1
|
Fu CN, Wicke S, Zhu AD, Li DZ, Gao LM. Distinctive plastome evolution in carnivorous angiosperms. BMC PLANT BIOLOGY 2023; 23:660. [PMID: 38124058 PMCID: PMC10731798 DOI: 10.1186/s12870-023-04682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Independent origins of carnivory in multiple angiosperm families are fabulous examples of convergent evolution using a diverse array of life forms and habitats. Previous studies have indicated that carnivorous plants have distinct evolutionary trajectories of plastid genome (plastome) compared to their non-carnivorous relatives, yet the extent and general characteristics remain elusive. RESULTS We compared plastomes from 9 out of 13 carnivorous families and their non-carnivorous relatives to assess carnivory-associated evolutionary patterns. We identified inversions in all sampled Droseraceae species and four species of Utricularia, Pinguicula, Darlingtonia and Triphyophyllum. A few carnivores showed distinct shifts in inverted repeat boundaries and the overall repeat contents. Many ndh genes, along with some other genes, were independently lost in several carnivorous lineages. We detected significant substitution rate variations in most sampled carnivorous lineages. A significant overall substitution rate acceleration characterizes the two largest carnivorous lineages of Droseraceae and Lentibulariaceae. We also observe moderate substitution rates acceleration in many genes of Cephalotus follicularis, Roridula gorgonias, and Drosophyllum lusitanicum. However, only a few genes exhibit significant relaxed selection. CONCLUSION Our results indicate that the carnivory of plants have different effects on plastome evolution across carnivorous lineages. The complex mechanism under carnivorous habitats may have resulted in distinctive plastome evolution with conserved plastome in the Brocchinia hechtioides to strongly reconfigured plastomes structures in Droseraceae. Organic carbon obtained from prey and the efficiency of utilizing prey-derived nutrients might constitute possible explanation.
Collapse
Affiliation(s)
- Chao-Nan Fu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China
| | - Susann Wicke
- Institute for Biology, Humboldt-University Berlin, Berlin, Germany
- Späth-Arboretum of the Humboldt-University Berlin, Berlin, Germany
| | - An-Dan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Lijiang Forest Biodiversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, Yunnan, China.
| |
Collapse
|
2
|
Fleck SJ, Jobson RW. Molecular Phylogenomics Reveals the Deep Evolutionary History of Carnivory across Land Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3356. [PMID: 37836100 PMCID: PMC10574757 DOI: 10.3390/plants12193356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023]
Abstract
Plastid molecular phylogenies that broadly sampled angiosperm lineages imply that carnivorous plants evolved at least 11 times independently in 13 families and 6 orders. Within and between these clades, the different prey capture strategies involving flypaper and pitfall structures arose in parallel with the subsequent evolution of snap traps and suction bladders. Attempts to discern the deep ontological history of carnivorous structures using multigene phylogenies have provided a plastid-level picture of sister relationships at the family level. Here, we present a molecular phylogeny of the angiosperms based on nuclear target sequence capture data (Angiosperms-353 probe set), assembled by the Kew Plant Trees of Life initiative, which aims to complete the tree of life for plants. This phylogeny encompasses all carnivorous and protocarnivorous families, although certain genera such as Philcoxia (Plantaginaceae) are excluded. This study offers a novel nuclear gene-based overview of relationships within and between carnivorous families and genera. Consistent with previous broadly sampled studies, we found that most carnivorous families are not affiliated with any single family. Instead, they emerge as sister groups to large clades comprising multiple non-carnivorous families. Additionally, we explore recent genomic studies across various carnivorous clades that examine the evolution of the carnivorous syndrome in relation to whole-genome duplication, subgenome dominance, small-scale gene duplication, and convergent evolution. Furthermore, we discuss insights into genome size evolution through the lens of carnivorous plant genomes.
Collapse
Affiliation(s)
- Steven J. Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Richard W. Jobson
- National Herbarium of New South Wales, Botanic Gardens of Sydney, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| |
Collapse
|
3
|
Silva SR, Miranda VFO, Michael TP, Płachno BJ, Matos RG, Adamec L, Pond SLK, Lucaci AG, Pinheiro DG, Varani AM. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae). Mol Phylogenet Evol 2023; 181:107711. [PMID: 36693533 DOI: 10.1016/j.ympev.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.
Collapse
Affiliation(s)
- Saura R Silva
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Vitor F O Miranda
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Todd P Michael
- Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, Gronostajowa 9 St., 30-387 Cracow, Poland.
| | - Ramon G Matos
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Biology, Laboratory of Plant Systematics, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Lubomir Adamec
- Department of Experimental and Functional Morphology, Institute of Botany CAS, Dukelská 135, CZ-379 01 Třeboň, Czech Republic.
| | - Sergei L K Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Alexander G Lucaci
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122, USA.
| | - Daniel G Pinheiro
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| | - Alessandro M Varani
- UNESP - São Paulo State University, School of Agricultural and Veterinarian Sciences, Department of Agricultural and Environmental Biotechnology, Campus Jaboticabal, CEP 14884-900 SP, Brazil.
| |
Collapse
|
4
|
Katayama N, Koi S, Sassa A, Kurata T, Imaichi R, Kato M, Nishiyama T. Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae. Commun Biol 2022; 5:75. [PMID: 35058542 PMCID: PMC8776956 DOI: 10.1038/s42003-022-03003-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/23/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular evolutionary rates vary among lineages and influence the evolutionary process. Here, we report elevated genome-wide mutation rates in Podostemaceae, a family of aquatic plants with a unique body plan that allows members to live on submerged rocks in fast-flowing rivers. Molecular evolutionary analyses using 1640 orthologous gene groups revealed two historical increases in evolutionary rates: the first at the emergence of the family and the second at the emergence of Podostemoideae, which is the most diversified subfamily. In both branches, synonymous substitution rates were elevated, indicating higher mutation rates. On early branches, mutations were biased in favour of AT content, which is consistent with a role for ultraviolet light-induced mutation and habitat shift. In ancestors of Podostemoideae, DNA-repair genes were enriched in genes under positive selection, which may have responded to the meristem architectural changes.
