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Nakayama H. Leaf form diversity and evolution: a never-ending story in plant biology. JOURNAL OF PLANT RESEARCH 2024; 137:547-560. [PMID: 38592658 PMCID: PMC11230983 DOI: 10.1007/s10265-024-01541-4] [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: 02/19/2024] [Accepted: 03/31/2024] [Indexed: 04/10/2024]
Abstract
Leaf form can vary at different levels, such as inter/intraspecies, and diverse leaf shapes reflect their remarkable ability to adapt to various environmental conditions. Over the past two decades, considerable progress has been made in unraveling the molecular mechanisms underlying leaf form diversity, particularly the regulatory mechanisms of leaf complexity. However, the mechanisms identified thus far are only part of the entire process, and numerous questions remain unanswered. This review aims to provide an overview of the current understanding of the molecular mechanisms driving leaf form diversity while highlighting the existing gaps in our knowledge. By focusing on the unanswered questions, this review aims to shed light on areas that require further research, ultimately fostering a more comprehensive understanding of leaf form diversity.
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Affiliation(s)
- Hokuto Nakayama
- Graduate School of Science, Department of Biological Sciences, The University of Tokyo, Science Build. #2, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-0033, Japan.
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2
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Ambrose BA, Stevenson DW. The evolution and development of sporangia-The fundamental reproductive organ of land plant sporophytes. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102563. [PMID: 38838582 DOI: 10.1016/j.pbi.2024.102563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/22/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
A key innovation of land plants is the origin and evolution of the sporangium, the fundamental reproductive structure of the diploid sporophyte. In vascular plants, whether the structure is a cone, fertile leaf, or flower-all are clusters of sporangia. The evolution of morphologically distinct sporangia (heterospory) and retention of the gametophyte evolved three times independently as a prerequisite for the evolution of seeds. This review summarizes the development of vascular plant sporangia, molecular genetics of angiosperm sporangia, and provides a framework to investigate evolution and development in vascular plant sporangia.
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Affiliation(s)
- Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, NY, 10458, USA.
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3
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Turner HA, Humpage M, Kerp H, Hetherington AJ. Leaves and sporangia developed in rare non-Fibonacci spirals in early leafy plants. Science 2023; 380:1188-1192. [PMID: 37319203 DOI: 10.1126/science.adg4014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
Lateral plant organs, including leaves and reproductive structures, are arranged on stems in distinct patterns termed phyllotaxis. Most extant plants exhibit phyllotactic patterns that are mathematically described by the Fibonacci series. However, it remains unclear what lateral organ arrangements were present in early leafy plants. To investigate this, we quantified phyllotaxis in fossils of the Early Devonian lycopod Asteroxylon mackiei. We report diverse phyllotaxis in leaves, including whorls and spirals. Spirals were all n:(n+1) non-Fibonacci types. We also show that leaves and reproductive structures occurred in the same phyllotactic series, indicating developmental similarities between the organs. Our findings shed light on the long-standing debate about leaf origins and demonstrate the antiquity of non-Fibonacci spirals in plants.
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Affiliation(s)
- Holly-Anne Turner
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Matthew Humpage
- Northern Rogue Studios, 18 Hunsdon Road, Iffley, Oxford OX4 4JE, UK
| | - Hans Kerp
- Research Group for Palaeobotany, Institute for Geology and Palaeontology, University Münster, Heisenbergstrasse 2, 48149 Münster, Germany
| | - Alexander J Hetherington
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
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4
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Jiang M, Jian J, Zhou C, Li L, Wang Y, Zhang W, Song Z, Yang J. Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development. FRONTIERS IN PLANT SCIENCE 2023; 13:1078248. [PMID: 36714739 PMCID: PMC9880897 DOI: 10.3389/fpls.2022.1078248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
The origin of seeds is one of the key innovations in land plant evolution. Ovules are the developmental precursors of seeds. The integument is the envelope structure surrounding the nucellus within the ovule and developing into the seed coat when ovules mature upon fertilization. The question of whether the integument arise de novo or evolve from elaboration of pre-existing structures has caused much debate. By exploring the origin and evolution of the key regulatory genes controlling integument development and their functions during both individual and historical developmental processes, we showed the widespread presence of the homologs of ANT, CUC, BEL1, SPL, C3HDZ, INO, ATS, and ETT in seedless plant genomes. All of these genes have undergone duplication-divergence events in their evolutionary history, with most of the descendant paralogous suffering motif gain and/or loss in the coding regions. Expression and functional characterization have shown that these genes are key components of the genetic program that patterns leaf-like lateral organs. Serial homology can thus be postulated between integuments and other lateral organs in terms of the shared master regulatory genes. Given that the genetic program patterning leaf-like lateral organs formed in seedless plants, and was reused during seed origin, the integument is unlikely to arise de novo but evolved from the stem segment-specific modification of pre-existing serially homologous structures. The master 'switches' trigging the modification to specify the integument identity remain unclear. We propose a successive transformation model of integument origin.
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Affiliation(s)
- Min Jiang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Jinjing Jian
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Chengchuan Zhou
- Institute of Tree Genetics Breeding and Cultivation, Jiangxi Academy of Forestry, Nanchang, China
| | - Linfeng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yuguo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Wenju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Center for Evolutionary Biology, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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5
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Kapoor B, Kumar P, Verma V, Irfan M, Sharma R, Bhargava B. How plants conquered land: evolution of terrestrial adaptation. J Evol Biol 2023; 36:5-14. [PMID: 36083189 DOI: 10.1111/jeb.14062] [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: 11/15/2021] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/11/2023]
Abstract
The transition of plants from water to land is considered one of the most significant events in the evolution of life on Earth. The colonization of land by plants, accompanied by their morphological, physiological and developmental changes, resulted in plant biodiversity. Besides significantly influencing oxygen levels in the air and on land, plants manufacture organic matter from CO2 and water with the help of sunlight, paving the way for the diversification of nonplant lineages ranging from microscopic organisms to animals. Land plants regulate the climate by adjusting total biomass and energy flow. At the genetic level, these innovations are achieved through the rearrangement of pre-existing genetic information. Advances in genome sequencing technology are revamping our understanding of plant evolution. This study highlights the morphological and genomic innovations that allow plants to integrate life on Earth.
