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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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Mahley JN, Pittermann J, Rowe N, Baer A, Watkins JE, Schuettpelz E, Wheeler JK, Mehltreter K, Windham M, Testo W, Beck J. Geometry, Allometry and Biomechanics of Fern Leaf Petioles: Their Significance for the Evolution of Functional and Ecological Diversity Within the Pteridaceae. FRONTIERS IN PLANT SCIENCE 2018; 9:197. [PMID: 29563920 PMCID: PMC5850050 DOI: 10.3389/fpls.2018.00197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 02/01/2018] [Indexed: 06/01/2023]
Abstract
Herbaceous plants rely on a combination of turgor, ground tissues and geometry for mechanical support of leaves and stems. Unlike most angiosperms however, ferns employ a sub-dermal layer of fibers, known as a hypodermal sterome, for support of their leaves. The sterome is nearly ubiquitous in ferns, but nothing is known about its role in leaf biomechanics. The goal of this research was to characterize sterome attributes in ferns that experience a broad range of mechanical stresses, as imposed by their aquatic, xeric, epiphytic, and terrestrial niches. Members of the Pteridaceae meet this criteria well. The anatomical and functional morphometrics along with published values of tissue moduli were used to model petiole flexural rigidity and susceptibility to buckling in 20 species of the Pteridaceae. Strong allometric relationships were observed between sterome thickness and leaf size, with the sterome contributing over 97% to petiole flexural rigidity. Surprisingly, the small-statured cheilanthoid ferns allocated the highest fraction of their petiole to the sterome, while large leaves exploited aspects of geometry (second moment of area) to achieve bending resistance. This pattern also revealed an economy of function in which increasing sterome thickness was associated with decreasing fiber cell reinforcement, and fiber wall fraction. Lastly, strong petioles were associated with durable leaves, as approximated by specific leaf area. This study reveals meaningful patterns in fern leaf biomechanics that align with species leaf size, sterome attributes and life-history strategy.
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Affiliation(s)
- Jennifer N. Mahley
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Jarmila Pittermann
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Nick Rowe
- Botanique et Modélisation de l'Architecture des Plantes et des Végétations (AMAP) TA A-51/PS2, Montpellier, France
| | - Alex Baer
- Department of Biology, California State University, Bakersfield, Bakersfield, CA, United States
| | - James E. Watkins
- Department of Biology, Colgate University, Hamilton, NY, United States
| | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - James K. Wheeler
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Klaus Mehltreter
- Red de Ecología Funcional, Instituto de Ecología, Xalapa, Mexico
| | - Michael Windham
- Department of Biology, Duke University, Durham, NC, United States
| | - Weston Testo
- Pringle Herbarium, Department of Plant Biology, University of Vermont, Burlington, VT, United States
| | - James Beck
- Biological Sciences, Wichita State University, Wichita, KS, United States
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Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. AMERICAN JOURNAL OF BOTANY 2018; 105:385-403. [PMID: 29746719 DOI: 10.1002/ajb2.1016] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/05/2017] [Indexed: 05/21/2023]
Abstract
PREMISE OF THE STUDY Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative. METHODS We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets. KEY RESULTS QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data. CONCLUSIONS Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.
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Affiliation(s)
- James B Pease
- Department of Biology, Wake Forest University, 455 Vine Street, Winston-Salem, North Carolina, 27101, USA
| | - Joseph W Brown
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109, USA
| | - Joseph F Walker
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109, USA
| | - Cody E Hinchliff
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, Idaho, 83844, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University, Ann Arbor, Michigan, 48109, USA
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Sessa EB, Chambers SM, Li D, Trotta L, Endara L, Burleigh JG, Baiser B. Community assembly of the ferns of Florida. AMERICAN JOURNAL OF BOTANY 2018; 105:549-564. [PMID: 29730880 DOI: 10.1002/ajb2.1073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/18/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. METHODS We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic distances and functional trait data for both spatial scales and compared the results to null models to assess significance. KEY RESULTS Our results for over vs. underdispersion in functional and phylogenetic diversity differed depending on spatial scale and metric considered. At the county scale, MPD revealed evidence for phylogenetic overdispersion, while MNTD revealed phylogenetic and functional underdispersion, and at the conservation area scale, MPD revealed phylogenetic and functional underdispersion while MNTD revealed evidence only of functional underdispersion. CONCLUSIONS Our results are consistent with environmental filtering playing a larger role at the smaller, conservation area scale. The smaller spatial units are likely composed of fewer local habitat types that are selecting for closely related species, with the larger-scale units more likely to be composed of multiple habitat types that bring together a larger pool of species from across the phylogeny. Several aspects of fern biology, including their unique physiology and water relations and the importance of the independent gametophyte stage of the life cycle, make ferns highly sensitive to local, microhabitat conditions.
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Affiliation(s)
- Emily B Sessa
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Sally M Chambers
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
- Marie Selby Botanical Gardens, 900 S. Palm Avenue, Sarasota, FL, 34236, USA
| | - Daijiang Li
- Department of Wildlife Ecology & Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | - Lauren Trotta
- Department of Wildlife Ecology & Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | - Lorena Endara
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - J Gordon Burleigh
- Department of Biology, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Benjamin Baiser
- Department of Wildlife Ecology & Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
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Harrison CJ, Morris JL. The origin and early evolution of vascular plant shoots and leaves. Philos Trans R Soc Lond B Biol Sci 2018; 373:20160496. [PMID: 29254961 PMCID: PMC5745332 DOI: 10.1098/rstb.2016.0496] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2017] [Indexed: 12/22/2022] Open
Abstract
The morphology of plant fossils from the Rhynie chert has generated longstanding questions about vascular plant shoot and leaf evolution, for instance, which morphologies were ancestral within land plants, when did vascular plants first arise and did leaves have multiple evolutionary origins? Recent advances combining insights from molecular phylogeny, palaeobotany and evo-devo research address these questions and suggest the sequence of morphological innovation during vascular plant shoot and leaf evolution. The evidence pinpoints testable developmental and genetic hypotheses relating to the origin of branching and indeterminate shoot architectures prior to the evolution of leaves, and demonstrates underestimation of polyphyly in the evolution of leaves from branching forms in 'telome theory' hypotheses of leaf evolution. This review discusses fossil, developmental and genetic evidence relating to the evolution of vascular plant shoots and leaves in a phylogenetic framework.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.
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Affiliation(s)
- C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Jennifer L Morris
- School of Earth Sciences, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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Ruiz-Estévez M, Bakkali M, Martín-Blázquez R, Garrido-Ramos MA. Identification and Characterization of TALE Homeobox Genes in the Endangered Fern Vandenboschia speciosa. Genes (Basel) 2017; 8:E275. [PMID: 29039766 PMCID: PMC5664125 DOI: 10.3390/genes8100275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 12/18/2022] Open
Abstract
We report and discuss the results of a quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the expression patterns of seven three amino acid loop extension (TALE) homeobox genes (four KNOTTED-like homeobox (KNOX) and three BEL1-like homeobox (BELL) genes) identified after next generation sequencing (NGS) and assembly of the sporophyte and gametophyte transcriptomes of the endangered fern species Vandenboschia speciosa. Among the four KNOX genes, two belonged to the KNOX1 class and the other two belonged to the KNOX2 class. Analysis of the deduced amino acid sequences supported the typical domain structure of both types of TALE proteins, and the homology to TALE proteins of mosses, lycophytes, and seed plant species. The expression analyses demonstrate that these homeodomain proteins appear to have a key role in the establishment and development of the gametophyte and sporophyte phases of V. speciosa lifecycle, as well as in the control of the transition between both phases. Vandenboschia speciosa VsKNAT3 (a KNOX2 class protein) as well as VsBELL4 and VsBELL10 proteins have higher expression levels during the sporophyte program. On the contrary, one V. speciosa KNOX1 protein (VsKNAT6) and one KNOX2 protein (VsKNAT4) seem important during the development of the gametophyte phase. TALE homeobox genes might be among the key regulators in the gametophyte-to-sporophyte developmental transition in regular populations that show alternation of generations, since some of the genes analyzed here (VsKNAT3, VsKNAT6, VsBELL4, and VsBELL6) are upregulated in a non-alternating population in which only independent gametophytes are found (they grow by vegetative reproduction outside of the range of sporophyte distribution). Thus, these four genes might trigger the vegetative propagation of the gametophyte and the repression of the sexual development in populations composed of independent gametophytes. This study represents a comprehensive identification and characterization of TALE homeobox genes in V. speciosa, and gives novel insights about the role of these genes in fern development.
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Affiliation(s)
- Mercedes Ruiz-Estévez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Mohammed Bakkali
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Rubén Martín-Blázquez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Manuel A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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57
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Bartels D, Classen B. Structural investigations on arabinogalactan-proteins from a lycophyte and different monilophytes (ferns) in the evolutionary context. Carbohydr Polym 2017; 172:342-351. [DOI: 10.1016/j.carbpol.2017.05.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 01/30/2023]
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Abstract
Plants provide unmatched opportunities to evaluate long debated evolutionary patterns in terms of the detailed biology of the fossil organisms. Leaves serve here as an example of how those advantages can be exploited. Over the history of vascular plants, three important transitions in leaf evolution—the origin of laminate leaves, the progressive loss of seed plant morphological diversity, and the evolution of more angiosperm-like leaves—also represent major shifts in leaf development and physiology. These transitions often occurred in parallel in different lineages, such as the evolution of marginal growth in each of at least four independent origins of laminate leaves during the Devonian and Carboniferous. Each also entailed dramatic reorganizations of leaf hydraulics. For example, the length of the finest distributary vein order varies from up to tens of centimeters down to hundreds of microns in successive groups of dominant seed plants. Angiosperms impose an additional trend upon these patterns with the evolution of their uniquely high vein densities. Vein density strongly influences and can provide a proxy for other physiological characteristics, such as assimilation and transpiration rates. The large increase in transpiration capacity accompanying the evolution of angiosperm leaf traits may even play an important role in feeding precipitation and thereby altering local climate.