Collapse
Affiliation(s)
- Natsu Katayama
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
- Research Fellow of Japan Society for the Promotion of Science, Tokyo, 102-0083, Japan.
| | - Satoshi Koi
- Botanical Gardens, Osaka City University, Osaka, 575-0004, Japan
| | - Akira Sassa
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Tetsuya Kurata
- Division of Biological Science, Nara Institute of Science and Technology, Nara, 630-0192, Japan
| | - Ryoko Imaichi
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Masahiro Kato
- Department of Botany, National Museum of Nature and Science, Tsukuba, 305-0005, Japan
| | - Tomoaki Nishiyama
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-0934, Japan.
| |
Collapse
|
5
|
Biogeographical patterns and speciation of the genus Pinguicula (Lentibulariaceae) inferred by phylogenetic analyses. PLoS One 2021; 16:e0252581. [PMID: 34097720 PMCID: PMC8184156 DOI: 10.1371/journal.pone.0252581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 05/18/2021] [Indexed: 11/19/2022] Open
Abstract
Earlier phylogenetic studies in the genus Pinguicua (Lentibulariaceae) suggested that the species within a geographical region was rather monophyletic, although the sampling was limited or was restricted to specific regions. Those results conflicted with the floral morphology-based classification, which has been widely accepted to date. In the current study, one nuclear ribosomal DNA (internal transcribed spacer; ITS) and two regions of chloroplast DNA (matK and rpl32-trnL), from up to ca. 80% of the taxa in the genus Pinguicula, covering all three subgenera, were sequenced to demonstrate the inconsistency and explore a possible evolutionary history of the genus. Some incongruence was observed between nuclear and chloroplast topologies and the results from each of the three DNA analyses conflicted with the morphology-based subgeneric divisions. Both the ITS tree and network, however, corresponded with the biogeographical patterns of the genus supported by life-forms (winter rosette or hibernaculum formation) and basic chromosome numbers (haploidy). The dormant strategy evolved in a specific geographical region is a phylogenetic constraint and a synapomorphic characteristic within a lineage. Therefore, the results denied the idea that the Mexican group, morphologically divided into the three subgenera, independently acquired winter rosette formations. Topological incongruence among the trees or reticulations, indicated by parallel edges in phylogenetic networks, implied that some taxa originated by introgressive hybridisation. Although there are exceptions, species within the same geographical region arose from a common ancestor. Therefore, the classification by the floral characteristics is rather unreliable. The results obtained from this study suggest that evolution within the genus Pinguicula has involved; 1) ancient expansions to geographical regions with gene flow and subsequent vicariance with genetic drift, 2) acquirement of a common dormant strategy within a specific lineage to adapt a local climate (i.e., synapomorphic characteristic), 3) recent speciation in a short time span linked to introgressive hybridisation or multiplying the ploidy level (i.e., divergence), and 4) parallel evolution in floral traits among lineages found in different geographical regions (i.e., convergence). As such, the floral morphology masks and obscures the phylogenetic relationships among species in the genus.
Collapse
|
6
|
Arai N, Ohno Y, Jumyo S, Hamaji Y, Ohyama T. Organ-specific expression and epigenetic traits of genes encoding digestive enzymes in the lance-leaf sundew (Drosera adelae). JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1946-1961. [PMID: 33247920 PMCID: PMC7921302 DOI: 10.1093/jxb/eraa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 11/25/2020] [Indexed: 05/16/2023]
Abstract
Over the last two decades, extensive studies have been performed at the molecular level to understand the evolution of carnivorous plants. As fruits, the repertoire of protein components in the digestive fluids of several carnivorous plants have gradually become clear. However, the quantitative aspects of these proteins and the expression mechanisms of the genes that encode them are still poorly understood. In this study, using the Australian sundew Drosera adelae, we identified and quantified the digestive fluid proteins. We examined the expression and methylation status of the genes corresponding to major hydrolytic enzymes in various organs; these included thaumatin-like protein, S-like RNase, cysteine protease, class I chitinase, β-1, 3-glucanase, and hevein-like protein. The genes encoding these proteins were exclusively expressed in the glandular tentacles. Furthermore, the promoters of the β-1, 3-glucanase and cysteine protease genes were demethylated only in the glandular tentacles, similar to the previously reported case of the S-like RNase gene da-I. This phenomenon correlated with high expression of the DNA demethylase DEMETER in the glandular tentacles, strongly suggesting that it performs glandular tentacle-specific demethylation of the genes. The current study strengthens and generalizes the relevance of epigenetics to trap organ-specific gene expression in D. adelae. We also suggest similarities between the trap organs of carnivorous plants and the roots of non-carnivorous plants.
Collapse
Affiliation(s)
- Naoki Arai
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Ohno
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Shinya Jumyo
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Yusuke Hamaji
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, Japan
| | - Takashi Ohyama
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, Japan
- Correspondence:
| |
Collapse
|
7
|
Lustofin K, Świątek P, Stolarczyk P, Miranda VFO, Płachno BJ. Do food trichomes occur in Pinguicula (Lentibulariaceae) flowers? ANNALS OF BOTANY 2020; 126:1039-1048. [PMID: 32592586 PMCID: PMC7596368 DOI: 10.1093/aob/mcaa123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/19/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS Floral food bodies (including edible trichomes) are a form of floral reward for pollinators. This type of nutritive reward has been recorded in several angiosperm families: Annonaceae, Araceae, Calycanthaceae, Eupomatiaceae, Himantandraceae, Nymphaeaceae, Orchidaceae, Pandanaceae and Winteraceae. Although these bodies are very diverse in their structure, their cells contain food material: starch grains, protein bodies or lipid droplets. In Pinguicula flowers, there are numerous multicellular clavate trichomes. Previous authors have proposed that these trichomes in the Pinguicula flower play the role of 'futterhaare' ('feeding hairs') and are eaten by pollinators. The main aim of this study was to investigate whether the floral non-glandular trichomes of Pinguicula contain food reserves and thus are a reward for pollinators. The trichomes from the Pinguicula groups, which differ in their taxonomy (species from the subgenera: Temnoceras, Pinguicula and Isoloba) as well as the types of their pollinators (butterflies/flies and bees/hummingbirds), were examined. Thus, it was determined whether there are any connections between the occurrence of food trichomes and phylogeny position or pollination biology. Additionally, we determined the phylogenetic history of edible trichomes and pollinator evolution in the Pinguicula species. METHODS The species that were sampled were: Pinguicula moctezumae, P. esseriana, P. moranensis, P. emarginata, P. rectifolia, P. mesophytica, P. hemiepiphytica, P. agnata, P. albida, P. ibarrae, P. martinezii, P. filifolia, P. gigantea, P. lusitanica, P. alpina and P. vulgaris. Light microscopy, histochemistry, and scanning and transmission electron microscopy were used to address our aims with a phylogenetic perspective based on matK/trnK DNA sequences. KEY RESULTS No accumulation of protein bodies or lipid droplets was recorded in the floral non-glandular trichomes of any of the analysed species. Starch grains occurred in the cells of the trichomes of the bee-/fly-pollinated species: P. agnata, P. albida, P. ibarrae, P. martinezii, P. filifolia and P. gigantea, but not in P. alpina or P. vulgaris. Moreover, starch grains were not recorded in the cells of the trichomes of the Pinguicula species that have long spurs, which are pollinated by Lepidoptera (P. moctezumae, P. esseriana, P. moranensis, P. emarginata and P. rectifolia) or birds (P. mesophytica and P. hemiepihytica), or in species with a small and whitish corolla that self-pollinate (P. lusitanica). The results on the occurrence of edible trichomes and pollinator syndromes were mapped onto a phylogenetic reconstruction of the genus. CONCLUSION Floral non-glandular trichomes play the role of edible trichomes in some Pinguicula species (P. agnata, P. albida, P. ibarrae, P. martinezii, P. filifolia and P. gigantea), which are mainly classified as bee-pollinated species that had originated from Central and South America. It seems that in the Pinguicula that are pollinated by other pollinator groups (Lepidoptera and hummingbirds), the non-glandular trichomes in the flowers play a role other than that of a floral reward for their pollinators. Edible trichomes are symplesiomorphic for the Pinguicula species, and thus do not support a monophyletic group such as a synapomorphy. Nevertheless, edible trichomes are derived and are possibly a specialization for fly and bee pollinators by acting as a food reward for these visitors.