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Affiliation(s)
- Bhuvnesh Kapoor
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, New York, USA
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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6
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Marchant DB, Chen G, Cai S, Chen F, Schafran P, Jenkins J, Shu S, Plott C, Webber J, Lovell JT, He G, Sandor L, Williams M, Rajasekar S, Healey A, Barry K, Zhang Y, Sessa E, Dhakal RR, Wolf PG, Harkess A, Li FW, Rössner C, Becker A, Gramzow L, Xue D, Wu Y, Tong T, Wang Y, Dai F, Hua S, Wang H, Xu S, Xu F, Duan H, Theißen G, McKain MR, Li Z, McKibben MTW, Barker MS, Schmitz RJ, Stevenson DW, Zumajo-Cardona C, Ambrose BA, Leebens-Mack JH, Grimwood J, Schmutz J, Soltis PS, Soltis DE, Chen ZH. Dynamic genome evolution in a model fern. NATURE PLANTS 2022; 8:1038-1051. [PMID: 36050461 PMCID: PMC9477723 DOI: 10.1038/s41477-022-01226-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
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Affiliation(s)
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Fei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | | | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Guifen He
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Laura Sandor
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Adam Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kerrie Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Emily Sessa
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Rijan R Dhakal
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL, USA
| | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Clemens Rössner
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Annette Becker
- Justus-Liebig-University, Department of Biology and Chemistry, Institute of Botany, Gießen, Germany
| | - Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuhuan Wu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuanyuan Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Shengchun Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Honglang Duan
- Institute for Forest Resources & Environment of Guizhou, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, China
| | - Günter Theißen
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Michael R McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | | | | | | | | | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, USA.
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia.
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
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7
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HD-Zip III Gene Family: Identification and Expression Profiles during Leaf Vein Development in Soybean. PLANTS 2022; 11:plants11131728. [PMID: 35807680 PMCID: PMC9269512 DOI: 10.3390/plants11131728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022]
Abstract
Leaf veins constitute the transport network for water and photosynthetic assimilates in vascular plants. The class III homeodomain-leucine zipper (HD-Zip III) gene family is central to the regulation of vascular development. In this research, we performed an overall analysis of the HD-Zip III genes in soybean (Glycine max L. Merr.). Our analysis included the phylogeny, conservation domains and cis-elements in the promoters of these genes. We used the quantitative reverse transcription-polymerase chain reaction to characterize the expression patterns of HD-Zip III genes in leaf vein development and analyze the effects of exogenous hormone treatments. In this study, twelve HD-Zip III genes were identified from the soybean genome and named. All soybean HD-Zip III proteins contained four highly conserved domains. GmHB15-L-1 transcripts showed steadily increasing accumulation during all stages of leaf vein development and were highly expressed in cambium cells. GmREV-L-1 and GmHB14-L-2 had nearly identical expression patterns in soybean leaf vein tissues. GmREV-L-1 and GmHB14-L-2 transcripts remained at stable high levels at all xylem developmental stages. GmREV-L-1 and GmHB14-L-2 were expressed at high levels in the vascular cambium and xylem cells. Overall, GmHB15-L-1 may be an essential regulator that is responsible for the formation or maintenance of soybean vein cambial cells. GmREV-L-1 and GmHB14-L-2 were correlated with xylem differentiation in soybean leaf veins. This study will pave the way for identifying the molecular mechanism of leaf vein development.
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8
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Perico C, Tan S, Langdale JA. Developmental regulation of leaf venation patterns: monocot versus eudicots and the role of auxin. THE NEW PHYTOLOGIST 2022; 234:783-803. [PMID: 35020214 PMCID: PMC9994446 DOI: 10.1111/nph.17955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Organisation and patterning of the vascular network in land plants varies in different taxonomic, developmental and environmental contexts. In leaves, the degree of vascular strand connectivity influences both light and CO2 harvesting capabilities as well as hydraulic capacity. As such, developmental mechanisms that regulate leaf venation patterning have a direct impact on physiological performance. Development of the leaf venation network requires the specification of procambial cells within the ground meristem of the primordium and subsequent proliferation and differentiation of the procambial lineage to form vascular strands. An understanding of how diverse venation patterns are manifest therefore requires mechanistic insight into how procambium is dynamically specified in a growing leaf. A role for auxin in this process was identified many years ago, but questions remain. In this review we first provide an overview of the diverse venation patterns that exist in land plants, providing an evolutionary perspective. We then focus on the developmental regulation of leaf venation patterns in angiosperms, comparing patterning in eudicots and monocots, and the role of auxin in each case. Although common themes emerge, we conclude that the developmental mechanisms elucidated in eudicots are unlikely to fully explain how parallel venation patterns in monocot leaves are elaborated.
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Affiliation(s)
- Chiara Perico
- Department of Plant SciencesUniversity of OxfordSouth Parks RdOxfordOX1 3RBUK
| | - Sovanna Tan
- Department of Plant SciencesUniversity of OxfordSouth Parks RdOxfordOX1 3RBUK
| | - Jane A. Langdale
- Department of Plant SciencesUniversity of OxfordSouth Parks RdOxfordOX1 3RBUK
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9
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Kinosian SP, Wolf PG. The biology of C. richardii as a tool to understand plant evolution. eLife 2022; 11:75019. [PMID: 35311640 PMCID: PMC8979586 DOI: 10.7554/elife.75019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/18/2022] [Indexed: 12/12/2022] Open
Abstract
The fern Ceratopteris richardii has been studied as a model organism for over 50 years because it is easy to grow and has a short life cycle. In particular, as the first homosporous vascular plant for which genomic resources were developed, C. richardii has been an important system for studying plant evolution. However, we know relatively little about the natural history of C. richardii. In this article, we summarize what is known about this aspect of C. richardii, and discuss how learning more about its natural history could greatly increase our understanding of the evolution of land plants.