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59
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Hidalgo O, Pellicer J, Christenhusz M, Schneider H, Leitch AR, Leitch IJ. Is There an Upper Limit to Genome Size? TRENDS IN PLANT SCIENCE 2017; 22:567-573. [PMID: 28506667 DOI: 10.1016/j.tplants.2017.04.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 05/08/2023]
Abstract
At 50-fold the size of the human genome (3 Gb), the staggeringly huge genome of 147.3 Gb recently discovered in the fern Tmesipteris obliqua is comparable in size to those of the other plant and animal record-holders (i.e., Paris japonica, a flowering plant with a genome size of 148.8 Gb, and Protopterus aethiopicus, a lungfish with a genome of 130 Gb). The synthesis of available information on giant genomes suggests that the biological limit to genome size expansion in eukaryotes may have been reached. We propose several explanations for why the genomes of ferns, flowering plants, and lungfish, all of which have independently undergone dramatic increases in genome size through a variety of mechanisms, do not exceed 150 Gb.
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Affiliation(s)
| | | | | | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London W7 5BD, UK; Xishuangbanna Tropical Botanical Garden, Centre for Integrative Conservation, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, PR China
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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Yang T, Du MF, Guo YH, Liu X. Two LEAFY homologs ILFY1 and ILFY2 control reproductive and vegetative developments in Isoetes L. Sci Rep 2017; 7:225. [PMID: 28331204 PMCID: PMC5412651 DOI: 10.1038/s41598-017-00297-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/17/2017] [Indexed: 11/09/2022] Open
Abstract
LEAFY (LFY) is a plant-specific transcription factor, which is found in algae and all land plants. LFY homologs exert ancestral roles in regulating cell division and obtain novel functions to control floral identity. Isoetes L. is an ancient genus of heterosporous lycophytes. However, characters about LFY homologs in lycophytes remain poorly investigated. In this study, two LFY homologs, ILFY1 and ILFY2, were cloned from five Isoetes species, including I. hypsophila, I. yunguiensis, I. sinensis, I. orientalis, and I. taiwanensis. The full length of ILFY1 was 1449-1456 bp with an open reading frame (ORF) of 927-936 bp. The full length of ILFY2 was 1768 bp with ORF of 726 bp. Phylogenetic tree revealed that ILFY1 and ILFY2 were separated into two clades, and I. hypsophila were separated with the others. Expression analysis demonstrated that IsLFY1 and IsLFY2 for I. sinensis did not show functional diversity. The two transcripts were similarly accumulated in both vegetative and reproductive tissues and highly expressed in juvenile tissues. In addition, the IsLFY1 and IsLFY2 transgenic Arabidopsis similarly did not promote precocious flowering, and they were inactive to rescue lfy mutants. The results facilitate general understandings about the characteristics of LFY in Isoetes and evolutionary process.
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Affiliation(s)
- Tao Yang
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Ming-Fang Du
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - You-Hao Guo
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China.
| | - Xing Liu
- Laboratory of Plant Systematics and Evolutionary Biology, College of Life Science, Wuhan University, Wuhan, Hubei, China.
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Simmons TJ, Fry SC. Bonds broken and formed during the mixed-linkage glucan : xyloglucan endotransglucosylase reaction catalysed by Equisetum hetero-trans-β-glucanase. Biochem J 2017; 474:1055-1070. [PMID: 28108640 PMCID: PMC5341106 DOI: 10.1042/bcj20160935] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/12/2017] [Accepted: 01/19/2017] [Indexed: 11/17/2022]
Abstract
Mixed-linkage glucan∶xyloglucan endotransglucosylase (MXE) is one of the three activities of the recently characterised hetero-trans-β-glucanase (HTG), which among land plants is known only from Equisetum species. The biochemical details of the MXE reaction were incompletely understood - details that would promote understanding of MXE's role in vivo and enable its full technological exploitation. We investigated HTG's site of attack on one of its donor substrates, mixed-linkage (1→3),(1→4)-β-d-glucan (MLG), with radioactive oligosaccharides of xyloglucan as the acceptor substrate. Comparing three different MLG preparations, we showed that the enzyme favours those with a high content of cellotetraose blocks. The reaction products were analysed by enzymic digestion, thin-layer chromatography (TLC), high-pressure liquid chromatography (HPLC) and gel-permeation chromatography (GPC). Equisetum HTG consistently cleaved the MLG at the third consecutive β-(1→4)-bond following (towards the reducing terminus) a β-(1→3)-bond. It then formed a β-(1→4)-bond between the MLG and the non-reducing terminal glucose residue of the xyloglucan oligosaccharide, consistent with its xyloglucan endotransglucosylase/hydrolase subfamily membership. Using size-homogeneous barley MLG as the donor substrate, we showed that HTG does not favour any particular region of the MLG chain relative to the polysaccharide's reducing and non-reducing termini; rather, it selects its target cellotetraosyl unit stochastically along the MLG molecule. This work improves our understanding of how enzymes can exhibit promiscuous substrate specificities and provides the foundations to explore strategies for engineering novel substrate specificities into transglycanases.
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Affiliation(s)
- Thomas J Simmons
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, U.K
| | - Stephen C Fry
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, U.K.
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Nitta JH, Meyer J, Taputuarai R, Davis CC. Life cycle matters:
DNA
barcoding reveals contrasting community structure between fern sporophytes and gametophytes. ECOL MONOGR 2017. [DOI: 10.1002/ecm.1246] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Joel H. Nitta
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria Harvard University Cambridge Massachusetts 02138 USA
| | - Jean‐Yves Meyer
- Délégation à la Recherche Government of French Polynesia B.P. 20981 Papeete, Tahiti French Polynesia
| | - Ravahere Taputuarai
- Association Te Rau Ati Ati a Tau a Hiti Noa Tu B.P. 11553 Mahina, Tahiti French Polynesia
| | - Charles C. Davis
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria Harvard University Cambridge Massachusetts 02138 USA
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Tomescu AMF, Escapa IH, Rothwell GW, Elgorriaga A, Cúneo NR. Developmental programmes in the evolution of Equisetum reproductive morphology: a hierarchical modularity hypothesis. ANNALS OF BOTANY 2017; 119:489-505. [PMID: 28365757 PMCID: PMC5458719 DOI: 10.1093/aob/mcw273] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 09/19/2016] [Accepted: 11/29/2016] [Indexed: 05/30/2023]
Abstract
BACKGROUND The origin of the Equisetum strobilus has long been debated and the fossil record has played an important role in these discussions. The paradigm underlying these debates has been the perspective of the shoot as node-internode alternation, with sporangiophores attached at nodes. However, fossils historically excluded from these discussions (e.g. Cruciaetheca and Peltotheca ) exhibit reproductive morphologies that suggest attachment of sporangiophores along internodes, challenging traditional views. This has rekindled discussions around the evolution of the Equisetum strobilus, but lack of mechanistic explanations has led discussions to a stalemate. SCOPE A shift of focus from the node-internode view to a perspective emphasizing the phytomer as a modular unit of the shoot, frees the debate of homology constraints on the nature of the sporangiophore and inspires a mechanism-based hypothesis for the evolution of the strobilus. The hypothesis, drawing on data from developmental anatomy, regulatory mechanisms and the fossil record, rests on two tenets: (1) the equisetalean shoot grows by combined activity of the apical meristem, laying down the phytomer pattern, and intercalary meristems responsible for internode elongation; and (2) activation of reproductive growth programmes in the intercalary meristem produces sporangiophore whorls along internodes. CONCLUSIONS Hierarchical expression of regulatory modules responsible for (1) transition to reproductive growth; (2) determinacy of apical growth; and (3) node-internode differentiation within phytomers, can explain reproductive morphologies illustrated by Cruciaetheca (module 1 only), Peltotheca (modules 1 and 2) and Equisetum (all three modules). This model has implications - testable by studies of the fossil record, phylogeny and development - for directionality in the evolution of reproductive morphology ( Cruciaetheca - Peltotheca - Equisetum ) and for the homology of the Equisetum stobilus. Furthermore, this model implies that sporangiophore development is independent of node-internode identity, suggesting that the sporangiophore represents the expression of an ancestral euphyllophyte developmental module that pre-dates the evolution of leaves.