Collapse
Affiliation(s)
- Krzysztof Lustofin
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa Street, 30-387 Cracow, Poland
| | - Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 9 Bankowa Street, 40-007 Katowice, Poland
| | - Piotr Stolarczyk
- Unit of Botany and Plant Physiology, Institute of Plant Biology and Biotechnology, University of Agriculture in Kraków, 29 Listopada 54 Street, 31-425 Kraków, Poland
| | - Vitor F O Miranda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa Street, 30-387 Cracow, Poland
| |
Collapse
|
8
|
Müller UK, Berg O, Schwaner JM, Brown MD, Li G, Voesenek CJ, van Leeuwen JL. Bladderworts, the smallest known suction feeders, generate inertia-dominated flows to capture prey. THE NEW PHYTOLOGIST 2020; 228:586-595. [PMID: 32506423 DOI: 10.1111/nph.16726] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/22/2020] [Indexed: 05/02/2023]
Abstract
Aquatic bladderworts (Utricularia gibba and U. australis) capture zooplankton in mechanically triggered underwater traps. With characteristic dimensions less than 1 mm, the trapping structures are among the smallest known to capture prey by suction, a mechanism that is not effective in the creeping-flow regime where viscous forces prevent the generation of fast and energy-efficient suction flows. To understand what makes suction feeding possible on the small scale of bladderwort traps, we characterised their suction flows experimentally (using particle image velocimetry) and mathematically (using computational fluid dynamics and analytical mathematical models). We show that bladderwort traps avoid the adverse effects of creeping flow by generating strong, fast-onset suction pressures. Our findings suggest that traps use three morphological adaptations: the trap walls' fast release of elastic energy ensures strong and constant suction pressure; the trap door's fast opening ensures effectively instantaneous onset of suction; the short channel leading into the trap ensures undeveloped flow, which maintains a wide effective channel diameter. Bladderwort traps generate much stronger suction flows than larval fish with similar gape sizes because of the traps' considerably stronger suction pressures. However, bladderworts' ability to generate strong suction flows comes at considerable energetic expense.
Collapse
Affiliation(s)
- Ulrike K Müller
- Department of Biology, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA, 93740, USA
| | - Otto Berg
- Department of Chemistry, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA, 93740, USA
| | - Janneke M Schwaner
- Biological Sciences, University of Idaho, 875 Perimeter Drive MS 3051, Moscow, ID, 83844-3051, USA
| | - Matthew D Brown
- Department of Biology, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA, 93740, USA
| | - Gen Li
- Department of Mathematical Science and Advanced Technology, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Showa-machi, Kanazawa-ku, Yokohama-city, Kanagawa, 3173-25, 236-0001, Japan
| | - Cees J Voesenek
- Experimental Zoology Group, Wageningen University, De Elst 1, Wageningen, 6708WD, the Netherlands
| | - Johan L van Leeuwen
- Experimental Zoology Group, Wageningen University, De Elst 1, Wageningen, 6708WD, the Netherlands
| |
Collapse
|
9
|
Oropeza-Aburto A, Cervantes-Pérez SA, Albert VA, Herrera-Estrella L. Agrobacterium tumefaciens mediated transformation of the aquatic carnivorous plant Utricularia gibba. PLANT METHODS 2020; 16:50. [PMID: 32308728 PMCID: PMC7149871 DOI: 10.1186/s13007-020-00592-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/31/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND The genus Utricularia belongs to Lentibulariaceae, the largest family of carnivorous plants, which includes terrestrial, epiphytic and aquatic species. The development of specialized structures that evolved for carnivory is a feature of this genus that has been of great interest to biologists since Darwin's early studies. Utricularia gibba is itself an aquatic plant with sophisticated bladder traps having one of the most complex suction mechanisms for trapping prey. However, the molecular characterization of the mechanisms that regulate trap development and the biophysical processes involved in prey trapping are still largely unknown due to the lack of a simple and reproducible gene transfer system. RESULTS Here, we report the establishment of a simple, fast and reproducible protocol for genetic transformation of U. gibba based on the T-DNA of Agrobacterium tumefaciens. An in vitro selection system using Phosphinotricin as a selective agent was established for U. gibba. Plant transformation was confirmed by histochemical GUS assays and PCR and qRT-PCR analyses. We report on the expression pattern of the 35S promoter and of the promoter of a trap-specific ribonuclease gene in transgenic U. gibba plants. CONCLUSIONS The genetic transformation protocol reported here is an effective method for studying developmental biology and functional genomics of this genus of carnivorous plants and advances the utility of U. gibba as a model system to study developmental processes involved in trap formation.