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Affiliation(s)
- Sylvia P Kinosian
- Negaunee Institute for Plant Conservation Science, Chicago Botanic Garden, Chicago, United States
| | - Paul G Wolf
- Department of Biological Sciences, University of Alabama, Huntsville, United States
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10
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Fossils and plant evolution: structural fingerprints and modularity in the evo-devo paradigm. EvoDevo 2022; 13:8. [PMID: 35236418 PMCID: PMC8892741 DOI: 10.1186/s13227-022-00192-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/29/2022] [Indexed: 11/30/2022] Open
Abstract
Fossils constitute the principal repository of data that allow for independent tests of hypotheses of biological evolution derived from observations of the extant biota. Traditionally, transformational series of structure, consisting of sequences of fossils of the same lineage through time, have been employed to reconstruct and interpret morphological evolution. More recently, a move toward an updated paradigm was fueled by the deliberate integration of developmental thinking in the inclusion of fossils in reconstruction of morphological evolution. The vehicle for this is provided by structural fingerprints—recognizable morphological and anatomical structures generated by (and reflective of) the deployment of specific genes and regulatory pathways during development. Furthermore, because the regulation of plant development is both modular and hierarchical in nature, combining structural fingerprints recognized in the fossil record with our understanding of the developmental regulation of those structures produces a powerful tool for understanding plant evolution. This is particularly true when the systematic distribution of specific developmental regulatory mechanisms and modules is viewed within an evolutionary (paleo-evo-devo) framework. Here, we discuss several advances in understanding the processes and patterns of evolution, achieved by tracking structural fingerprints with their underlying regulatory modules across lineages, living and fossil: the role of polar auxin regulation in the cellular patterning of secondary xylem and the parallel evolution of arborescence in lycophytes and seed plants; the morphology and life history of early polysporangiophytes and tracheophytes; the role of modularity in the parallel evolution of leaves in euphyllophytes; leaf meristematic activity and the parallel evolution of venation patterns among euphyllophytes; mosaic deployment of regulatory modules and the diverse modes of secondary growth of euphyllophytes; modularity and hierarchy in developmental regulation and the evolution of equisetalean reproductive morphology. More generally, inclusion of plant fossils in the evo-devo paradigm has informed discussions on the evolution of growth patterns and growth responses, sporophyte body plans and their homology, sequences of character evolution, and the evolution of reproductive systems.
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11
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Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
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12
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Heisler MG. Integration of Core Mechanisms Underlying Plant Aerial Architecture. FRONTIERS IN PLANT SCIENCE 2021; 12:786338. [PMID: 34868186 PMCID: PMC8637408 DOI: 10.3389/fpls.2021.786338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/27/2021] [Indexed: 06/03/2023]
Abstract
Over the last decade or so important progress has been made in identifying and understanding a set of patterning mechanisms that have the potential to explain many aspects of plant morphology. These include the feedback loop between mechanical stresses and interphase microtubules, the regulation of plant cell polarity and the role of adaxial and abaxial cell type boundaries. What is perhaps most intriguing is how these mechanisms integrate in a combinatorial manner that provides a means to generate a large variety of commonly seen plant morphologies. Here, I review our current understanding of these mechanisms and discuss the links between them.
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Affiliation(s)
- Marcus G. Heisler
- School of Life and Environmental Science, University of Sydney, Camperdown, NSW, Australia
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13
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Zumajo-Cardona C, Little DP, Stevenson D, Ambrose BA. Expression analyses in Ginkgo biloba provide new insights into the evolution and development of the seed. Sci Rep 2021; 11:21995. [PMID: 34754044 PMCID: PMC8578549 DOI: 10.1038/s41598-021-01483-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Although the seed is a key morphological innovation, its origin remains unknown and molecular data outside angiosperms is still limited. Ginkgo biloba, with a unique place in plant evolution, being one of the first extant gymnosperms where seeds evolved, can testify to the evolution and development of the seed. Initially, to better understand the development of the ovules in Ginkgo biloba ovules, we performed spatio-temporal expression analyses in seeds at early developing stages, of six candidate gene homologues known in angiosperms: WUSCHEL, AINTEGUMENTA, BELL1, KANADI, UNICORN, and C3HDZip. Surprisingly, the expression patterns of most these ovule homologues indicate that they are not wholly conserved between angiosperms and Ginkgo biloba. Consistent with previous studies on early diverging seedless plant lineages, ferns, lycophytes, and bryophytes, many of these candidate genes are mainly expressed in mega- and micro-sporangia. Through in-depth comparative transcriptome analyses of Ginkgo biloba developing ovules, pollen cones, and megagametophytes we have been able to identify novel genes, likely involved in ovule development. Finally, our expression analyses support the synangial or neo-synangial hypotheses for the origin of the seed, where the sporangium developmental network was likely co-opted and restricted during integument evolution.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Damon P Little
- New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Dennis Stevenson
- New York Botanical Garden, Bronx, NY, USA.,The Graduate Center, City University of New York, New York, NY, USA
| | - Barbara A Ambrose
- New York Botanical Garden, Bronx, NY, USA. .,The Graduate Center, City University of New York, New York, NY, USA.
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14
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Toledo S, Bippus AC, Atkinson BA, Bronson AW, Tomescu AMF. Taxon sampling and alternative hypotheses of relationships in the euphyllophyte plexus that gave rise to seed plants: insights from an Early Devonian radiatopsid. THE NEW PHYTOLOGIST 2021; 232:914-927. [PMID: 34031894 DOI: 10.1111/nph.17511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
An abrupt transition in the fossil record separates Early Devonian euphyllophytes with a simple structure from a broad diversity of structurally complex Middle-Late Devonian plants. Morphological evolution and phylogeny across this transition are poorly understood due to incomplete sampling of the fossil record. We document a new Early Devonian radiatopsid and integrate it in analyses addressing euphyllophyte relationships. Anatomically preserved Emsian fossils (402-394 Ma) from the Battery Point Formation (Gaspé, Quebec, Canada) are studied in serial sections. The phylogenetic analysis is based on a matrix of 31 taxa and 50 characters emphasising vegetative morphology (41 discrete, nine continuous). The new plant, Kenrickia bivena gen. et sp. nov., is one of very few structurally complex euphyllophytes documented in the Early Devonian. Inclusion of Kenrickia overturns previously established phylogenetic relationships among Radiatopses, reiterating the need for increased density of Early Devonian taxon sampling. Kenrickia is recovered as the sister lineage to all other radiatopsids, a clade in which paraphyletic Stenokoleales led to a lignophyte clade where archaeopterids and seed plants fall into sister clades. Our results shed light on early euphyllophyte relationships and evolution, indicating early exploration of structural complexity by multiple lineages and reiterating the potential of a single origin of secondary growth in euphyllophytes.