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Key Words
- Cruciaetheca, development, Equisetum, Equisetales, evolution, fossil, hierarchy, modularity, Peltotheca, phytomer, sphenopsid, strobilus
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Affiliation(s)
| | - Ignacio H. Escapa
- CONICET, Museo Paleontológico Egidio Feruglio, Avenida Fontana 140, 9100 Trelew, Chubut, Argentina
| | - Gar W. Rothwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Andrés Elgorriaga
- Museo Paleontológico Egidio Feruglio, Avenida Fontana 140, 9100 Trelew, Chubut, Argentina
| | - N. Rubén Cúneo
- Museo Paleontológico Egidio Feruglio, Avenida Fontana 140, 9100 Trelew, Chubut, Argentina
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64
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Gachet MS, Schubert A, Calarco S, Boccard J, Gertsch J. Targeted metabolomics shows plasticity in the evolution of signaling lipids and uncovers old and new endocannabinoids in the plant kingdom. Sci Rep 2017; 7:41177. [PMID: 28120902 PMCID: PMC5264637 DOI: 10.1038/srep41177] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/16/2016] [Indexed: 12/28/2022] Open
Abstract
The remarkable absence of arachidonic acid (AA) in seed plants prompted us to systematically study the presence of C20 polyunsaturated fatty acids, stearic acid, oleic acid, jasmonic acid (JA), N-acylethanolamines (NAEs) and endocannabinoids (ECs) in 71 plant species representative of major phylogenetic clades. Given the difficulty of extrapolating information about lipid metabolites from genetic data we employed targeted metabolomics using LC-MS/MS and GC-MS to study these signaling lipids in plant evolution. Intriguingly, the distribution of AA among the clades showed an inverse correlation with JA which was less present in algae, bryophytes and monilophytes. Conversely, ECs co-occurred with AA in algae and in the lower plants (bryophytes and monilophytes), thus prior to the evolution of cannabinoid receptors in Animalia. We identified two novel EC-like molecules derived from the eicosatetraenoic acid juniperonic acid, an omega-3 structural isomer of AA, namely juniperoyl ethanolamide and 2-juniperoyl glycerol in gymnosperms, lycophytes and few monilophytes. Principal component analysis of the targeted metabolic profiles suggested that distinct NAEs may occur in different monophyletic taxa. This is the first report on the molecular phylogenetic distribution of apparently ancient lipids in the plant kingdom, indicating biosynthetic plasticity and potential physiological roles of EC-like lipids in plants.
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Affiliation(s)
- María Salomé Gachet
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Alexandra Schubert
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Serafina Calarco
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Julien Boccard
- School of Pharmaceutical Science, University of Geneva, University of Lausanne, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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Li X, Han JD, Fang YH, Bai SN, Rao GY. Expression Analyses of Embryogenesis-Associated Genes during Somatic Embryogenesis of Adiantum capillus-veneris L. In vitro: New Insights into the Evolution of Reproductive Organs in Land Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:658. [PMID: 28496454 PMCID: PMC5406782 DOI: 10.3389/fpls.2017.00658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/11/2017] [Indexed: 05/07/2023]
Abstract
An efficient in vitro regeneration system via somatic embryogenesis (SE) was developed for a fern species Adiantum capillus-veneris. Adventitious shoots, green globular bodies (GGBs) and calli were obtained with the maximal induction rate on the Murashige and Skoog (MS) medium of low concentrations of 6-benzyladenine (BA) (0-1.0 mg/L), 2.0 mg/L BA without 2,4-dichlorophenoxyacetic acid (2,4-D), 0.5 mg/L 2,4-D and 0.5-1.0 mg/L 6-BA, respectively. Cyto-morphological and histological changes in the shoot development via calli and GGBs were examined. For a better understanding of these developmental events, expression patterns of six genes, AcLBD16, AcAGL, AcBBM, AcWUS, AcRKD, and AcLEC1, were characterized during SE. AcBBM and AcLEC1 were ubiquitously expressed in direct SE (adventitious shoots and GGBs) the maximal expression of AcBBM in mature GGBs, and the high expression of AcLEC1 in GGB initiation and adventitious shoots. During the indirect SE, AcLBD16, AcLEC1, AcRKD, and AcWUS were highly expressed in mature calli. Additionally, phylogenetic analyses showed that AcWUS, AcBBM, AcLBD, AcAGL, AcRKD, and their homologs of other green plants formed monophyletic clades, respectively. Some of these gene families, however, diversified rapidly with the occurrence of embryophytes, suggesting that embryogenesis-associated genes could experience a rapid evolution with the colonization of plants to terrestrial environments. Expression and phylogenetic analyses of those embryogenesis-associated genes by the aid of in vitro regeneration system of A. capillus-veneris provide new insights into the evolution of reproductive organs in land plants.
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Affiliation(s)
- Xia Li
- RDFZ XiShan SchoolBeijing, China
| | - Jing-Dan Han
- School of Life Sciences, Peking UniversityBeijing, China
| | - Yu-Han Fang
- School of Life Sciences, Peking UniversityBeijing, China
| | - Shu-Nong Bai
- School of Life Sciences, Peking UniversityBeijing, China
| | - Guang-Yuan Rao
- School of Life Sciences, Peking UniversityBeijing, China
- *Correspondence: Guang-Yuan Rao
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66
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Phylogenetic Relationships of the Fern Cyrtomium falcatum (Dryopteridaceae) from Dokdo Island Based on Chloroplast Genome Sequencing. Genes (Basel) 2016; 7:genes7120115. [PMID: 28009803 PMCID: PMC5192491 DOI: 10.3390/genes7120115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/17/2022] Open
Abstract
Cyrtomium falcatum is a popular ornamental fern cultivated worldwide. Native to the Korean Peninsula, Japan, and Dokdo Island in the Sea of Japan, it is the only fern present on Dokdo Island. We isolated and characterized the chloroplast (cp) genome of C. falcatum, and compared it with those of closely related species. The genes trnV-GAC and trnV-GAU were found to be present within the cp genome of C. falcatum, whereas trnP-GGG and rpl21 were lacking. Moreover, cp genomes of Cyrtomium devexiscapulae and Adiantum capillus-veneris lack trnP-GGG and rpl21, suggesting these are not conserved among angiosperm cp genomes. The deletion of trnR-UCG, trnR-CCG, and trnSeC in the cp genomes of C. falcatum and other eupolypod ferns indicates these genes are restricted to tree ferns, non-core leptosporangiates, and basal ferns. The C. falcatum cp genome also encoded ndhF and rps7, with GUG start codons that were only conserved in polypod ferns, and it shares two significant inversions with other ferns, including a minor inversion of the trnD-GUC region and an approximate 3 kb inversion of the trnG-trnT region. Phylogenetic analyses showed that Equisetum was found to be a sister clade to Psilotales-Ophioglossales with a 100% bootstrap (BS) value. The sister relationship between Pteridaceae and eupolypods was also strongly supported by a 100% BS, but Bayesian molecular clock analyses suggested that C. falcatum diversified in the mid-Paleogene period (45.15 ± 4.93 million years ago) and might have moved from Eurasia to Dokdo Island.
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67
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A 4000-species dataset provides new insight into the evolution of ferns. Mol Phylogenet Evol 2016; 105:200-211. [DOI: 10.1016/j.ympev.2016.09.003] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/03/2016] [Accepted: 09/07/2016] [Indexed: 01/17/2023]
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68
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Vasco A, Smalls TL, Graham SW, Cooper ED, Wong GKS, Stevenson DW, Moran RC, Ambrose BA. Challenging the paradigms of leaf evolution: Class III HD-Zips in ferns and lycophytes. THE NEW PHYTOLOGIST 2016; 212:745-758. [PMID: 27385116 DOI: 10.1111/nph.14075] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/23/2016] [Indexed: 05/06/2023]
Abstract
Despite the extraordinary significance leaves have for life on Earth, their origin and development remain vigorously debated. More than a century of paleobotanical, morphological, and phylogenetic research has still not resolved fundamental questions about leaves. Developmental genetic data are sparse in ferns, and comparative studies of lycophytes and seed plants have reached opposing conclusions on the conservation of a leaf developmental program. We performed phylogenetic and expression analyses of a leaf developmental regulator (Class III HD-Zip genes; C3HDZs) spanning lycophytes and ferns. We show that a duplication and neofunctionalization of C3HDZs probably occurred in the ancestor of euphyllophytes, and that there is a common leaf developmental mechanism conserved between ferns and seed plants. We show C3HDZ expression in lycophyte and fern sporangia and show that C3HDZs have conserved expression patterns during initiation of lateral primordia (leaves or sporangia). This expression is maintained throughout sporangium development in lycophytes and ferns and indicates an ancestral role of C3HDZs in sporangium development. We hypothesize that there is a deep homology of all leaves and that a sporangium-specific developmental program was coopted independently for the development of lycophyte and euphyllophyte leaves. This provides molecular genetic support for a paradigm shift in theories of lycophyte leaf evolution.
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Affiliation(s)
- Alejandra Vasco
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
- Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Mexico DF, 04510, Mexico
| | - Tynisha L Smalls
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
| | - Endymion D Cooper
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Robbin C Moran
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA
| | - Barbara A Ambrose
- The New York Botanical Garden, 2900 Southern Blvd, Bronx, NY, 10458-5126, USA.
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69
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Haufler CH, Pryer KM, Schuettpelz E, Sessa EB, Farrar DR, Moran R, Schneller JJ, Watkins JE, Windham MD. Sex and the Single Gametophyte: Revising the Homosporous Vascular Plant Life Cycle in Light of Contemporary Research. Bioscience 2016. [DOI: 10.1093/biosci/biw108] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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70
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Knie N, Grewe F, Knoop V. Monilophyte mitochondrial rps1 genes carry a unique group II intron that likely originated from an ancient paralog in rpl2. RNA (NEW YORK, N.Y.) 2016; 22:1338-48. [PMID: 27354706 PMCID: PMC4986890 DOI: 10.1261/rna.056572.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/19/2016] [Indexed: 05/10/2023]
Abstract
Intron patterns in plant mitochondrial genomes differ significantly between the major land plant clades. We here report on a new, clade-specific group II intron in the rps1 gene of monilophytes (ferns). This intron, rps1i25g2, is strikingly similar to rpl2i846g2 previously identified in the mitochondrial rpl2 gene of seed plants, ferns, and the lycophyte Phlegmariurus squarrosus Although mitochondrial ribosomal protein genes are frequently subject to endosymbiotic gene transfer among plants, we could retrieve the mitochondrial rps1 gene in a taxonomically wide sampling of 44 monilophyte taxa including basal lineages such as the Ophioglossales, Psilotales, and Marattiales with the only exception being the Equisetales (horsetails). Introns rps1i25g2 and rpl2i846g2 were likewise consistently present with only two exceptions: Intron rps1i25g2 is lost in the genus Ophioglossum and intron rpl2i846g2 is lost in Equisetum bogotense Both intron sequences are moderately affected by RNA editing. The unprecedented primary and secondary structure similarity of rps1i25g2 and rpl2i846g2 suggests an ancient retrotransposition event copying rpl2i846g2 into rps1, for which we suggest a model. Our phylogenetic analysis adding the new rps1 locus to a previous data set is fully congruent with recent insights on monilophyte phylogeny and further supports a sister relationship of Gleicheniales and Hymenophyllales.