Collapse
Affiliation(s)
- A. Oropeza-Aburto
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824 Irapuato, Guanajuato Mexico
| | - S. A. Cervantes-Pérez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824 Irapuato, Guanajuato Mexico
| | - V. A. Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260 USA
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551 Singapore
| | - L. Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824 Irapuato, Guanajuato Mexico
- Institute of Genomics for Crop Abiotic Stress Tolerance, Plant and Soil Department, Texas Tech University, Lubbock, USA
| |
Collapse
|
10
|
Lustofin K, Świątek P, Miranda VFO, Płachno BJ. Flower nectar trichome structure of carnivorous plants from the genus butterworts Pinguicula L. (Lentibulariaceae). PROTOPLASMA 2020; 257:245-259. [PMID: 31428856 PMCID: PMC6982637 DOI: 10.1007/s00709-019-01433-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 08/07/2019] [Indexed: 05/22/2023]
Abstract
Pinguicula (Lentibulariaceae) is a genus comprising around 96 species of herbaceous, carnivorous plants, which are extremely diverse in flower size, colour and spur length and structure as well as pollination strategy. In Pinguicula, nectar is formed in the flower spur; however, there is a gap in the knowledge about the nectary trichome structure in this genus. Our aim was to compare the nectary trichome structure of various Pinguicula species in order to determine whether there are any differences among the species in this genus. The taxa that were sampled were Pinguicula moctezumae, P. moranensis, P. rectifolia, P. emarginata and P. esseriana. We used light microscopy, histochemistry, scanning and transmission electron microscopy to address those aims. We show a conservative nectary trichome structure and spur anatomy in various Mexican Pinguicula species. The gross structural similarities between the examined species were the spur anatomy, the occurrence of papillae, the architecture of the nectary trichomes and the ultrastructure characters of the trichome cells. However, there were some differences in the spur length, the size of spur trichomes, the occurrence of starch grains in the spur parenchyma and the occurrence of cell wall ingrowths in the terminal cells of the nectary trichomes. Similar nectary capitate trichomes, as are described here, were recorded in the spurs of species from other Lentibulariaceae genera. There are many ultrastructural similarities between the cells of nectary trichomes in Pinguicula and Utricularia.
Collapse
Affiliation(s)
- Krzysztof Lustofin
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St, 30-387, Kraków, Poland
| | - Piotr Świątek
- Department of Animal Histology and Embryology, University of Silesia in Katowice, 9 Bankowa St, 40-007, Katowice, Poland
| | - Vitor F O Miranda
- Departamento de Biologia Aplicada à Agropecuária, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, São Paulo, Brazil
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Institute of Botany, Faculty of Biology, Jagiellonian University in Kraków, 9 Gronostajowa St, 30-387, Kraków, Poland.
| |
Collapse
|
11
|
Lee KJI, Bushell C, Koide Y, Fozard JA, Piao C, Yu M, Newman J, Whitewoods C, Avondo J, Kennaway R, Marée AFM, Cui M, Coen E. Shaping of a three-dimensional carnivorous trap through modulation of a planar growth mechanism. PLoS Biol 2019; 17:e3000427. [PMID: 31600203 PMCID: PMC6786542 DOI: 10.1371/journal.pbio.3000427] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
Leaves display a remarkable range of forms, from flat sheets with simple outlines to cup-shaped traps. Although much progress has been made in understanding the mechanisms of planar leaf development, it is unclear whether similar or distinctive mechanisms underlie shape transformations during development of more complex curved forms. Here, we use 3D imaging and cellular and clonal analysis, combined with computational modelling, to analyse the development of cup-shaped traps of the carnivorous plant Utricularia gibba. We show that the transformation from a near-spherical form at early developmental stages to an oblate spheroid with a straightened ventral midline in the mature form can be accounted for by spatial variations in rates and orientations of growth. Different hypotheses regarding spatiotemporal control predict distinct patterns of cell shape and size, which were tested experimentally by quantifying cellular and clonal anisotropy. We propose that orientations of growth are specified by a proximodistal polarity field, similar to that hypothesised to account for Arabidopsis leaf development, except that in Utricularia, the field propagates through a highly curved tissue sheet. Independent evidence for the polarity field is provided by the orientation of glandular hairs on the inner surface of the trap. Taken together, our results show that morphogenesis of complex 3D leaf shapes can be accounted for by similar mechanisms to those for planar leaves, suggesting that simple modulations of a common growth framework underlie the shaping of a diverse range of morphologies. Many plant and animal organs derive from tissue sheets, but how are they shaped to create the diversity of forms observed in nature? This study uses a combination of imaging and mathematical modelling to show how carnivorous plant traps shape themselves in 3D by a growth framework oriented by tissue polarity, similar to that found in planar leaves.
Collapse
Affiliation(s)
- Karen J. I. Lee
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Claire Bushell
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Yohei Koide
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - John A. Fozard
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Chunlan Piao
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Linan, Zhejiang, China
| | - Man Yu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jacob Newman
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Christopher Whitewoods
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jerome Avondo
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Richard Kennaway
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Athanasius F. M. Marée
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Minlong Cui
- College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Linan, Zhejiang, China
- * E-mail: (EC); (MC)
| | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- * E-mail: (EC); (MC)
| |
Collapse
|
12
|
Ravee R, Mohd Salleh F‘I, Goh HH. Discovery of digestive enzymes in carnivorous plants with focus on proteases. PeerJ 2018; 6:e4914. [PMID: 29888132 PMCID: PMC5993016 DOI: 10.7717/peerj.4914] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/16/2018] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Carnivorous plants have been fascinating researchers with their unique characters and bioinspired applications. These include medicinal trait of some carnivorous plants with potentials for pharmaceutical industry. METHODS This review will cover recent progress based on current studies on digestive enzymes secreted by different genera of carnivorous plants: Drosera (sundews), Dionaea (Venus flytrap), Nepenthes (tropical pitcher plants), Sarracenia (North American pitcher plants), Cephalotus (Australian pitcher plants), Genlisea (corkscrew plants), and Utricularia (bladderworts). RESULTS Since the discovery of secreted protease nepenthesin in Nepenthes pitcher, digestive enzymes from carnivorous plants have been the focus of many studies. Recent genomics approaches have accelerated digestive enzyme discovery. Furthermore, the advancement in recombinant technology and protein purification helped in the identification and characterisation of enzymes in carnivorous plants. DISCUSSION These different aspects will be described and discussed in this review with focus on the role of secreted plant proteases and their potential industrial applications.
