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Abstract
The liverwort Marchantia polymorpha has been known to man for millennia due to its inclusion Greek herbals. Perhaps due to its familiarity and association with growth in, often, man-made disturbed habitats, it was readily used to address fundamental biological questions of the day, including elucidation of land plant life cycles in the late 18th century, the formulation of cell theory early in the 19th century and the discovery of the alternation of generations in land plants in the mid-19th century. Subsequently, Marchantia was used as model in botany classes. With the arrival of the molecular era, its organellar genomes, the chloroplast and mitochondrial, were some of the first to be sequenced from any plant. In the past two decades, molecular genetic tools have been applied such that genes may be manipulated seemingly at will. Here, are past, present, and some views to the future of Marchantia as a model.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
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2
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Abstract
Computers are able to systematically exploit RNA-seq data allowing us to efficiently detect RNA editing sites in a genome-wide scale. This chapter introduces a very flexible computational framework for detecting RNA editing sites in plant organelles. This framework comprises three major steps: RNA-seq data processing, RNA read alignment, and RNA editing site detection. Each step is discussed in sufficient detail to be implemented by the reader. As a study case, the framework will be used with publicly available sequencing data to detect C-to-U RNA editing sites in the coding sequences of the mitochondrial genome of Nicotiana tabacum.
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Affiliation(s)
- Alejandro A Edera
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown, Argentina.
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
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3
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Moody LA. Three-dimensional growth: a developmental innovation that facilitated plant terrestrialization. J Plant Res 2020; 133:283-290. [PMID: 32095969 PMCID: PMC7214384 DOI: 10.1007/s10265-020-01173-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/11/2020] [Indexed: 05/18/2023]
Abstract
One of the most transformative events in the history of life on earth was the transition of plants from water to land approximately 470 million years ago. Within the Charophyte green algae, the closest living relatives of land plants, body plans have evolved from those that comprise simple unicells to those that are morphologically complex, large and multicellular. The Charophytes developed these broad ranging body plans by exploiting a range of one-dimensional and two-dimensional growth strategies to produce filaments, mats and branches. When plants were confronted with harsh conditions on land, they were required to make significant changes to the way they shaped their body plans. One of the fundamental developmental transitions that occurred was the evolution of three-dimensional growth and the acquisition of apical cells with three or more cutting faces. Plants subsequently developed a range of morphological adaptations (e.g. vasculature, roots, flowers, seeds) that enabled them to colonise progressively drier environments. 3D apical growth also evolved convergently in the brown algae, completely independently of the green lineage. This review summarises the evolving developmental complexities observed in the early divergent Charophytes all the way through to the earliest conquerors of land, and investigates 3D apical growth in the brown algae.
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Affiliation(s)
- Laura A Moody
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Kondou Y, Miyagi Y, Morito T, Fujihira K, Miyauchi W, Moriyama A, Terasawa T, Ishida S, Iwabuchi K, Kubo H, Nishihama R, Ishizaki K, Kohchi T. Physiological function of photoreceptor UVR8 in UV-B tolerance in the liverwort Marchantia polymorpha. Planta 2019; 249:1349-1364. [PMID: 30840176 DOI: 10.1007/s00425-019-03090-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/04/2019] [Indexed: 05/08/2023]
Abstract
The physiological importance of MpUVR8 in UV-B resistance and translocation in a UV-B-dependent manner from the cytosol into the nucleus is characterized in Marchantia polymorpha. UV RESISTANCE LOCUS 8 (UVR8) is an ultraviolet-B (UV-B) light receptor functioning for UV-B sensing and tolerance in Arabidopsis thaliana and other species. It is unclear whether UVR8 physiologically functions in UV-B-induced defense responses in Marchantia polymorpha, which belongs to the earliest diverging group of embryophyte lineages. Here, we demonstrate that UVR8 has a physiological function in UV-B tolerance and that there is a UVR8-dependent pathway involved. In addition, a UVR8-independent pathway is revealed. We examine the tissue-specific expression pattern of M. polymorpha UVR8 (MpUVR8), showing that it is highly expressed in the apical notch in thalli and gametangiophores, as well as in antheridial and archegonial heads. Furthermore, Mpuvr8KO plant transformants, in which the MpUVR8 locus was disrupted, were produced and analyzed to understand the physiological and molecular function of MpUVR8. Analysis using these plants indicates the important roles of MpUVR8 and MpUVR8-regulated genes, and of MpUVR8-independent pathways in UV-B tolerance. Subcellular localization of Citrine-fused MpUVR8 in M. polymorpha cells was also investigated. It was found to translocate from the cytosol into the nucleus in response to UV-B irradiation. Our findings indicate strong conservation of the physiological function of UVR8 and the molecular mechanisms for UVR8-dependent signal transduction through regulation of gene expression in embryophytes.
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Affiliation(s)
- Youichi Kondou
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan.
| | - Yuta Miyagi
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Takeshi Morito
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Kenta Fujihira
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Wataru Miyauchi
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Asami Moriyama
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Takuya Terasawa
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Sakiko Ishida
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Kosei Iwabuchi
- Faculty of Science and Engineering, Konan University, Kobe, 658-8501, Japan
| | - Hiroyoshi Kubo
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto, 390-8621, Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | | | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
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Abstract
BACKGROUND Lateral Organ Boundaries Domain (LBD) genes arise from charophyte algae and evolve essential functions in land plants in regulating organ development and secondary metabolism. Although diverse plant species have been investigated to construct the phylogeny of LBD gene family, a detailed and reliable ancestry that characterizes their evolutionary patterns has not been revealed. RESULTS We develop an improved bioinformatic method that allows robust detection of 431 LBD genes in 11 high-quality land plant genomes. Phylogenetic analysis classifies the LBD genes into six subfamilies which support the existence of 7 ancient gene lineages. Phylogenetic relationship and gene collinearity are combined to retrace 11 ancestor genes for seed plants and 18 ancestor genes for angiosperms, which improves the resolution of LBD gene ancestry. The ancient gene lineages are strictly preserved in current plant genomes, including the previously controversial class IB gene in Selaginella moellendorphii, suggesting extreme reluctance of LBD genes to be lost during evolution. Meanwhile, whole-genome and dispersed gene duplications substantially expand LBD gene family in angiosperms, and elaborate functions of LBD genes through frequent expression pattern change and protein sequence variation. CONCLUSIONS Through phylogenetic and gene collinearity analyses, we retrace the landscape of LBD gene ancestry which lays foundation for elucidating evolutionary diversification of LBD genes in land plants.
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Affiliation(s)
- Yimeng Kong
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Peng Xu
- National Key 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 Sciences, Shanghai, 200032, China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Longxian Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Laigeng Li
- National Key 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 Sciences, Shanghai, 200032, China.
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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