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Affiliation(s)
- Selin Toledo
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Alexander C Bippus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Brian A Atkinson
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Allison W Bronson
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
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15
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Zumajo-Cardona C, Ambrose BA. Deciphering the evolution of the ovule genetic network through expression analyses in Gnetum gnemon. ANNALS OF BOTANY 2021; 128:217-230. [PMID: 33959756 PMCID: PMC8324035 DOI: 10.1093/aob/mcab059] [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: 03/18/2021] [Accepted: 04/30/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS The ovule is a synapomorphy of all seed plants (gymnosperms and angiosperms); however, there are some striking differences in ovules among the major seed plant lineages, such as the number of integuments or the orientation of the ovule. The genetics involved in ovule development have been well studied in the model species Arabidopsis thaliana, which has two integuments and anatropous orientation. This study is approached from what is known in arabidopsis, focusing on the expression patterns of homologues of four genes known to be key for the proper development of the integuments in arabidopsis: AINTEGUMENTA (ANT), BELL1, (BEL1), KANADIs (KANs) and UNICORN (UCN). METHODS We used histology to describe the morphoanatomical development from ovules to seeds in Gnetum gnemon. We carried out spatiotemporal expression analyses in G. gnemon, a gymnosperm, which has a unique ovule morphology with an integument covering the nucellus, two additional envelopes where the outermost becomes fleshy as the seed matures, and an orthotropous orientation. KEY RESULTS Our anatomical and developmental descriptions provide a framework for expression analyses in the ovule of G. gnemon. Our expression results show that although ANT, KAN and UCN homologues are expressed in the inner integument, their spatiotemporal patterns differ from those found in angiosperms. Furthermore, all homologues studied here are expressed in the nucellus, revealing major differences in seed plants. Finally, no expression of the studied homologues was detected in the outer envelopes. CONCLUSIONS Altogether, these analyses provide significant comparative data that allows us to better understand the functional evolution of these gene lineages, providing a compelling framework for evolutionary and developmental studies of seeds. Our findings suggest that these genes were most likely recruited from the sporangium development network and became restricted to the integuments of angiosperm ovules.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- New York Botanical Garden, Bronx, NY, USA
- The Graduate Center, City University of New York, New York, NY, USA
| | - Barbara A Ambrose
- The Graduate Center, City University of New York, New York, NY, USA
- For correspondence. E-mail
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16
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Vasco A, Matos FB, Sundue MA. Robbin C. Moran, Fern and Lycophyte Curator- an Appreciation. THE BOTANICAL REVIEW; INTERPRETING BOTANICAL PROGRESS 2021; 87:151-166. [PMID: 34219751 PMCID: PMC8241203 DOI: 10.1007/s12229-021-09254-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To mark the commencement of his retirement as Nathaniel Lord Britton Curator of Botany, and appointment as Curator Emeritus at the New York Botanical Garden, we pay tribute to Robbin Moran and impact on the botanical community with a brief synopsis of his career. Naturalist, fern expert, adored teacher-it is difficult to adequately pay tribute to his accomplishments, and his impact on botany in a single article. Robbin has published four books, 13 monographs of neotropical fern clades, over 170 scientific papers, and dozens of popular articles. He has named 115 new species, five new genera, and one family of ferns. He is eponymized by seven new species and the genus Moranopteris. We recount his earliest days and academic trajectory to become a leading researcher and educator in pteridology. We highlight his major influences, scientific accomplishments, and outreach to the botanical community.
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Affiliation(s)
- Alejandra Vasco
- Botanical Research Institute of Texas, 1700 University Drive, Fort Worth, TX 76107 USA
| | - Fernando B. Matos
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. Purdue s.n., Viçosa, Minas Gerais CEP 36570-900 Brazil
| | - Michael A. Sundue
- Department of Plant Biology, The Pringle Herbarium, University of Vermont, 111 Jeffords Hall, Burlington, 05405 VT USA
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17
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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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18
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Romanova MA, Maksimova AI, Pawlowski K, Voitsekhovskaja OV. YABBY Genes in the Development and Evolution of Land Plants. Int J Mol Sci 2021; 22:4139. [PMID: 33923657 PMCID: PMC8074164 DOI: 10.3390/ijms22084139] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/27/2022] Open
Abstract
Mounting evidence from genomic and transcriptomic studies suggests that most genetic networks regulating the morphogenesis of land plant sporophytes were co-opted and modified from those already present in streptophyte algae and gametophytes of bryophytes sensu lato. However, thus far, no candidate genes have been identified that could be responsible for "planation", a conversion from a three-dimensional to a two-dimensional growth pattern. According to the telome theory, "planation" was required for the genesis of the leaf blade in the course of leaf evolution. The key transcription factors responsible for leaf blade development in angiosperms are YABBY proteins, which until recently were thought to be unique for seed plants. Yet, identification of a YABBY homologue in a green alga and the recent findings of YABBY homologues in lycophytes and hornworts suggest that YABBY proteins were already present in the last common ancestor of land plants. Thus, these transcriptional factors could have been involved in "planation", which fosters our understanding of the origin of leaves. Here, we summarise the current data on functions of YABBY proteins in the vegetative and reproductive development of diverse angiosperms and gymnosperms as well as in the development of lycophytes. Furthermore, we discuss a putative role of YABBY proteins in the genesis of multicellular shoot apical meristems and in the evolution of leaves in early divergent terrestrial plants.
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Affiliation(s)
- Marina A. Romanova
- Department of Botany, St. Petersburg State University, Universitetskaya Nab. 7/9, 190034 Saint Petersburg, Russia
| | - Anastasiia I. Maksimova
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, ul. Professora Popova 2, 197376 Saint Petersburg, Russia;
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden;
| | - Olga V. Voitsekhovskaja
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, ul. Professora Popova 2, 197376 Saint Petersburg, Russia;
- Saint Petersburg Electrotechnical University “LETI”, ul. Professora Popova 5, 197022 Saint Petersburg, Russia
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19
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Ambrose BA, Smalls TL, Zumajo-Cardona C. All type II classic MADS-box genes in the lycophyte Selaginella moellendorffii are broadly yet discretely expressed in vegetative and reproductive tissues. Evol Dev 2021; 23:215-230. [PMID: 33666357 DOI: 10.1111/ede.12375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/13/2021] [Accepted: 01/30/2021] [Indexed: 11/29/2022]
Abstract
The MADS-box genes constitute a large transcription factor family that appear to have evolved by duplication and diversification of function. Two types of MADS-box genes are distinguished throughout eukaryotes, types I and II. Type II classic MADS-box genes, also known as MIKC-type, are key developmental regulators in flowering plants and are particularly well-studied for their role in floral organ specification. However, very little is known about the role that these genes might play outside of the flowering plants. We investigated the evolution of type II classic MADS-box genes across land plants by performing a maximum likelihood analysis with a particular focus on lycophytes. Here, we present the expression patterns of all three type II classic MADS-box homologs throughout plant development in the lycophyte Selaginella moellendorffii: SmMADS1, SmMADS3, and SmMADS6. We used scanning electron microscopy and histological analyses to define stages of sporangia development in S. moellendorffii. We performed phylogenetic analyses of this gene lineage across land plants and found that lycophyte sequences appeared before the multiple duplication events that gave rise to the major MADS-box gene lineages in seed plants. Our expression analyses by in situ hybridization show that all type II classic MADS-box genes in S. moellendorffii have broad but distinct patterns of expression in vegetative and reproductive tissues, where SmMADS1 and SmMADS6 only differ during late sporangia development. The broad expression during S. moellendorffii development suggests that MADS-box genes have undergone neofunctionalization and subfunctionalization after duplication events in seed plants.