Collapse
Affiliation(s)
- Rishiesvari Ravee
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Faris ‘Imadi Mohd Salleh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| |
Collapse
|
13
|
Villegas SG, Alcalá RE. Reproductive ecology of the carnivorous plant Pinguicula moranensis (Lentibulariaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:205-212. [PMID: 29083079 DOI: 10.1111/plb.12652] [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: 06/07/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
The interaction of plants with pollinators can be a determinant of their reproductive fitness. However, information about the pollination biology of carnivorous plants is scarce. To increase knowledge of reproductive ecology of carnivorous plants we focused on Pinguicula moranensis. Specifically, based on the presence of large, zygomorphic and spurred flowers, we predicted higher reproductive fitness in cross-pollinated than in self-pollinated flowers. Within a plot of 51 m2 we characterised the reproductive phenology, including flower lifespan and stigmatic receptivity. We identified pollinators and their movement patterns within the plot. Breeding system was experimentally evaluated using hand-pollination (i.e. autonomous, self- and cross-pollination). Flowers of P. moranensis were visited by long-tongued pollinators, mainly members of the Lepidoptera. Hand-pollination experiments confirmed our prediction and suggest that flower traits might favour cross-pollination. We mainly discuss the implications of the patchy distribution of plants and behaviour of pollinators on gene movement in this plant species, as pollination between genetically related individuals could be occurring.
Collapse
Affiliation(s)
- S G Villegas
- Departamento de Ecología Evolutiva, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - R E Alcalá
- Departamento de Ecología Evolutiva, Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| |
Collapse
|
14
|
Silva SR, Michael TP, Meer EJ, Pinheiro DG, Varani AM, Miranda VFO. Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes. PLoS One 2018; 13:e0190321. [PMID: 29293597 PMCID: PMC5749785 DOI: 10.1371/journal.pone.0190321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/12/2017] [Indexed: 11/18/2022] Open
Abstract
In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.
Collapse
Affiliation(s)
- Saura R. Silva
- Universidade Estadual Paulista (Unesp), Botucatu, Instituto de Biociências, São Paulo, Brazil
| | - Todd P. Michael
- J. Craig Venter Institute, La Jolla, CA, United States of America
| | - Elliott J. Meer
- 10X Genomics, Pleasanton, California, United States of America
| | - Daniel G. Pinheiro
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, São Paulo, Brazil
| | - Alessandro M. Varani
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Tecnologia, São Paulo, Brazil
| | - Vitor F. O. Miranda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| |
Collapse
|
15
|
Płachno BJ, Świątek P, Jobson RW, Małota K, Brutkowski W. Serial block face SEM visualization of unusual plant nuclear tubular extensions in a carnivorous plant (Utricularia, Lentibulariaceae). ANNALS OF BOTANY 2017; 120:673-680. [PMID: 28541416 PMCID: PMC5691799 DOI: 10.1093/aob/mcx042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/09/2017] [Accepted: 03/23/2017] [Indexed: 05/22/2023]
Abstract
Background and Aims In Utricularia nelumbifolia , the nuclei of placental nutritive tissue possess unusually shaped projections not known to occur in any other flowering plant. The main aim of the study was to document the morphology and ultrastructure of these unusual nuclei. In addition, the literature was searched to find examples of nuclear tubular projections in other plant groups, and the nuclei of closely related species of Utricularia (i.e. sects Iperua , Orchidioides , Foliosa and Utricularia ) were examined. Methods To visualize the complexity of the nuclear structures, transmission electron microscopy (TEM) was used, and 3-D ultrastructural reconstructions were made using the serial block face scanning electron microscopy (SBEM) technique. The nuclei of 11 Utricularia species, i.e. U. nelumbifolia , U. reniformis , U. cornigera , U. nephrophylla (sect. Iperua ), U. asplundii , U. alpina , U. quelchii (sect. Orchidioides ), U. longifolia (sect. Foliosa ), U. intermedia , U. minor and U. gibba (sect. Utricularia ) were examined. Key Results Of the 11 Utricularia species examined, the spindle-like tubular projections (approx. 5 μm long) emanating from resident nuclei located in placental nutritive tissues were observed only in U. nelumbifolia . These tubular nuclear extensions contained chromatin distributed along hexagonally shaped tubules. The apices of the projections extended into the cell plasma membrane, and in many cases also made contact at the two opposing cellular poles, and with plasmodesmata via a short cisterna of the cortical endoplasmic reticulum. Images from the SBEM provide some evidence that the nuclear projections are making contact with those of neighbouring cells. Conclusions The term chromatubules (chromatin-filled tubules) for the nuclear projections of U. nelumbifolia placental tissue was proposed here. Due to the apparent association with the plasma membrane and plasmodesmata, it was also speculated that chromatubules are involved in nucleus-cell-cell communication. However, further experimental evidence is required before any functional hypothesis can be entertained.
Collapse
Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University in Kraków, 9 Gronostajowa St., Cracow, Poland
| | - Piotr Świątek
- Department of Animal Histology and Embryology, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland
| | - Richard W Jobson
- National Herbarium of New South Wales, Mrs Macquaries Road, Sydney, NSW 2000 Australia
| | - Karol Małota
- Department of Animal Histology and Embryology, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland
| | - Wojciech Brutkowski
- Laboratory for Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., 02-093 Warszawa, Poland
| |
Collapse
|
16
|
Gomes Rodrigues F, Franco Marulanda N, Silva SR, Płachno BJ, Adamec L, Miranda VFO. Phylogeny of the 'orchid-like' bladderworts (gen. Utricularia sect. Orchidioides and Iperua: Lentibulariaceae) with remarks on the stolon-tuber system. ANNALS OF BOTANY 2017; 120:709-723. [PMID: 28673037 PMCID: PMC5691873 DOI: 10.1093/aob/mcx056] [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: 02/25/2017] [Revised: 03/22/2017] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Background and Aims The 'orchid-like' bladderworts ( Utricularia ) comprise 15 species separated into two sections: Orchidioides and Iperua . These robust and mostly epiphytic species were originally grouped within the section Orchidioides by the first taxonomical systems. These species were later split into two sections when sect. Iperua was proposed. Due to the lack of strong evidence based on a robust phylogenetic perspective, this study presents a phylogenetic proposal based on four different DNA sequences (plastid and nuclear) and morphology to test the monophyly of the two sections. Methods In comparison with all previous phylogenetic studies, the largest number of species across the sections was covered: 11 species from sections Orchidioides and Iperua with 14 species as an external group. Maximum likelihood and Bayesian inferences were applied to DNA sequences of rps16 , trnL-F , matK , the internal transcribed spacer (ITS) and three morphological characters: (1) the crest of the corolla; (2) the primary organs in the embryo; and (3) tubers. Additionally, a histochemical analysis of the stolons and tubers is presented from an evolutionary perspective. Key Results The analyses showed the paraphyly of sect. Iperua , since Utricularia humboldtii is more related to the clade of sect. Orchidioides . Utricularia cornigera is grouped in the sect. Iperua clade based on chloroplast DNA sequences, but it is nested to sect. Orchidioides according to ITS dataset. Morphological characters do not support the breaking up of the 'orchid-like' species into two sections, either. Moreover, the stolon-tuber systems of both sections serve exclusively for water storage, according to histological analyses. Conclusions This study provides strong evidence, based on DNA sequences from two genomic compartments (plastid and nucleus) and morphology to group the Utricularia sect. Orchidioides into the sect. Iperua . The tubers are important adaptations for water storage and have been derived from stolons at least twice in the phylogenetic history of 'orchid-like' bladderworts.