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Affiliation(s)
- Nils Knie
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, D-53115 Bonn, Germany
| | - Felix Grewe
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, D-53115 Bonn, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, IZMB-Institut für Zelluläre und Molekulare Botanik, Universität Bonn, D-53115 Bonn, Germany
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71
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Cullen E, Rudall PJ. The remarkable stomata of horsetails (Equisetum): patterning, ultrastructure and development. ANNALS OF BOTANY 2016; 118:207-18. [PMID: 27268485 PMCID: PMC4970360 DOI: 10.1093/aob/mcw094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/18/2016] [Accepted: 03/31/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS The stomata of Equisetum - the sole extant representative of an ancient group of land plants - are unique with respect to both structure and development, yet little is known about details of ultrastructure and patterning, and existing accounts of key developmental stages are conflicting. METHODS We used light and electron microscopy to examine mature stomata and stomatal development in Equisetum myriochaetum, and compared them with other land plants, including another putative fern relative, Psilotum We reviewed published reports of stomatal development to provide a comprehensive discussion of stomata in more distantly related taxa. KEY RESULTS Stomatal development in Equisetum is basipetal and sequential in strict linear cell files, in contrast with Psilotum, in which stomatal development occurs acropetally. In Equisetum, cell asymmetry occurs in the axial stomatal cell file, resulting in a meristemoidal mother cell that subsequently undergoes two successive asymmetric mitoses. Each stomatal cell complex is formed from a single precursor meristemoid, and consists of four cells: two guard cells and two mesogene subsidiary cells. Late periclinal divisions occur in the developing intervening cells. CONCLUSIONS In addition to the unique mature structure, several highly unusual developmental features include a well-defined series of asymmetric and symmetric mitoses in Equisetum, which differs markedly from Psilotum and other land plants. The results contribute to our understanding of the diverse patterns of stomatal development in land plants, including contrasting pathways to paracytic stomata. They add to a considerable catalogue of highly unusual traits of horsetails - one of the most evolutionarily isolated land-plant taxa.
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Affiliation(s)
- Erin Cullen
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
| | - Paula J Rudall
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK
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72
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Knie N, Grewe F, Fischer S, Knoop V. Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles. BMC Evol Biol 2016; 16:134. [PMID: 27329857 PMCID: PMC4915041 DOI: 10.1186/s12862-016-0707-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA editing by C-to-U conversions is nearly omnipresent in land plant chloroplasts and mitochondria, where it mainly serves to reconstitute conserved codon identities in the organelle mRNAs. Reverse U-to-C RNA editing in contrast appears to be restricted to hornworts, some lycophytes, and ferns (monilophytes). A well-resolved monilophyte phylogeny has recently emerged and now allows to trace the side-by-side evolution of both types of pyrimidine exchange editing in the two endosymbiotic organelles. RESULTS Our study of RNA editing in four selected mitochondrial genes show a wide spectrum of divergent RNA editing frequencies including a dominance of U-to-C over the canonical C-to-U editing in some taxa like the order Schizaeales. We find that silent RNA editing leaving encoded amino acids unchanged is highly biased with more than ten-fold amounts of silent C-to-U over U-to-C edits. In full contrast to flowering plants, RNA editing frequencies are low in early-branching monilophyte lineages but increase in later emerging clades. Moreover, while editing rates in the two organelles are usually correlated, we observe uncoupled evolution of editing frequencies in fern mitochondria and chloroplasts. Most mitochondrial RNA editing sites are shared between the recently emerging fern orders whereas chloroplast editing sites are mostly clade-specific. Finally, we observe that chloroplast RNA editing appears to be completely absent in horsetails (Equisetales), the sister clade of all other monilophytes. CONCLUSIONS C-to-U and U-to-C RNA editing in fern chloroplasts and mitochondria follow disinct evolutionary pathways that are surprisingly different from what has previously been found in flowering plants. The results call for careful differentiation of the two types of RNA editing in the two endosymbiotic organelles in comparative evolutionary studies.
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Affiliation(s)
- Nils Knie
- Abteilung Molekulare Evolution, IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany
| | - Felix Grewe
- Present address: Department of Science and Education, Field Museum of Natural History, Integrative Research Center, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Simon Fischer
- Present address: Protrans medizinisch diagnostische Produkte GmbH, Ketschau 2, D-68766, Hockenheim, Germany
| | - Volker Knoop
- Abteilung Molekulare Evolution, IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Kirschallee 1, D-53115, Bonn, Germany.
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73
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Clark J, Hidalgo O, Pellicer J, Liu H, Marquardt J, Robert Y, Christenhusz M, Zhang S, Gibby M, Leitch IJ, Schneider H. Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. THE NEW PHYTOLOGIST 2016; 210:1072-82. [PMID: 26756823 DOI: 10.1111/nph.13833] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/16/2015] [Indexed: 05/06/2023]
Abstract
The genome evolution of ferns has been considered to be relatively static compared with angiosperms. In this study, we analyse genome size data and chromosome numbers in a phylogenetic framework to explore three hypotheses: the correlation of genome size and chromosome number, the origin of modern ferns from ancestors with high chromosome numbers, and the occurrence of several whole-genome duplications during the evolution of ferns. To achieve this, we generated new genome size data, increasing the percentage of fern species with genome sizes estimated to 2.8% of extant diversity, and ensuring a comprehensive phylogenetic coverage including at least three species from each fern order. Genome size was correlated with chromosome number across all ferns despite some substantial variation in both traits. We observed a trend towards conservation of the amount of DNA per chromosome, although Osmundaceae and Psilotaceae have substantially larger chromosomes. Reconstruction of the ancestral genome traits suggested that the earliest ferns were already characterized by possessing high chromosome numbers and that the earliest divergences in ferns were correlated with substantial karyological changes. Evidence for repeated whole-genome duplications was found across the phylogeny. Fern genomes tend to evolve slowly, albeit genome rearrangements occur in some clades.
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Affiliation(s)
- James Clark
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Hongmei Liu
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & The Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Jeannine Marquardt
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Yannis Robert
- 18, Rue des Capucines, F-97431, La Plaine des Palmistes, La Réunion, France
| | - Maarten Christenhusz
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
- Plant Gateway, 5 Talbot Street, Hertford, Hertfordshire, SG13 7BX, UK
| | - Shouzhou Zhang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & The Chinese Academy of Sciences, Shenzhen, 518004, China
| | - Mary Gibby
- Department of Science, Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Harald Schneider
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
- School of Life Sciences, Sun Yatsen University, Guangzhou, 510275, Guangdong, China
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Blanke A, Rühr PT, Mokso R, Villanueva P, Wilde F, Stampanoni M, Uesugi K, Machida R, Misof B. Structural mouthpart interaction evolved already in the earliest lineages of insects. Proc Biol Sci 2016. [PMID: 26203002 DOI: 10.1098/rspb.2015.1033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In butterflies, bees, flies and true bugs specific mouthparts are in close contact or even fused to enable piercing, sucking or sponging of particular food sources. The common phenomenon behind these mouthpart types is a complex composed of several consecutive mouthparts which structurally interact during food uptake. The single mouthparts are thus only functional in conjunction with other adjacent mouthparts, which is fundamentally different to biting-chewing. It is, however, unclear when structural mouthpart interaction (SMI) evolved since this principle obviously occurred multiple times independently in several extant and extinct winged insect groups. Here, we report a new type of SMI in two of the earliest wingless hexapod lineages--Diplura and Collembola. We found that the mandible and maxilla interact with each other via an articulatory stud at the dorsal side of the maxillary stipes, and they are furthermore supported by structures of the hypopharynx and head capsule. These interactions are crucial stabilizing elements during food uptake. The presence of SMI in these ancestrally wingless insects, and its absence in those crustacean groups probably ancestral to insects, indicates that SMI is a groundplan apomorphy of insects. Our results thus contradict the currently established view of insect mouthpart evolution that biting-chewing mouthparts without any form of SMI are the ancestral configuration. Furthermore, SMIs occur in the earliest insects in a high anatomical variety. SMIs in stemgroup representatives of insects may have triggered efficient exploitation and fast adaptation to new terrestrial food sources much earlier than previously supposed.
