supports the view of the early sporophyte being energetically and nutritionally dependent on the gametophyte, provides a profile of homologues to genes involved in angiosperm stomatal development and physiology which suggests a deeply conserved mechanism of stomatal control, and identifies a novel series of transcription factors associated with moss sporophyte development.
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Affiliation(s)
| | - Caspar Chater
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Simon Wallace
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Julie E. Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - David J. Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Andrew J. Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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