Collapse
Affiliation(s)
- Fernanda Gomes Rodrigues
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| | - Néstor Franco Marulanda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| | - Saura R Silva
- Universidade Estadual Paulista (Unesp), Instituto de Biociências, Botucatu, São Paulo, Brazil
| | - Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University in Kraków, 9 Gronostajowa St., 30-387 Kraków, Poland
| | - Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Třeboň, Czech Republic
| | - Vitor F O Miranda
- Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil
| |
Collapse
|
17
|
Westermeier AS, Fleischmann A, Müller K, Schäferhoff B, Rubach C, Speck T, Poppinga S. Trap diversity and character evolution in carnivorous bladderworts (Utricularia, Lentibulariaceae). Sci Rep 2017; 7:12052. [PMID: 28935893 PMCID: PMC5608911 DOI: 10.1038/s41598-017-12324-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/07/2017] [Indexed: 01/12/2023] Open
Abstract
Bladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations between life-forms, trapping mechanisms, and functional-morphological traits. Our investigations show the existence of two functional trap principles (passive trap in U. multifida vs. active suction traps), and - in active suction traps - three main trapdoor movement types (with several subtypes). The trapdoor movement types and their corresponding functional-morphological features most presumably represent adaptations to the respective habitat. We furthermore give insights into fluid dynamics during suction in three representatives of the main types of trapdoor movement. The results on functional morphology and trapdoor movement were mapped onto a new phylogenetic reconstruction of the genus, derived from the rapidly evolving chloroplast regions trnK, rps16 and trnQ-rps16 and a sampling of 105 Utricularia species in total. We discuss potential scenarios of trap character evolution and species radiation, highlighting possible key innovations that enable such a unique carnivorous lifestyle in different habitats.
Collapse
Affiliation(s)
- Anna Sofia Westermeier
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg im Breisgau, Germany
| | - Andreas Fleischmann
- Botanische Staatssammlung München, Menzinger Straße 67, D-80638, München, Germany
- GeoBio-Center LMU, Center of Geobiology and Biodiversity Research, Ludwig-Maximilians-University, München, Germany
| | - Kai Müller
- Westfälische Wilhelms-Universität Münster, Institut für Evolution und Biodiversität, AG Evolution und Biodiversität der Pflanzen, Hüfferstraße 1, D-48149, Münster, Germany
| | - Bastian Schäferhoff
- Westfälische Wilhelms-Universität Münster, Institut für Evolution und Biodiversität, AG Evolution und Biodiversität der Pflanzen, Hüfferstraße 1, D-48149, Münster, Germany
- PAN Institut für Endokrinologie und Reproduktionsmedizin, Zeppelinstraße 1, D-50667, Köln, Germany
| | - Carmen Rubach
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany
| | - Thomas Speck
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, D-79110, Freiburg im Breisgau, Germany
| | - Simon Poppinga
- Plant Biomechanics Group, Botanic Garden, University of Freiburg, Schänzlestraße 1, D-79104, Freiburg im Breisgau, Germany.
| |
Collapse
|
18
|
Coelho N, Gomes-Klein VL, Dantas-Queiroz MV. Lentibulariaceae from Serra dos Pireneus, Goiás, Brazil. RODRIGUÉSIA 2017. [DOI: 10.1590/2175-7860201768416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Abstract This study provides a floristic survey of Lentibulariaceae occurring in Serra dos Pireneus (SDP), state of Goiás, Brazil. The phytogeographic domain in which SDP is located is the Cerrado, with different vegetation, including floodplain grasslands (campos úmidos) where Lentibulariaceae usually occur. Samples were collected from 2007 to 2010 and herbarium samples were consulted as well. We recorded nine species of Lentibulariaceae: the genera Genlisea (2 spp.) and Utricularia (7 spp.). Descriptions, illustrations, photographs and identification keys are presented in this study.
Collapse
|
19
|
Brewer JS. Stochastic losses of fire-dependent endemic herbs revealed by a 65-year chronosequence of dispersal-limited woody plant encroachment. Ecol Evol 2017. [PMID: 28649349 PMCID: PMC5478063 DOI: 10.1002/ece3.3020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The factors responsible for maintaining diverse groundcover plant communities of high conservation value in frequently burned wet pine savannas are poorly understood. While most management involves manipulating extrinsic factors important in maintaining species diversity (e.g., fire regimes), most ecological theory (e.g., niche theory and neutral theory) examines how traits exhibited by the species promote species coexistence. Furthermore, although many ecologists focus on processes that maintain local species diversity, conservation biologists have argued that other indices (e.g., phylogenetic diversity) are better for evaluating assemblages in terms of their conservation value. I used a null model that employed beta‐diversity calculations based on Raup–Crick distances to test for deterministic herbaceous species losses associated with a 65‐year chronosequence of woody species encroachment within each of three localities. I quantified conservation value of assemblages by measuring taxonomic distinctness, endemism, and floristic quality of plots with and without woody encroachment. Reductions in herb species richness per plot attributable to woody encroachment were largely stochastic, as indicated by a lack of change in the mean or variance in beta‐diversity caused by woody encroachment in the savannas studied here. Taxonomic distinctness, endemism, and floristic quality (when summed across all species) were all greater in areas that had not experienced woody encroachment. However, when corrected for local species richness, only average endemism and floristic quality of assemblages inclusive of herbs and woody plants were greater in areas that had not experienced woody encroachment, due to the more restricted ranges and habitat requirements of herbs. Results suggest that frequent fires maintain diverse assemblages of fire‐dependent herb species endemic to the region. The stochastic loss of plant species, irrespective of their taxonomic distinctness, to woody encroachment suggests that the relevance of niche partitioning or phylogenetic diversity to the management of biodiversity in wet pine savannas is minimal.