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Affiliation(s)
- Alexander Blanke
- Sugadaira Montane Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Peter T Rühr
- Zentrum für Molekulare Biodiversitätsforschung, Zoologisches Forschungsmuseum Alexander Koenig, Bonn 53113, Germany
| | - Rajmund Mokso
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Pablo Villanueva
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | - Fabian Wilde
- Helmholtz-Zentrum Geesthacht, Zentrum für Material- und Küstenforschung GmbH, Geesthacht 21502, Germany
| | - Marco Stampanoni
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Kentaro Uesugi
- Japan Synchrotron Radiation Research Institute/SPring-8, Sayo, Hyogo 679-5198, Japan
| | - Ryuichiro Machida
- Sugadaira Montane Research Center, University of Tsukuba, Sugadaira Kogen, Ueda, Nagano 386-2204, Japan
| | - Bernhard Misof
- Zentrum für Molekulare Biodiversitätsforschung, Zoologisches Forschungsmuseum Alexander Koenig, Bonn 53113, Germany
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Pinson JB, Schuettpelz E. Unraveling the origin of the Appalachian gametophyte, Vittaria appalachiana. AMERICAN JOURNAL OF BOTANY 2016; 103:668-676. [PMID: 27033317 DOI: 10.3732/ajb.1500522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/25/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF STUDY Ferns and lycophytes are distinct among plants in producing two free-living life stages: a long-lived sporophyte phase and a (usually) short-lived gametophyte phase. Notably, however, some species have perennial, vegetatively reproducing gametophytes. Vittaria appalachiana is one of just three species in which mature sporophytes are unknown. It has a wide range throughout the Appalachian Mountains and Plateau, where it reproduces asexually via gemmae. The origin of V. appalachiana, however, has long been a mystery, with most previous studies suggesting it may have resulted from hybridization of two closely related Vittaria species (V. graminifolia and V. lineata). METHODS A four-gene plastid data set including 32 samples of six Vittaria species, plus samples of five outgroup species, was analyzed to uncover phylogenetic relationships. Additional analyses of nuclear DET1 gene sequences allowed for the examination of hypotheses involving a hybrid origin for V. appalachiana. KEY RESULTS In the plastid phylogeny, V. appalachiana is well supported as monophyletic, but is embedded within V. graminifolia. With the exception of a single aberrant allele, this result is mirrored in the nuclear tree. CONCLUSIONS Through analyses of plastid and nuclear data sets, this study demonstrates that a hybrid origin for V. appalachiana is unlikely. Instead, it appears that this species emerged from within the V. graminifolia lineage. Further work is needed to fully elucidate the genetic structure within this group.
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Affiliation(s)
- Jerald B Pinson
- Department of Biology, University of Florida, Gainesville, Florida 32611-8525 USA
| | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, MRC 166 PO Box 37012 Washington, District of Columbia 20013-7012 USA
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76
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Arana MD, Larsen C, Ponce MM. Revisión y análisis panbiogeográfico de las Hymenophyllaceae de las Yungas meridionales de Argentina (Selva Tucumano-Boliviana). RODRIGUÉSIA 2016. [DOI: 10.1590/2175-7860201667105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hymenophyllaceae constituye uno de los linajes más tempranamente divergente dentro de los helechos, habitan lugares hiperhúmedos y su aparición se ha datado en el cretácico temprano, previa a la ruptura de Gondwana; estas características determinan que sean especialmente útiles para establecer patrones biogeográficos. En este trabajo se discuten la diversidad de la familia Hymenophyllaceae en las Yungas meridionales y sus vinculaciones biogeográficas, mediante un análisis panbiogeográfico. Se han encontrado nueve especies, comprendidas en cuatro géneros: Crepidomanes, Didymoglossum, Hymenophyllum y Polyphlebium; Crepidomanes pyxidiferum constituye una novedad florística a nivel genérico para Argentina. Se brindan una clave para todos los géneros de Hymenophyllaceae presentes en Argentina, así como claves entre todas las especies presentes en las Yungas, que además son descriptas e ilustradas.
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Affiliation(s)
| | - Cristian Larsen
- Academia Nacional de Ciencias Exactas, Físicas y Naturales, Argentina
| | - M. Mónica Ponce
- Academia Nacional de Ciencias Exactas, Físicas y Naturales, Argentina
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77
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AVCI MK, AYVAZ M, UYSAL H, SEVİNDİK E, ÖRENAY BOYACIOĞLU S, YAMANER Ç. Order-wide in silico comparative analysis and identification ofgrowth-regulating factor proteins in Malpighiales. Turk J Biol 2016. [DOI: 10.3906/biy-1502-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Ge Y, Liu J, Zeng M, He J, Qin P, Huang H, Xu L. Identification of WOX Family Genes in Selaginella kraussiana for Studies on Stem Cells and Regeneration in Lycophytes. FRONTIERS IN PLANT SCIENCE 2016; 7:93. [PMID: 26904063 PMCID: PMC4742569 DOI: 10.3389/fpls.2016.00093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/18/2016] [Indexed: 05/02/2023]
Abstract
Plant stem cells give rise to all tissues and organs and also serve as the source for plant regeneration. The organization of plant stem cells has undergone a progressive change from simple to complex during the evolution of vascular plants. Most studies on plant stem cells have focused on model angiosperms, the most recently diverged branch of vascular plants. However, our knowledge of stem cell function in other vascular plants is limited. Lycophytes and euphyllophytes (ferns, gymnosperms, and angiosperms) are two existing branches of vascular plants that separated more than 400 million years ago. Lycophytes retain many of the features of early vascular plants. Based on genome and transcriptome data, we identified WUSCHEL-RELATED HOMEOBOX (WOX) genes in Selaginella kraussiana, a model lycophyte that is convenient for in vitro culture and observations of organ formation and regeneration. WOX genes are key players controlling stem cells in plants. Our results showed that the S. kraussiana genome encodes at least eight members of the WOX family, which represent an early stage of WOX family evolution. Identification of WOX genes in S. kraussiana could be a useful tool for molecular studies on the function of stem cells in lycophytes.
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Affiliation(s)
- Yachao Ge
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Jie Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Minhuan Zeng
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Jianfeng He
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Peng Qin
- Department of Instrumentation Science and Engineering, Shanghai Jiao Tong UniversityShanghai, China
| | - Hai Huang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Lin Xu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Lin Xu,
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79
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Morozov SY, Milyutina IA, Bobrova VK, Ryazantsev DY, Erokhina TN, Zavriev SK, Agranovsky AA, Solovyev AG, Troitsky AV. Structural evolution of the 4/1 genes and proteins in non-vascular and lower vascular plants. Biochimie 2015; 119:125-36. [PMID: 26542289 DOI: 10.1016/j.biochi.2015.10.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 10/29/2015] [Indexed: 12/19/2022]
Abstract
The 4/1 protein of unknown function is encoded by a single-copy gene in most higher plants. The 4/1 protein of Nicotiana tabacum (Nt-4/1 protein) has been shown to be alpha-helical and predominantly expressed in conductive tissues. Here, we report the analysis of 4/1 genes and the encoded proteins of lower land plants. Sequences of a number of 4/1 genes from liverworts, lycophytes, ferns and gymnosperms were determined and analyzed together with sequences available in databases. Most of the vascular plants were found to encode Magnoliophyta-like 4/1 proteins exhibiting previously described gene structure and protein properties. Identification of the 4/1-like proteins in hornworts, liverworts and charophyte algae (sister lineage to all land plants) but not in mosses suggests that 4/1 proteins are likely important for plant development but not required for a primary metabolic function of plant cell.
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Affiliation(s)
- Sergey Y Morozov
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, Moscow 119992, Russia; A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia.
| | - Irina A Milyutina
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Vera K Bobrova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Dmitry Y Ryazantsev
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia
| | - Tatiana N Erokhina
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia
| | - Sergey K Zavriev
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia
| | - Alexey A Agranovsky
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexey V Troitsky
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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81
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Simmons TJ, Mohler KE, Holland C, Goubet F, Franková L, Houston DR, Hudson AD, Meulewaeter F, Fry SC. Hetero-trans-β-glucanase, an enzyme unique to Equisetum plants, functionalizes cellulose. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:753-69. [PMID: 26185964 PMCID: PMC4950035 DOI: 10.1111/tpj.12935] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/12/2015] [Accepted: 06/24/2015] [Indexed: 05/18/2023]
Abstract
Cell walls are metabolically active components of plant cells. They contain diverse enzymes, including transglycanases (endotransglycosylases), enzymes that 'cut and paste' certain structural polysaccharide molecules and thus potentially remodel the wall during growth and development. Known transglycanase activities modify several cell-wall polysaccharides (xyloglucan, mannans, mixed-linkage β-glucan and xylans); however, no transglycanases were known to act on cellulose, the principal polysaccharide of biomass. We now report the discovery and characterization of hetero-trans-β-glucanase (HTG), a transglycanase that targets cellulose, in horsetails (Equisetum spp., an early-diverging genus of monilophytes). HTG is also remarkable in predominantly catalysing hetero-transglycosylation: its preferred donor substrates (cellulose or mixed-linkage β-glucan) differ qualitatively from its acceptor substrate (xyloglucan). HTG thus generates stable cellulose-xyloglucan and mixed-linkage β-glucan-xyloglucan covalent bonds, and may therefore strengthen ageing Equisetum tissues by inter-linking different structural polysaccharides of the cell wall. 3D modelling suggests that only three key amino acid substitutions (Trp → Pro, Gly → Ser and Arg → Leu) are responsible for the evolution of HTG's unique specificity from the better-known xyloglucan-acting homo-transglycanases (xyloglucan endotransglucosylase/hydrolases; XTH). Among land plants, HTG appears to be confined to Equisetum, but its target polysaccharides are widespread, potentially offering opportunities for enhancing crop mechanical properties, such as wind resistance. In addition, by linking cellulose to xyloglucan fragments previously tagged with compounds such as dyes or indicators, HTG may be useful biotechnologically for manufacturing stably functionalized celluloses, thereby potentially offering a commercially valuable 'green' technology for industrially manipulating biomass.