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Affiliation(s)
| | | | - Cecilia Zumajo-Cardona
- New York Botanical Garden, Bronx, Bronx, New York, USA.,The Graduate Center, City University of New York, New York, New York, USA
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20
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Tomescu AMF. The stele - a developmental perspective on the diversity and evolution of primary vascular architecture. Biol Rev Camb Philos Soc 2021; 96:1263-1283. [PMID: 33655608 DOI: 10.1111/brv.12699] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/15/2022]
Abstract
The stele concept is one of the oldest enduring concepts in plant biology. Here, I review the history of the concept and build an argument for an updated view of steles and their evolution. Studies of stelar organization have generated a widely ranging array of definitions that determine the way we classify steles and construct scenarios about the evolution of stelar architecture. Because at the organismal level biological evolution proceeds by changes in development, concepts of structure need to be grounded in development to be relevant in an evolutionary perspective. For the stele, most traditional definitions that incorporate development have viewed it as the totality of tissues that either originate from procambium - currently the prevailing view - or are bordered by a boundary layer (e.g. endodermis). Consensus between these two perspectives can be reached by recasting the stele as a structural entity of dual nature. Following a brief review of the history of the stele concept, basic terminology related to stelar organization, and traditional classifications of the steles, I revisit boundary layers from the perspective of histogenesis as a dynamic mosaic of developmental domains. I review anatomical and molecular data to explore and reaffirm the importance of boundary layers for stelar organization. Drawing on information from comparative anatomy, developmental regulation, and the fossil record, I propose a stele concept that integrates both the boundary layer and the procambial perspectives, consistent with a dual nature of the stele. This dual stele model posits that stelar architecture is determined at the apical meristem by two major cell fate specification events: a first one that specifies a provascular domain and its boundaries, and a second event that specifies a procambial domain (which will mature into conducting tissues) from cell subpopulations of the provascular domain. If the position and extent of the developmental domains defined by the two events are determined by different concentrations of the same morphogen (most likely auxin), then the distribution of this organizer factor in the shoot apical meristem, as modulated by changes in axis size and the effect of lateral organs, can explain the different stelar configurations documented among tracheophytes. This model provides working hypotheses that incorporate assumptions and generate implications that can be tested empirically. The model also offers criteria for an updated classification of steles in line with current understanding of plant development. In this classification, steles fall into two major categories determined by the configuration of boundary layers: boundary protosteles and boundary siphonosteles, each with subtypes defined by the architecture of the vascular tissues. Validation of the dual stele model and, more generally, in-depth understanding of the regulation of stelar architecture, will necessitate targeted efforts in two areas: (i) the regulation of procambium, vascular tissue, and boundary layer specification in all extant vascular plants, considering that most of the diversity in stelar architecture is hosted by seed-free plants, which are the least explored in terms of developmental regulation; (ii) the configuration of vascular tissues and, especially, boundary layers, in as many extinct lineages as possible.
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Affiliation(s)
- Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, U.S.A
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21
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Dijkhuizen LW, Tabatabaei BES, Brouwer P, Rijken N, Buijs VA, Güngör E, Schluepmann H. Far-Red Light-Induced Azolla filiculoides Symbiosis Sexual Reproduction: Responsive Transcripts of Symbiont Nostoc azollae Encode Transporters Whilst Those of the Fern Relate to the Angiosperm Floral Transition. FRONTIERS IN PLANT SCIENCE 2021; 12:693039. [PMID: 34456937 PMCID: PMC8386757 DOI: 10.3389/fpls.2021.693039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/22/2021] [Indexed: 05/02/2023]
Abstract
Water ferns of the genus Azolla and the filamentous cyanobacteria Nostoc azollae constitute a model symbiosis that enabled the colonization of the water surface with traits highly desirable for the development of more sustainable crops: their floating mats capture CO2 and fix N2 at high rates using light energy. Their mode of sexual reproduction is heterosporous. The regulation of the transition from the vegetative phase to the spore forming phase in ferns is largely unknown, yet a prerequisite for Azolla domestication, and of particular interest as ferns represent the sister lineage of seed plants. Sporocarps induced with far red light could be crossed so as to verify species attribution of strains from the Netherlands but not of the strain from the Anzali lagoon in Iran; the latter strain was assigned to a novel species cluster from South America. Red-dominated light suppresses the formation of dissemination stages in both gametophyte- and sporophyte-dominated lineages of plants, the response likely is a convergent ecological strategy to open fields. FR-responsive transcripts included those from MIKCC homologues of CMADS1 and miR319-controlled GAMYB transcription factors in the fern, transporters in N. azollae, and ycf2 in chloroplasts. Loci of conserved microRNA (miRNA) in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159. Phylogenomic analyses of MIKCC TFs suggested that the control of flowering and flower organ specification may have originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.
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Affiliation(s)
- Laura W. Dijkhuizen
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Paul Brouwer
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Niels Rijken
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Valerie A. Buijs
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Erbil Güngör
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Henriette Schluepmann
- Laboratory of Molecular Plant Physiology, Department of Biology, Utrecht University, Utrecht, Netherlands
- *Correspondence: Henriette Schluepmann
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Aragón-Raygoza A, Vasco A, Blilou I, Herrera-Estrella L, Cruz-Ramírez A. Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii. Genes (Basel) 2020; 11:E1455. [PMID: 33291610 PMCID: PMC7761924 DOI: 10.3390/genes11121455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.
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Affiliation(s)
- Alejandro Aragón-Raygoza
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
| | - Alejandra Vasco
- Botanical Research Institute of Texas (BRIT), Fort Worth, TX 76107-3400, USA;
| | - Ikram Blilou
- Laboratory of Plant Cell and Developmental Biology, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Luis Herrera-Estrella
- Metabolic Engineering Group, Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Alfredo Cruz-Ramírez
- Molecular and Developmental Complexity Group at Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav Sede Irapuato, Km. 9.6 Libramiento Norte Carretera, Irapuato-León, Irapuato 36821, Guanajuato, Mexico;
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23
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Sun J, Li GS. Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides. AMERICAN JOURNAL OF BOTANY 2020; 107:1470-1480. [PMID: 33216953 DOI: 10.1002/ajb2.1570] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
PREMISE Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question. METHODS ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF. RESULTS ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it. CONCLUSIONS Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.