Collapse
|
20
|
De Castro O, Innangi M, Di Maio A, Menale B, Bacchetta G, Pires M, Noble V, Gestri G, Conti F, Peruzzi L. Disentangling Phylogenetic Relationships in a Hotspot of Diversity: The Butterworts (Pinguicula L., Lentibulariaceae) Endemic to Italy. PLoS One 2016; 11:e0167610. [PMID: 28030566 PMCID: PMC5193322 DOI: 10.1371/journal.pone.0167610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 11/04/2016] [Indexed: 11/20/2022] Open
Abstract
The genus Pinguicula (Lentibulariaceae) consists of about 100 carnivorous species, also known as butterworts. Eleven taxa are endemic to Italy, which represents a biodiversity hotspot for butterworts in Europe. The aim of our study was to provide a phylogenetic framework for the Italian endemics, in order to: a) investigate the relationships between species in this group; b) evaluate their actual taxonomic value. To achieve this, we analysed all the taxa endemic to Italy, along with several other species, by means of ITS nrDNA analysis. Our results clarify the relationships between Italian endemics and other Pinguicula taxa identifying a basal polytomy defined by five clades. All of the Italian endemics (with the exception of P. lavalvae) fall within a single large clade, which includes P. vulgaris and allied species. Among them, P. poldinii represents the most isolated lineage. Other taxa show strong molecular similarities and form a single subclade, although their taxonomic ranks can be retained. Pinguicula lattanziae sp. nov., seemingly endemic to Liguria (NW Italy), is also described.
Collapse
Affiliation(s)
- Olga De Castro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Michele Innangi
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Seconda Università degli Studi di Napoli, Caserta, Italy
| | - Antonietta Di Maio
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Bruno Menale
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Gianluigi Bacchetta
- Centro Conservazione Biodiversità, Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cagliari, Italy
| | - Mathias Pires
- Conservatoire Botanique National Méditerranéen, Hyères, France
| | - Virgile Noble
- Conservatoire Botanique National Méditerranéen, Hyères, France
| | | | - Fabio Conti
- Scuola di Bioscienze e Medicina Veterinaria, Università di Camerino—Centro Ricerche Floristiche dell’Appennino, Parco Nazionale del Gran Sasso e Monti della Laga, Barisciano (L’Aquila), Italy
| | - Lorenzo Peruzzi
- Dipartimento di Biologia, Università degli Studi di Pisa, Pisa, Italy
| |
Collapse
|
21
|
Silva SR, Pinheiro DG, Meer EJ, Michael TP, Varani AM, Miranda VFO. The complete chloroplast genome sequence of the leafy bladderwort, Utricularia foliosa L. (Lentibulariaceae). CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0653-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
22
|
Silva SR, Diaz YCA, Penha HA, Pinheiro DG, Fernandes CC, Miranda VFO, Michael TP, Varani AM. The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family. PLoS One 2016; 11:e0165176. [PMID: 27764252 PMCID: PMC5072713 DOI: 10.1371/journal.pone.0165176] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/08/2016] [Indexed: 02/06/2023] Open
Abstract
Lentibulariaceae is the richest family of carnivorous plants spanning three genera including Pinguicula, Genlisea, and Utricularia. Utricularia is globally distributed, and, unlike Pinguicula and Genlisea, has both aquatic and terrestrial forms. In this study we present the analysis of the chloroplast (cp) genome of the terrestrial Utricularia reniformis. U. reniformis has a standard cp genome of 139,725bp, encoding a gene repertoire similar to essentially all photosynthetic organisms. However, an exclusive combination of losses and pseudogenization of the plastid NAD(P)H-dehydrogenase (ndh) gene complex were observed. Comparisons among aquatic and terrestrial forms of Pinguicula, Genlisea, and Utricularia indicate that, whereas the aquatic forms retained functional copies of the eleven ndh genes, these have been lost or truncated in terrestrial forms, suggesting that the ndh function may be dispensable in terrestrial Lentibulariaceae. Phylogenetic scenarios of the ndh gene loss and recovery among Pinguicula, Genlisea, and Utricularia to the ancestral Lentibulariaceae cladeare proposed. Interestingly, RNAseq analysis evidenced that U. reniformis cp genes are transcribed, including the truncated ndh genes, suggesting that these are not completely inactivated. In addition, potential novel RNA-editing sites were identified in at least six U. reniformis cp genes, while none were identified in the truncated ndh genes. Moreover, phylogenomic analyses support that Lentibulariaceae is monophyletic, belonging to the higher core Lamiales clade, corroborating the hypothesis that the first Utricularia lineage emerged in terrestrial habitats and then evolved to epiphytic and aquatic forms. Furthermore, several truncated cp genes were found interspersed with U. reniformis mitochondrial and nuclear genome scaffolds, indicating that as observed in other smaller plant genomes, such as Arabidopsis thaliana, and the related and carnivorous Genlisea nigrocaulis and G. hispidula, the endosymbiotic gene transfer may also shape the U. reniformis genome in a similar fashion. Overall the comparative analysis of the U. reniformis cp genome provides new insight into the ndh genes and cp genome evolution of carnivorous plants from Lentibulariaceae family.
Collapse
Affiliation(s)
- Saura R. Silva
- Instituto de Biociências, UNESP - Univ Estadual Paulista, Câmpus Botucatu, São Paulo, Brazil
| | - Yani C. A. Diaz
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Helen Alves Penha
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Camila C. Fernandes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Vitor F. O. Miranda
- Departamento de Biologia Aplicada à Agropecuária, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| | - Todd P. Michael
- Ibis Bioscience, Computational Genomics, Carlsbad, California, United States of America
| | - Alessandro M. Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Câmpus Jaboticabal, São Paulo, Brazil
| |
Collapse
|
23
|
Tran TD, Šimková H, Schmidt R, Doležel J, Schubert I, Fuchs J. Chromosome identification for the carnivorous plant Genlisea margaretae. Chromosoma 2016; 126:389-397. [PMID: 27153834 DOI: 10.1007/s00412-016-0599-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/20/2016] [Accepted: 04/26/2016] [Indexed: 10/21/2022]
Abstract
Genlisea margaretae, subgenus Genlisea, section Recurvatae (184 Mbp/1C), belongs to a plant genus with a 25-fold genome size difference and an extreme genome plasticity. Its 19 chromosome pairs could be distinguished individually by an approach combining optimized probe pooling and consecutive rounds of multicolor fluorescence in situ hybridization (mcFISH) with bacterial artificial chromosomes (BACs) selected for repeat-free inserts. Fifty-one BACs were assigned to 18 chromosome pairs. They provide a tool for future assignment of genomic sequence contigs to distinct chromosomes as well as for identification of homeologous chromosome regions in other species of the carnivorous Lentibulariaceae family, and potentially of chromosome rearrangements, in cases where more than one BAC per chromosome pair was identified.