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Affiliation(s)
- Thomas J Simmons
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Kyle E Mohler
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Claire Holland
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Florence Goubet
- Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052, Gent, Belgium
| | - Lenka Franková
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Douglas R Houston
- Institute of Structural and Molecular Biology, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JR, UK
| | - Andrew D Hudson
- Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Frank Meulewaeter
- Bayer CropScience NV, Innovation Center, Technologiepark 38, 9052, Gent, Belgium
| | - Stephen C Fry
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, The University of Edinburgh, Edinburgh, EH9 3BF, UK
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82
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Nishida K, Kodama N, Yonemura S, Hanba YT. Rapid response of leaf photosynthesis in two fern species Pteridium aquilinum and Thelypteris dentata to changes in CO2 measured by tunable diode laser absorption spectroscopy. JOURNAL OF PLANT RESEARCH 2015; 128:777-89. [PMID: 26038271 PMCID: PMC4550647 DOI: 10.1007/s10265-015-0736-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 04/20/2015] [Indexed: 05/10/2023]
Abstract
We investigated stomatal conductance (g(s)) and mesophyll conductance (g(m)) in response to atmospheric CO2 concentration [CO2] in two primitive land plants, the fern species Pteridium aquilinum and Thelypteris dentata, using the concurrent measurement of leaf gas exchange and carbon isotope discrimination. [CO2] was initially decreased from 400 to 200 μmol mol(-1), and then increased from 200 to 700 μmol mol(-1), and finally decreased from 700 to 400 μmol mol(-1). Analysis by tunable diode laser absorption spectroscopy (TDLAS) revealed a rapid and continuous response in g m within a few minutes. In most cases, both ferns showed rapid and significant responses of g m to changes in [CO2]. The largest changes (quote % decrease) were obtained when [CO2] was decreased from 400 to 200 μmol mol(-1). This is in contrast to angiosperms where an increase in g(m) is commonly observed at low [CO2]. Similarly, fern species observed little or no response of g(s) to changes in [CO2] whereas, a concomitant decline of g(m) and g(s) with [CO2] is often reported in angiosperms. Together, these results suggest that regulation of g(m) to [CO2] may differ between angiosperms and ferns.
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Affiliation(s)
- Keisuke Nishida
- The Graduate School of Science, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan,
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83
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Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns. Mol Phylogenet Evol 2015; 90:140-9. [DOI: 10.1016/j.ympev.2015.05.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/09/2015] [Accepted: 05/11/2015] [Indexed: 11/23/2022]
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84
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Wolf PG, Sessa EB, Marchant DB, Li FW, Rothfels CJ, Sigel EM, Gitzendanner MA, Visger CJ, Banks JA, Soltis DE, Soltis PS, Pryer KM, Der JP. An Exploration into Fern Genome Space. Genome Biol Evol 2015; 7:2533-44. [PMID: 26311176 PMCID: PMC4607520 DOI: 10.1093/gbe/evv163] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
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Affiliation(s)
- Paul G Wolf
- Ecology Center and Department of Biology, Utah State University
| | - Emily B Sessa
- Department of Biology, University of Florida Genetics Institute, University of Florida
| | - Daniel Blaine Marchant
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | | | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley
| | - Erin M Sigel
- Department of Biology, Duke University Present address: Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Clayton J Visger
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University
| | - Douglas E Soltis
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Pamela S Soltis
- Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | | | - Joshua P Der
- Department of Biological Science, California State University, Fullerton
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85
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Zhou XM, Rothfels CJ, Zhang L, He ZR, Le Péchon T, He H, Lu NT, Knapp R, Lorence D, He XJ, Gao XF, Zhang LB. A large-scale phylogeny of the lycophyte genusSelaginella(Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci. Cladistics 2015; 32:360-389. [DOI: 10.1111/cla.12136] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Xin-Mao Zhou
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
- School of Life Sciences; Sichuan University; Chengdu Sichuan 610064 China
| | - Carl J. Rothfels
- Department of Zoology; University of British Columbia; #4200-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- University Herbarium and Department of Integrative Biology; University of California; Berkeley CA 94720-2465 USA
| | - Liang Zhang
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
| | - Zhao-Rong He
- School of Life Science; Yunnan University; Kunming Yunnan 650091 China
| | - Timothée Le Péchon
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
- School of Life Sciences; University of KwaZulu-Natal; Private Bag X01 Scottsville Pietermaritzburg 3209 South Africa
| | - Hai He
- Department of Biology; Chongqing Normal University; Shapingba, Chongqing 400047 China
| | - Ngan Thi Lu
- Department of Botany, Vietnam National Museum of Nature; Vietnam Academy of Science and Technology; 18th Hoang Quoc Viet Road Cau Giay, Ha Noi Viet Nam
| | - Ralf Knapp
- Correspondent of the Muséum national d'Histoire naturelle (MNHN, Paris, France); Steigestrasse 78 69412 Eberbach Germany
| | - David Lorence
- National Tropical Botanical Garden; 3530 Papalina Road Kalaheo HI 96741 USA
| | - Xing-Jin He
- School of Life Sciences; Sichuan University; Chengdu Sichuan 610064 China
| | - Xin-Fen Gao
- Chengdu Institute of Biology; Chinese Academy of Sciences; PO Box 416 Chengdu Sichuan 610041 China
| | - Li-Bing Zhang
- Missouri Botanical Garden; PO Box 299 St Louis MO 63166-0299 USA
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86
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Frank MH, Edwards MB, Schultz ER, McKain MR, Fei Z, Sørensen I, Rose JKC, Scanlon MJ. Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages. THE NEW PHYTOLOGIST 2015; 207:893-904. [PMID: 25900772 DOI: 10.1111/nph.13407] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/04/2015] [Indexed: 05/18/2023]
Abstract
Shoot apical meristem (SAM) structure varies markedly within the land plants. The SAMs of many seedless vascular plants contain a conspicuous inverted, pyramidal cell called the apical cell (AC), which is unidentified in angiosperms. In this study, we use transcriptomic sequencing with precise laser microdissections of meristem subdomains to define the molecular signatures of anatomically distinct zones from the AC-type SAMs of a lycophyte (Selaginella moellendorffii) and a monilophyte (Equisetum arvense). The two model species for this study represent vascular plant lineages that diverged > 400 million yr ago. Our data comprise comprehensive molecular signatures for the distinct subdomains within AC-type SAMs, an anatomical anomaly whose functional significance has been debated in the botanical literature for over two centuries. Moreover, our data provide molecular support for distinct gene expression programs between the AC-type SAMs of Selaginella and Equisetum, as compared with the SAM transcriptome of the angiosperm maize. The results are discussed in light of the functional significance and evolutionary success of the AC-type SAM within the embryophytes.
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Affiliation(s)
- Margaret H Frank
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Molly B Edwards
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Eric R Schultz
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, 14853, USA
- USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Iben Sørensen
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Jocelyn K C Rose
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Michael J Scanlon
- Department of Plant Biology, Cornell University, Ithaca, NY, 14853, USA
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87
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Abotsi KE, Radji AR, Rouhan G, Dubuisson JY, Kokou K. The Pteridaceae family diversity in Togo. Biodivers Data J 2015; 3:e5078. [PMID: 26312048 PMCID: PMC4549653 DOI: 10.3897/bdj.3.e5078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/10/2015] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The Pteridaceae family is the largest fern family in Togo by its specific and generic diversity. Like all other families of ferns in the country, Pteridaceae are poorly studied and has no identification key. The objective of this study is to perform a taxonomic revision and list establishment of this family of leptosporangiate ferns in the light of current available knowledge about the family. Pteridaceae was also assessed in terms of its diversity and conservation status, this was conducted through the recent field data and the existing herbaria specimens. The current study permits to confirm the presence of Pteris similis Kuhn. which brought the number of Pteridaceae to 17 in Togo. NEW INFORMATION This study provides first local scientific information about the fern flora of Togo. It confirmed the presence of Pterissimilis Kuhn. in Togo and brought the Pteridaceae family diversity to 17 species. A species identification key is provided for the easy identification of the Pteridaceae of Togo.
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Affiliation(s)
| | | | - Germinal Rouhan
- Museum National d'Histoire Naturelle, Paris cedex 05, France
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88
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Rothfels CJ, Li FW, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GKS, Pryer KM. The evolutionary history of ferns inferred from 25 low-copy nuclear genes. AMERICAN JOURNAL OF BOTANY 2015. [PMID: 26199366 DOI: 10.3732/ajb.1500089] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data.• METHODS Here we take a curated phylogenomics approach to infer the first broad fern phylogeny from multiple nuclear loci, by combining broad taxon sampling (73 ferns and 12 outgroup species) with focused character sampling (25 loci comprising 35877 bp), along with rigorous alignment, orthology inference and model selection.• KEY RESULTS Our phylogeny corroborates some earlier inferences and provides novel insights; in particular, we find strong support for Equisetales as sister to the rest of ferns, Marattiales as sister to leptosporangiate ferns, and Dennstaedtiaceae as sister to the eupolypods. Our divergence-time analyses reveal that divergences among the extant fern orders all occurred prior to ∼200 MYA. Finally, our species-tree inferences are congruent with analyses of concatenated data, but generally with lower support. Those cases where species-tree support values are higher than expected involve relationships that have been supported by smaller plastid datasets, suggesting that deep coalescence may be reducing support from the concatenated nuclear data.• CONCLUSIONS Our study demonstrates the utility of a curated phylogenomics approach to inferring fern phylogeny, and highlights the need to consider underlying data characteristics, along with data quantity, in phylogenetic studies.