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Affiliation(s)
- Jun Sun
- 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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24
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Du H, Ran JH, Feng YY, Wang XQ. The flattened and needlelike leaves of the pine family (Pinaceae) share a conserved genetic network for adaxial-abaxial polarity but have diverged for photosynthetic adaptation. BMC Evol Biol 2020; 20:131. [PMID: 33028198 PMCID: PMC7542717 DOI: 10.1186/s12862-020-01694-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/21/2020] [Indexed: 11/10/2022] Open
Abstract
Background Leaves have highly diverse morphologies. However, with an evolutionary history of approximately 200 million years, leaves of the pine family are relatively monotonous and often collectively called “needles”, although they vary in length, width and cross-section shapes. It would be of great interest to determine whether Pinaceae leaves share similar morpho-physiological features and even consistent developmental and adaptive mechanisms. Results Based on a detailed morpho-anatomical study of leaves from all 11 Pinaceae genera, we particularly investigated the expression patterns of adaxial-abaxial polarity genes in two types of leaves (needlelike and flattened) and compared their photosynthetic capacities. We found that the two types of leaves share conserved spatial patterning of vasculatures and genetic networks for adaxial-abaxial polarity, although they display different anatomical structures in the mesophyll tissue differentiation and distribution direction. In addition, the species with needlelike leaves exhibited better photosynthetic capacity than the species with flattened leaves. Conclusions Our study provides the first evidence for the existence of a conserved genetic module controlling adaxial-abaxial polarity in the development of different Pinaceae leaves.
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Affiliation(s)
- Hong Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China
| | - Jin-Hua Ran
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan-Yuan Feng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing, 100093, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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25
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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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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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Wong GKS, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M. Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:741-765. [PMID: 31851546 DOI: 10.1146/annurev-arplant-042916-041040] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C4 photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.
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Affiliation(s)
- Gane Ka-Shu Wong
- Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E9, Canada;
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Douglas E Soltis
- Florida Museum of Natural History, Gainesville, Florida 32611, USA
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, Glencoe, Illinois 60022, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Michael Melkonian
- Faculty of Biology, University of Duisburg-Essen, D-45141 Essen, Germany
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The Evolution of the KANADI Gene Family and Leaf Development in Lycophytes and Ferns. PLANTS 2019; 8:plants8090313. [PMID: 31480252 PMCID: PMC6783990 DOI: 10.3390/plants8090313] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/23/2022]
Abstract
Leaves constitute the main photosynthetic plant organ and even though their importance is not debated, the origin and development of leaves still is. The leaf developmental network has been elucidated for angiosperms, from genes controlling leaf initiation, to leaf polarity and shape. There are four KANADI (KAN) paralogs in Arabidopsisthaliana needed for organ polarity with KAN1 and KAN2 specifying abaxial leaf identity. Yet, studies of this gene lineage outside angiosperms are required to better understand the evolutionary patterns of leaf development and the role of KAN homologs. We studied the evolution of KAN genes across vascular plants and their expression by in situ hybridization in the fern, Equisetum hyemale and the lycophyte Selaginella moellendorffii. Our results show that the expression of KAN genes in leaves is similar between ferns and angiosperms. However, the expression patterns observed in the lycophyte S. moellendorffii are significantly different compared to all other vascular plants, suggesting that the KAN function in leaf polarity is likely only conserved across ferns, gymnosperms, and angiosperms. This study indicates that mechanisms for leaf development are different in lycophytes compared to other vascular plants.
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Conway SJ, Di Stilio VS. An ontogenetic framework for functional studies in the model fern Ceratopteris richardii. Dev Biol 2019; 457:20-29. [PMID: 31470018 DOI: 10.1016/j.ydbio.2019.08.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 01/02/2023]
Abstract
As the sister group to seed plants, ferns are a phylogenetically informative lineage. Functional studies in representatives of the fern lineage are helping bridge the knowledge gap in developmental mechanisms between angiosperms and non-vascular plants. The fern life cycle has the advantage of combining a sizable free-living haploid gametophyte, more amenable for developmental studies than the reduced seed plant gametophyte, with an indeterminate and complex diploid sporophyte. Ceratopteris richardii has long been proposed as a model fern and has recently become tractable due to stable transgenesis and increasing genomic resources, allowing researchers to test explicit questions about gene function in a fern for the first time. As with any model system, a detailed understanding of wild-type morphology and a staged ontogeny are indispensable for the characterization of mutant phenotypes resulting from genetic manipulations. Therefore, the goal of this study is to provide a unified reference ontogeny for this emerging model fern as a tool for comparative evolutionary and developmental studies. It complements earlier research by filling gaps in major stages of development of the haploid gametophyte and diploid sporophyte generations, and provides additional descriptions of the shoot apical meristem and early leaf development. This resource is meant to facilitate not only studies of candidate genes within C. richardii, but also broader ontogenetic comparisons to other model plants.
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Affiliation(s)
- Stephanie J Conway
- Department of Biology, University of Washington, Seattle, WA, 98195-1800, USA.
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Tomescu AMF, Groover AT. Mosaic modularity: an updated perspective and research agenda for the evolution of vascular cambial growth. THE NEW PHYTOLOGIST 2019; 222:1719-1735. [PMID: 30552764 DOI: 10.1111/nph.15640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Secondary growth from a vascular cambium, present today only in seed plants and isoetalean lycophytes, has a 400-million-yr evolutionary history that involves considerably broader taxonomic diversity, most of it hidden in the fossil record. Approaching vascular cambial growth as a complex developmental process, we review data from living plants and fossils that reveal diverse modes of secondary growth. These are consistent with a modular nature of secondary growth, when considered as a tracheophyte-wide structural feature. This modular perspective identifies putative constituent developmental modules of cambial growth, for which we review developmental anatomy and regulation. Based on these data, we propose a hypothesis that explains the sources of diversity of secondary growth, considered across the entire tracheophyte clade, and opens up new avenues for exploring the origin of secondary growth. In this hypothesis, various modes of secondary growth reflect a mosaic pattern of expression of different developmental-regulatory modules among different lineages. We outline an approach that queries three information systems (living seed plants, living seed-free plants, and fossils) and integrates data on developmental regulation, anatomy, gene evolution and phylogeny to test the mosaic modularity hypothesis and its implications, and to inform efforts aimed at understanding the evolution of secondary growth.
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Affiliation(s)
- Alexandru M F Tomescu
- Department of Biological Sciences, Humboldt State University, Arcata, CA, 95521, USA
| | - Andrew T Groover
- Pacific Southwest Research Station, USDA Forest Service, Davis, CA, 95618, USA
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
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32
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Abstract
Land plants evolved from an ancestral alga from which they inherited developmental and physiological characters. A key innovation of land plants is a life cycle with an alternation of generations, with both haploid gametophyte and diploid sporophyte generations having complex multicellular bodies. The origins of the developmental genetic programs patterning these bodies, whether inherited from an algal ancestor or evolved de novo, and whether programs were co-opted between generations, are largely open questions. We first provide a framework for land plant evolution and co-option of developmental regulatory pathways and then examine two cases in more detail.
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33
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Qi X, Kuo LY, Guo C, Li H, Li Z, Qi J, Wang L, Hu Y, Xiang J, Zhang C, Guo J, Huang CH, Ma H. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. Mol Phylogenet Evol 2018; 127:961-977. [PMID: 29981932 DOI: 10.1016/j.ympev.2018.06.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.
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Affiliation(s)
- Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | | | - Chunce Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Hao Li
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Zhongyang Li
- College of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Linbo Wang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianying Xiang
- College of Biodiversity Conservation and Utilization, Southwest Forestry University, 300 Bailong Road, Kunming 650224, China
| | - Caifei Zhang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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Romani F, Reinheimer R, Florent SN, Bowman JL, Moreno JE. Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. THE NEW PHYTOLOGIST 2018; 219:408-421. [PMID: 29635737 DOI: 10.1111/nph.15133] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 02/26/2018] [Indexed: 05/15/2023]
Abstract
Plant transition to land required several regulatory adaptations. The mechanisms behind these changes remain unknown. Since the evolution of transcription factors (TFs) families accompanied this transition, we studied the HOMEODOMAIN LEUCINE ZIPPER (HDZ) TF family known to control key developmental and environmental responses. We performed a phylogenetic and bioinformatics analysis of HDZ genes using transcriptomic and genomic datasets from a wide range of Viridiplantae species. We found evidence for the existence of HDZ genes in chlorophytes and early-divergent charophytes identifying several HDZ members belonging to the four known classes (I-IV). Furthermore, we inferred a progressive incorporation of auxiliary motifs. Interestingly, most of the structural features were already present in ancient lineages. Our phylogenetic analysis inferred that the origin of classes I, III, and IV is monophyletic in land plants in respect to charophytes. However, class IIHDZ genes have two conserved lineages in charophytes and mosses that differ in the CPSCE motif. Our results indicate that the HDZ family was already present in green algae. Later, the HDZ family expanded accompanying critical plant traits. Once on land, the HDZ family experienced multiple duplication events that promoted fundamental neo- and subfunctionalizations for terrestrial life.
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Affiliation(s)
- Facundo Romani
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No. 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Renata Reinheimer
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Ciencias Agrarias, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No. 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
| | - Stevie N Florent
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Vic., 3800, Australia
| | - Javier E Moreno
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional No. 168 km. 0, Paraje El Pozo, Santa Fe, 3000, Argentina
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Lu Z, Huang Q, Zhang T, Hu B, Chang Y. Global transcriptome analysis and characterization of Dryopteris fragrans (L.) Schott sporangium in different developmental stages. BMC Genomics 2018; 19:471. [PMID: 29914367 PMCID: PMC6006573 DOI: 10.1186/s12864-018-4843-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 05/31/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Dryopteris fragrans (D. fragrans) is a potential medicinal fern distributed in volcanic magmatic rock areas under tough environmental condition. Sporangia are important organs for fern reproduction. This study was designed to characterize the transcriptome characteristics of the wild D. fragrans sporangia in three stages (stage A, B, and C) with the aim of uncovering its molecular mechanism of growth and development. RESULTS Using a HiSeq 4000, 79.81 Gb clean data (each sample is at least 7.95 GB) were obtained from nine samples, with three being supplied from each period, and assembled into 94,705 Unigenes, among which 44,006 Unigenes were annotated against public protein databases (NR, Swiss-Prot, KEGG, COG, KOG, GO, eggNOG and Pfam). Furthermore, we observed 7126 differentially expressed genes (DEG) (Fold Change > 4, FDR < 0.001), 349,885 SNP loci, and 10,584 SSRs. DEGs involved in DNA replication and homologous recombination were strongly expressed in stage A, and several DEGs involved in cutin, suberin and wax biosynthesis had undergone dramatic changes during development, which was consistent with morphological observations. DEGs responsible for secondary metabolism and plant hormone signal transduction changed clearly in the last two stages. DEGs homologous to those known genes associated with the development of reproductive organs of flowering plants have also been validated and discussed, such as AGL61, AGL62, ONAC010. In particular, a Unigene encoding TFL1, an important flower-development regulator in flowering plants, was identified and exhibited the highest expression level in stage B in D. fragrans sporangia. CONCLUSIONS This study is the first report on global transcriptome analysis in the development of sporangia of wild D. fragrans. DEGs related to development and homologous to flower-seed development in flowering plants were discussed. All DEGs involved in DNA replication and homologous recombination were consistent with morphological observations of paraffin slices. The results of this study provide rare resources for further investigation of the D. fragrans sporangium development, stress resistance and secondary metabolism.
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Affiliation(s)
- Zhen Lu
- Laboratory of Plant Research, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | - Qingyang Huang
- Laboratory of Plant Research, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin, 150040, China
| | - Tong Zhang
- Laboratory of Plant Research, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China
| | | | - Ying Chang
- Laboratory of Plant Research, College of Life Sciences, Northeast Agricultural University, Harbin, 150030, China.