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Affiliation(s)
- Carl J Rothfels
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Fay-Wei Li
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Erin M Sigel
- Department of Botany (MRC 166), National Museum of Natural History, Smithsonian Institution, P.O. Box 37012 Washington, District of Columbia 20013-7012 USA
| | - Layne Huiet
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
| | - Anders Larsson
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dylan O Burge
- California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 USA
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, Scotland, UK
| | - Michael Deyholos
- Department of Biology, University of British Columbia, Okanagan Campus, 1177 Research Road, Kelowna, British Columbia V1V 1V7, Canada
| | - Douglas E Soltis
- Florida Museum of Natural History, Department of Biology, and the Genetics Institute. University of Florida. Gainesville, Florida 32611 USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | | | - Lisa Pokorny
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico-Consejo Superior de Investigaciones Científicas, 28014 Madrid, Spain
| | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Claude dePamphilis
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 USA
| | - Lisa DeGironimo
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Li Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Xiao Sun
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Petra Korall
- Systematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
| | - Dennis W Stevenson
- The New York Botanical Garden, 2900 Southern Blvd., Bronx, New York 10458 USA
| | - Sean W Graham
- Department of Botany & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6J 3S7, Canada
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada Department of Medicine, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Kathleen M Pryer
- Department of Biology, Duke University, Durham, North Carolina 27708 USA
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89
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Silvestro D, Cascales‐Miñana B, Bacon CD, Antonelli A. Revisiting the origin and diversification of vascular plants through a comprehensive Bayesian analysis of the fossil record. THE NEW PHYTOLOGIST 2015; 207:425-436. [PMID: 25619401 PMCID: PMC4949670 DOI: 10.1111/nph.13247] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 11/23/2014] [Indexed: 05/18/2023]
Abstract
Plants have a long evolutionary history, during which mass extinction events dramatically affected Earth's ecosystems and its biodiversity. The fossil record can shed light on the diversification dynamics of plant life and reveal how changes in the origination-extinction balance have contributed to shaping the current flora. We use a novel Bayesian approach to estimate origination and extinction rates in plants throughout their history. We focus on the effect of the 'Big Five' mass extinctions and on estimating the timing of origin of vascular plants, seed plants and angiosperms. Our analyses show that plant diversification is characterized by several shifts in origination and extinction rates, often matching the most important geological boundaries. The estimated origin of major plant clades predates the oldest macrofossils when considering the uncertainties associated with the fossil record and the preservation process. Our findings show that the commonly recognized mass extinctions have affected each plant group differently and that phases of high extinction often coincided with major floral turnovers. For instance, after the Cretaceous-Paleogene boundary we infer negligible shifts in diversification of nonflowering seed plants, but find significantly decreased extinction in spore-bearing plants and increased origination rates in angiosperms, contributing to their current ecological and evolutionary dominance.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental SciencesUniversity of GothenburgCarl Skottsbergs gata 22BSE‐413 19GöteborgSweden
| | - Borja Cascales‐Miñana
- CNRSUMR Botanique et Bioinformatique de l'Architecture des Plantes (AMAP)MontpellierF‐34000France
- Present address: PPPDépartement de GéologieUniversité de LiègeAllée du 6 AoûtB18 Sart TilmanB4000LiègeBelgium
| | - Christine D. Bacon
- Department of Biological and Environmental SciencesUniversity of GothenburgCarl Skottsbergs gata 22BSE‐413 19GöteborgSweden
- Laboratório de Biología Molecular (CINBIN)Department of BiologyUniversidad Industrial de SantanderBucaramangaColombia
| | - Alexandre Antonelli
- Department of Biological and Environmental SciencesUniversity of GothenburgCarl Skottsbergs gata 22BSE‐413 19GöteborgSweden
- Gothenburg Botanical GardenCarl Skottsbergs gata 22ASE‐413 19GöteborgSweden
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90
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Mikuła A, Pożoga M, Tomiczak K, Rybczyński JJ. Somatic embryogenesis in ferns: a new experimental system. PLANT CELL REPORTS 2015; 34:783-794. [PMID: 25599853 PMCID: PMC4405229 DOI: 10.1007/s00299-015-1741-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/16/2014] [Accepted: 01/06/2015] [Indexed: 05/30/2023]
Abstract
Somatic embryogenesis has never been reported in ferns. The study showed that it is much easier to evoke the acquisition and expression of embryogenic competence in ferns than in spermatophytes. We discovered that the tree fern Cyathea delgadii offers an effective model for the reproducible and rapid formation of somatic embryos on hormone-free medium. Our study provides cyto-morphological evidence for the single cell origin and development of somatic embryos. Somatic embryogenesis (SE) in both primary and secondary explants was induced on half-strength micro- and macro-nutrients Murashige and Skoog medium without the application of exogenous plant growth regulators, in darkness. The early stage of SE was characterized by sequential perpendicular cell divisions of an individual epidermal cell of etiolated stipe explant. These resulted in the formation of a linear pro-embryo. Later their development resembled that of the zygotic embryo. We defined three morphogenetic stages of fern somatic embryo development: linear, early and late embryonic leaf stage. The transition from somatic embryo to juvenile sporophyte was quick and proceeded without interruption caused by dormancy. Following 9 weeks of culture the efficiency of somatic embryogenesis reached 12-13 embryos per responding explant. Spontaneous formation of somatic embryos and callus production, which improved the effectiveness of the process sevenfold in 10-month-long culture, occurred without subculturing. The tendency for C. delgadii to propagate by SE in vitro makes this species an excellent model for studies relating to asexual embryogenesis and the endogenous hormonal regulation of that process and opens new avenues of experimentation.
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Affiliation(s)
- Anna Mikuła
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-973, Warsaw, Poland,
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91
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Inamine S, Onaga S, Ohnuma T, Fukamizo T, Taira T. Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (Equisetum arvense). Biosci Biotechnol Biochem 2015; 79:1296-304. [PMID: 25818933 DOI: 10.1080/09168451.2015.1025693] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chitinase-A (EaChiA), molecular mass 36 kDa, was purified from the vegetative stems of a horsetail (Equisetum arvense) using a series of column chromatography. The N-terminal amino acid sequence of EaChiA was similar to the lysin motif (LysM). A cDNA encoding EaChiA was cloned by rapid amplification of cDNA ends and polymerase chain reaction. It consisted of 1320 nucleotides and encoded an open reading frame of 361 amino acid residues. The deduced amino acid sequence indicated that EaChiA is composed of a N-terminal LysM domain and a C-terminal plant class IIIb chitinase catalytic domain, belonging to the glycoside hydrolase family 18, linked by proline-rich regions. EaChiA has strong chitin-binding activity, however, no antifungal activity. This is the first report of a chitinase from Equisetopsida, a class of fern plants, and the second report of a LysM-containing chitinase from a plant.
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Affiliation(s)
- Saki Inamine
- a Graduate School of Science and Engineering , Kagoshima University , Kagoshima , Japan
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92
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Plackett ARG, Di Stilio VS, Langdale JA. Ferns: the missing link in shoot evolution and development. FRONTIERS IN PLANT SCIENCE 2015; 6:972. [PMID: 26594222 PMCID: PMC4635223 DOI: 10.3389/fpls.2015.00972] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 10/23/2015] [Indexed: 05/02/2023]
Abstract
Shoot development in land plants is a remarkably complex process that gives rise to an extreme diversity of forms. Our current understanding of shoot developmental mechanisms comes almost entirely from studies of angiosperms (flowering plants), the most recently diverged plant lineage. Shoot development in angiosperms is based around a layered multicellular apical meristem that produces lateral organs and/or secondary meristems from populations of founder cells at its periphery. In contrast, non-seed plant shoots develop from either single apical initials or from a small population of morphologically distinct apical cells. Although developmental and molecular information is becoming available for non-flowering plants, such as the model moss Physcomitrella patens, making valid comparisons between highly divergent lineages is extremely challenging. As sister group to the seed plants, the monilophytes (ferns and relatives) represent an excellent phylogenetic midpoint of comparison for unlocking the evolution of shoot developmental mechanisms, and recent technical advances have finally made transgenic analysis possible in the emerging model fern Ceratopteris richardii. This review compares and contrasts our current understanding of shoot development in different land plant lineages with the aim of highlighting the potential role that the fern C. richardii could play in shedding light on the evolution of underlying genetic regulatory mechanisms.
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Affiliation(s)
- Andrew R. G. Plackett
- Department of Plant Sciences, University of OxfordOxford, UK
- *Correspondence: Andrew R. G. Plackett,
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93
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Abstract
The independent origin and evolution of leaves as small, simple microphylls or larger, more complex megaphylls in plants has shaped and influenced the natural composition of the environment. Significant contributions have come from megaphyllous leaves, characterized usually as flat, thin lamina entrenched with photosynthetic organelles and stomata, which serve as the basis of primary productivity. During the course of evolution, the megaphylls have attained complexity not only in size or venation patterns but also in shape. This has fascinated scientists worldwide, and research has progressed tremendously in understanding the concept of leaf shape determination. Here, we review these studies and discuss the various factors that contributed towards shaping the leaf; initiated as a small bulge on the periphery of the shoot apical meristem (SAM) followed by asymmetric outgrowth, expansion and maturation until final shape is achieved. We found that the underlying factors governing these processes are inherently genetic: PIN1 and KNOX1 are indicators of leaf initiation, HD-ZIPIII, KANADI, and YABBY specify leaf outgrowth while ANGUSTIFOLIA3 and GROWTH-REGULATING FACTOR5 control leaf expansion and maturation; besides, recent research has identified new players such as APUM23, known to specify leaf polarity. In addition to genetic control, environmental factors also play an important role during the final adjustment of leaf shape. This immense amount of information available will serve as the basis for studying and understanding innovative leaf morphologies viz. the pitchers of the carnivorous plant Nepenthes which have evolved to provide additional support to the plant survival in its nutrient-deficient habitat. In hindsight, formation of the pitcher tube in Nepenthes might involve the recruitment of similar genetic mechanisms that occur during sympetaly in Petunia.