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Evkaikina AI, Berke L, Romanova MA, Proux-Wéra E, Ivanova AN, Rydin C, Pawlowski K, Voitsekhovskaja OV. The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves. Genome Biol Evol 2018; 9:2444-2460. [PMID: 28957460 PMCID: PMC5622374 DOI: 10.1093/gbe/evx169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2017] [Indexed: 12/21/2022] Open
Abstract
Lycopodiophyta—consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)—form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls—that is, leaves with a single, unbranched vein, emerging from the protostele without a leaf gap—not megaphylls. All leaves represent determinate organs originating on the flanks of indeterminate SAMs. Thus, leaf formation requires the suppression of indeterminacy, that is, of KNOX transcription factors. In seed plants, this is mediated by different groups of transcription factors including ARP and YABBY. We generated a shoot tip transcriptome of Huperzia selago (Lycopodiales) to examine the genes involved in leaf formation. Our H. selago transcriptome does not contain any ARP homolog, although transcriptomes of Selaginella spp. do. Surprisingly, we discovered a YABBY homolog, although these transcription factors were assumed to have evolved only in seed plants. The existence of a YABBY homolog in H. selago suggests that YABBY evolved already in the common ancestor of the vascular plants, and subsequently was lost in some lineages like Selaginellales, whereas ARP may have been lost in Lycopodiales. The presence of YABBY in the common ancestor of vascular plants would also support the hypothesis that this common ancestor had a simplex SAM. Furthermore, a comparison of the expression patterns of ARP in shoot tips of Selaginella kraussiana (Harrison CJ, etal. 2005. Independent recruitment of a conserved developmental mechanism during leaf evolution. Nature 434(7032):509–514.) and YABBY in shoot tips of H. selago implies that the development of microphylls, unlike megaphylls, does not seem to depend on the combined activities of ARP and YABBY. Altogether, our data show that Lycopodiophyta are a diverse group; so, in order to understand the role of Lycopodiophyta in evolution, representatives of Lycopodiales, Selaginellales, as well as of Isoetales, have to be examined.
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Affiliation(s)
- Anastasiia I Evkaikina
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Lidija Berke
- Department of Plant Sciences, Wageningen University, The Netherlands
| | - Marina A Romanova
- Department of Botany, St. Petersburg State University, St. Petersburg, Russia
| | - Estelle Proux-Wéra
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Alexandra N Ivanova
- Laboratory of Anatomy and Morphology, Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Olga V Voitsekhovskaja
- Laboratory of Molecular and Ecological Physiology, Komarov Botanical Institute, Russian Academy of Sciences, St. Petersburg, Russia
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Rensing SA. Why we need more non-seed plant models. THE NEW PHYTOLOGIST 2017; 216:355-360. [PMID: 28191633 DOI: 10.1111/nph.14464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 12/18/2016] [Indexed: 05/24/2023]
Abstract
Contents 355 I. 355 II. 356 III. 356 IV. 357 V. 358 VI. 359 359 References 359 SUMMARY: Out of a hundred sequenced and published land plant genomes, four are not of flowering plants. This severely skewed taxonomic sampling hinders our comprehension of land plant evolution at large. Moreover, most genetically accessible model species are flowering plants as well. If we are to gain a deeper understanding of how plants evolved and still evolve, and which of their developmental patterns are ancestral or derived, we need to study a more diverse set of plants. Here, I thus argue that we need to sequence genomes of so far neglected lineages, and that we need to develop more non-seed plant model species.
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Affiliation(s)
- Stefan A Rensing
- Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
- BIOSS Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
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38
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Thomas H, Ougham H. On plant growth and form. THE NEW PHYTOLOGIST 2017; 216:337-338. [PMID: 28921560 DOI: 10.1111/nph.14807] [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)
- Howard Thomas
- IBERS, Aberystwyth University, Edward Llwyd Building, Aberystwyth, Ceredigion, SY23 3DA, UK
| | - Helen Ougham
- IBERS, Aberystwyth University, Edward Llwyd Building, Aberystwyth, Ceredigion, SY23 3DA, UK
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Berruezo F, de Souza FSJ, Picca PI, Nemirovsky SI, Martínez Tosar L, Rivero M, Mentaberry AN, Zelada AM. Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microrna repertoire in land plants. PLoS One 2017; 12:e0177573. [PMID: 28494025 PMCID: PMC5426797 DOI: 10.1371/journal.pone.0177573] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/28/2017] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, playing key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plants. Among these, the fern group (monilophytes) occupies a key phylogenetic position, as it represents the closest extant cousin taxon of seed plants, i.e. gymno- and angiosperms. However, in spite of their evolutionary, economic and ecological importance, no fern genome has been sequenced yet and few genomic resources are available for this group. Here, we sequenced the small RNA fraction of an epiphytic South American fern, Pleopeltis minima (Polypodiaceae), and compared it to plant miRNA databases, allowing for the identification of miRNA families that are shared by all land plants, shared by all vascular plants (tracheophytes) or shared by euphyllophytes (ferns and seed plants) only. Using the recently described transcriptome of another fern, Lygodium japonicum, we also estimated the degree of conservation of fern miRNA targets in relation to other plant groups. Our results pinpoint the origin of several miRNA families in the land plant evolutionary tree with more precision and are a resource for future genomic and functional studies of fern miRNAs.
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Affiliation(s)
- Florencia Berruezo
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Flávio S. J. de Souza
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET), Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Pablo I. Picca
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sergio I. Nemirovsky
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN, CONICET-UBA), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leandro Martínez Tosar
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
| | - Mercedes Rivero
- Instituto de Agrobiotecnología de Rosario (INDEAR), Rosario, Santa Fe, Argentina
| | - Alejandro N. Mentaberry
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
| | - Alicia M. Zelada
- Laboratorio de Agrobiotecnología, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires (IBBEA, CONICET-UBA), Buenos Aires, Argentina
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Ramachandran P, Carlsbecker A, Etchells JP. Class III HD-ZIPs govern vascular cell fate: an HD view on patterning and differentiation. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:55-69. [PMID: 27794018 DOI: 10.1093/jxb/erw370] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Plant vasculature is required for the transport of water and solutes throughout the plant body. It is constituted of xylem, specialized for transport of water, and phloem, that transports photosynthates. These two differentiated tissues are specified early in development and arise from divisions in the procambium, which is the vascular meristem during primary growth. During secondary growth, the xylem and phloem are further expanded via differentiation of cells derived from divisions in the cambium. Almost all of the developmental fate decisions in this process, including vascular specification, patterning, and differentiation, are regulated by transcription factors belonging to the class III homeodomain-leucine zipper (HD-ZIP III) family. This review draws together the literature describing the roles that these genes play in vascular development, looking at how HD-ZIP IIIs are regulated, and how they in turn influence other regulators of vascular development. Themes covered vary, from interactions between HD-ZIP IIIs and auxin, cytokinin, and brassinosteroids, to the requirement for exquisite spatial and temporal regulation of HD-ZIP III expression through miRNA-mediated post-transcriptional regulation, and interactions with other transcription factors. The literature described places the HD-ZIP III family at the centre of a complex network required for initiating and maintaining plant vascular tissues.
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Affiliation(s)
- Prashanth Ramachandran
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls väg 24E, SE-756 51 Uppsala, Sweden
| | - Annelie Carlsbecker
- Physiological Botany, Department of Organismal Biology and Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls väg 24E, SE-756 51 Uppsala, Sweden
| | - J Peter Etchells
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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