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Affiliation(s)
- Jeremy Dkhar
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
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94
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Floyd SK, Ryan JG, Conway SJ, Brenner E, Burris KP, Burris JN, Chen T, Edger PP, Graham SW, Leebens-Mack JH, Pires JC, Rothfels CJ, Sigel EM, Stevenson DW, Neal Stewart C, Wong GKS, Bowman JL. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Mol Phylogenet Evol 2014; 81:159-73. [DOI: 10.1016/j.ympev.2014.06.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/02/2014] [Accepted: 06/02/2014] [Indexed: 10/24/2022]
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95
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Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GKS, Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci U S A 2014; 111:E4859-68. [PMID: 25355905 PMCID: PMC4234587 DOI: 10.1073/pnas.1323926111] [Citation(s) in RCA: 767] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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Affiliation(s)
- Norman J Wickett
- Chicago Botanic Garden, Glencoe, IL 60022; Program in Biological Sciences, Northwestern University, Evanston, IL 60208;
| | - Siavash Mirarab
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Nam Nguyen
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Tandy Warnow
- Department of Computer Science, University of Texas, Austin, TX 78712
| | - Eric Carpenter
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Naim Matasci
- iPlant Collaborative, Tucson, AZ 85721; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | | | - Matthew A Gitzendanner
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611
| | - Brad R Ruhfel
- Department of Biology and Department of Biological Sciences, Eastern Kentucky University, Richmond, KY 40475; Florida Museum of Natural History, Gainesville, FL 32611
| | - Eric Wafula
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | - Joshua P Der
- Department of Biology, Pennsylvania State University, University Park, PA 16803
| | | | - Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, MA 02138
| | | | - Douglas E Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | - Pamela S Soltis
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611; Florida Museum of Natural History, Gainesville, FL 32611
| | | | - Carl J Rothfels
- Department of Biology, Duke University, Durham, NC 27708; Department of Zoology, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Lisa Pokorny
- Department of Biology, Duke University, Durham, NC 27708; Department of Biodiversity and Conservation, Real Jardín Botánico-Consejo Superior de Investigaciones Cientificas, 28014 Madrid, Spain
| | | | | | | | - Barbara Surek
- Botanical Institute, Universität zu Köln, Cologne D-50674, Germany
| | - Juan Carlos Villarreal
- Department fur Biologie, Systematische Botanik und Mykologie, Ludwig-Maximilians-Universitat, 80638 Munich, Germany
| | - Béatrice Roure
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7
| | - Hervé Philippe
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale Centre-Ville, Montreal, QC, Canada H3C 3J7; CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | | | - Tao Chen
- Shenzhen Fairy Lake Botanical Garden, The Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China
| | - Michael K Deyholos
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Toni M Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO 63132
| | | | - Jun Wang
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Yong Zhang
- CNRS, Station d' Ecologie Expérimentale du CNRS, Moulis, 09200, France
| | - Zhijian Tian
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Zhixiang Yan
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiaolei Wu
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Xiao Sun
- BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E9; BGI-Shenzhen, Bei shan Industrial Zone, Yantian District, Shenzhen 518083, China; and Department of Medicine, University of Alberta, Edmonton, AB, Canada T6G 2E1
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96
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Sessa EB, Banks JA, Barker MS, Der JP, Duffy AM, Graham SW, Hasebe M, Langdale J, Li FW, Marchant DB, Pryer KM, Rothfels CJ, Roux SJ, Salmi ML, Sigel EM, Soltis DE, Soltis PS, Stevenson DW, Wolf PG. Between two fern genomes. Gigascience 2014; 3:15. [PMID: 25324969 PMCID: PMC4199785 DOI: 10.1186/2047-217x-3-15] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 09/18/2014] [Indexed: 11/10/2022] Open
Abstract
Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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Affiliation(s)
- Emily B Sessa
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, 1041 East Lowell Street, Tucson, AZ 85721, USA
| | - Joshua P Der
- Department of Biology, Penn State University, 201 Life Science Building, University Park, PA 16801, USA ; Current address: Department of Biological Science, California State University, 800 N. State College Blvd., Fullerton, CA 92831, USA
| | - Aaron M Duffy
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
| | - Sean W Graham
- Department of Botany, University of British Columbia, 3529-6720 University Blvd., Vancouver, BC V6T 1Z4, Canada
| | - Mitsuyasu Hasebe
- National Institute for Basic Biology, 38 Nishigounaka, Myo-daiji-cho, Okazaki 444-8585, Japan
| | - Jane Langdale
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Fay-Wei Li
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - D Blaine Marchant
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Kathleen M Pryer
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Carl J Rothfels
- Department of Zoology, University of British Columbia, 2329 W. Mall, WAITING Vancouver, BC V6T 1Z4, Canada ; Current address: University Herbarium and Department of Integrative Biology, University of California, 1001 Valley Life Sciences Building, Berkeley, Berkeley, CA 94720, USA
| | - Stanley J Roux
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Mari L Salmi
- Department of Molecular Biosciences, University of Texas, 205 W. 24th Street, Austin, TX 78712, USA
| | - Erin M Sigel
- Department of Biology, Duke University, Post Office Box 90338, Durham, NC 27708, USA
| | - Douglas E Soltis
- Department of Biology, Box 118525, University of Florida, Gainesville, FL 32611, USA ; Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Genetics Institute, University of Florida, Box 103610, Gainesville, FL 32611, USA ; Florida Museum of Natural History, Dickinson Hall, University of Florida, Gainesville, FL 32611, USA
| | - Dennis W Stevenson
- New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Paul G Wolf
- Ecology Center and Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
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97
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Cooper ED. Overly simplistic substitution models obscure green plant phylogeny. TRENDS IN PLANT SCIENCE 2014; 19:576-582. [PMID: 25023343 DOI: 10.1016/j.tplants.2014.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/25/2014] [Accepted: 06/05/2014] [Indexed: 06/03/2023]
Abstract
Phylogenetic analysis is an increasingly common and valuable component of plant science. Knowledge of the phylogenetic relationships between plant groups is a prerequisite for understanding the origin and evolution of important plant features, and phylogenetic analysis of individual genes and gene families provides fundamental insights into how those genes and their functions evolved. However, despite an active research community exploring and improving phylogenetic methods, the analytical methods commonly used, and the phylogenetic results they produce, are accorded far more confidence than they warrant. In this opinion article, I emphasise that important parts of the green plant phylogeny are inconsistently resolved and I argue that the lack of consistency arises due to inadequate modelling of changes in the substitution process.
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Affiliation(s)
- Endymion D Cooper
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4407, USA.
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98
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Tracing the origin and evolution of plant TIR-encoding genes. Gene 2014; 546:408-16. [DOI: 10.1016/j.gene.2014.04.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/17/2014] [Accepted: 04/24/2014] [Indexed: 01/16/2023]
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99
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Som A. Causes, consequences and solutions of phylogenetic incongruence. Brief Bioinform 2014; 16:536-48. [PMID: 24872401 DOI: 10.1093/bib/bbu015] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/05/2014] [Indexed: 11/14/2022] Open
Abstract
Phylogenetic analysis is used to recover the evolutionary history of species, genes or proteins. Understanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. Moreover, it is important because of its wide applications that include understanding genome organization, epidemiological investigations, predicting protein functions, and deciding the genes to be analyzed in comparative studies. Despite immense progress in recent years, phylogenetic reconstruction involves many challenges that create uncertainty with respect to the true evolutionary relationships of the species or genes analyzed. One of the most notable difficulties is the widespread occurrence of incongruence among methods and also among individual genes or different genomic regions. Presence of widespread incongruence inhibits successful revealing of evolutionary relationships and applications of phylogenetic analysis. In this article, I concisely review the effect of various factors that cause incongruence in molecular phylogenies, the advances in the field that resolved some factors, and explore unresolved factors that cause incongruence along with possible ways for tackling them.
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100
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Plackett AR, Huang L, Sanders HL, Langdale JA. High-efficiency stable transformation of the model fern species Ceratopteris richardii via microparticle bombardment. PLANT PHYSIOLOGY 2014; 165:3-14. [PMID: 24623851 PMCID: PMC4012588 DOI: 10.1104/pp.113.231357] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 03/11/2014] [Indexed: 05/18/2023]
Abstract
Ferns represent the most closely related extant lineage to seed plants. The aquatic fern Ceratopteris richardii has been subject to research for a considerable period of time, but analyses of the genetic programs underpinning developmental processes have been hampered by a large genome size, a lack of available mutants, and an inability to create stable transgenic lines. In this paper, we report a protocol for efficient stable genetic transformation of C. richardii and a closely related species Ceratopteris thalictroides using microparticle bombardment. Indeterminate callus was generated and maintained from the sporophytes of both species using cytokinin treatment. In proof-of-principle experiments, a 35S::β-glucuronidase (GUS) expression cassette was introduced into callus cells via tungsten microparticles, and stable transformants were selected via a linked hygromycin B resistance marker. The presence of the transgene in regenerated plants and in subsequent generations was validated using DNA-blot analysis, reverse transcription-polymerase chain reaction, and GUS staining. GUS staining patterns in most vegetative tissues corresponded with constitutive gene expression. The protocol described in this paper yields transformation efficiencies far greater than those previously published and represents a significant step toward the establishment of a tractable fern genetic model.
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