Collapse
Affiliation(s)
- Trung D Tran
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany.,Plant Resource Center, Vietnam Academy of Agricultural Science, Ankhanh, Hoaiduc, Hanoi, Vietnam
| | - Hana Šimková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic
| | - Renate Schmidt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Jaroslav Doležel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, CZ-78371, Olomouc, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany.,Central European Institute of Technology and Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany.
| |
Collapse
|
24
|
Rutishauser R. Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification. ANNALS OF BOTANY 2016; 117:811-32. [PMID: 26589968 PMCID: PMC4845801 DOI: 10.1093/aob/mcv172] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 08/19/2015] [Accepted: 09/25/2015] [Indexed: 05/22/2023]
Abstract
BACKGROUND Various groups of flowering plants reveal profound ('saltational') changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps 'hopeful monsters') that gave rise to new evolutionary lines of organisms, based on (major) genetic changes. SCOPE This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized. CONCLUSIONS Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves - as still distinguishable in related flowering plants - are blurred ('fuzzy'). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.
Collapse
Affiliation(s)
- Rolf Rutishauser
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland
| |
Collapse
|
25
|
Poppinga S, Weisskopf C, Westermeier AS, Masselter T, Speck T. Fastest predators in the plant kingdom: functional morphology and biomechanics of suction traps found in the largest genus of carnivorous plants. AOB PLANTS 2015; 8:plv140. [PMID: 26602984 PMCID: PMC4717191 DOI: 10.1093/aobpla/plv140] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/07/2015] [Indexed: 05/18/2023]
Abstract
Understanding the physics of plant movements, which describe the interplay between plant architecture, movement speed and actuation principles, is essential for the comprehension of important processes like plant morphogenesis. Recent investigations especially on rapid plant movements at the interface of biology, physics and engineering sciences highlight how such fast motions can be achieved without the presence of muscles, nerves and technical hinge analogies. The suction traps (bladders) of carnivorous bladderworts (Utricularia spp., Lentibulariaceae, Lamiales) are considered as some of the most elaborate moving structures in the plant kingdom. A complex interplay of morphological and physiological adaptations allows the traps to pump water out of their body and to store elastic energy in the deformed bladder walls. Mechanical stimulation by prey entails opening of the otherwise watertight trapdoor, followed by trap wall relaxation, sucking in of water and prey, and consecutive trapdoor closure. Suction can also occur spontaneously in non-stimulated traps. We review the current state of knowledge about the suction trap mechanism with a focus on architectonically homogeneous traps of aquatic bladderwort species from section Utricularia (the so-called 'Utricularia vulgaris trap type'). The functional morphology and biomechanics of the traps are described in detail. We discuss open questions and propose promising aspects for future studies on these sophisticated ultra-fast trapping devices.
Collapse
Affiliation(s)
- Simon Poppinga
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg im Breisgau, Germany
| | - Carmen Weisskopf
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany Present address: Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Anna Sophia Westermeier
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany
| | - Tom Masselter
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany
| | - Thomas Speck
- Plant Biomechanics Group, University of Freiburg, Botanic Garden, Schänzlestrasse 1, 79104 Freiburg im Breisgau, Germany Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Straße 21, 79104 Freiburg im Breisgau, Germany
| |
Collapse
|
26
|
Tran TD, Cao HX, Jovtchev G, Novák P, Vu GTH, Macas J, Schubert I, Fuchs J. Chromatin organization and cytological features of carnivorous Genlisea species with large genome size differences. FRONTIERS IN PLANT SCIENCE 2015; 6:613. [PMID: 26347752 PMCID: PMC4542322 DOI: 10.3389/fpls.2015.00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/24/2015] [Indexed: 05/07/2023]
Abstract
The monophyletic carnivorous genus Genlisea (Lentibulariaceae) is characterized by a bi-directional genome size evolution resulting in a 25-fold difference in nuclear DNA content. This is one of the largest ranges found within a genus so far and makes Genlisea an interesting subject to study mechanisms of genome and karyotype evolution. Genlisea nigrocaulis, with 86 Mbp one of the smallest plant genomes, and the 18-fold larger genome of G. hispidula (1,550 Mbp) possess identical chromosome numbers (2n = 40) but differ considerably in chromatin organization, nuclear and cell size. Interphase nuclei of G. nigrocaulis and of related species with small genomes, G. aurea (133 Mbp, 2n ≈ 104) and G. pygmaea (179 Mbp, 2n = 80), are hallmarked by intensely DAPI-stained chromocenters, carrying typical heterochromatin-associated methylation marks (5-methylcytosine, H3K9me2), while in G. hispidula and surprisingly also in the small genome of G. margaretae (184 Mbp, 2n = 38) the heterochromatin marks are more evenly distributed. Probes of tandem repetitive sequences together with rDNA allow the unequivocal discrimination of 13 out of 20 chromosome pairs of G. hispidula. One of the repetitive sequences labeled half of the chromosome set almost homogenously supporting an allopolyploid status of G. hispidula and its close relative G. subglabra (1,622 Mbp, 2n = 40). In G. nigrocaulis 11 chromosome pairs could be individualized using a combination of rDNA and unique genomic probes. The presented data provide a basis for future studies of karyotype evolution within the genus Genlisea.
Collapse
Affiliation(s)
- Trung D. Tran
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Hieu X. Cao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Gabriele Jovtchev
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Petr Novák
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czech Republic
| | - Giang T. H. Vu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| | - Jiří Macas
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of SciencesČeské Budějovice, Czech Republic
| | - Ingo Schubert
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
- Central European Institute of Technology and Faculty of Science, Masaryk UniversityBrno, Czech Republic
| | - Joerg Fuchs
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben, Germany
| |
Collapse
|
27
|
Bárta J, Stone JD, Pech J, Sirová D, Adamec L, Campbell MA, Štorchová H. The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba. BMC PLANT BIOLOGY 2015; 15:78. [PMID: 25848894 PMCID: PMC4358910 DOI: 10.1186/s12870-015-0467-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/23/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The species of Utricularia attract attention not only owing to their carnivorous lifestyle, but also due to an elevated substitution rate and a dynamic evolution of genome size leading to its dramatic reduction. To better understand the evolutionary dynamics of genome size and content as well as the great physiological plasticity in this mostly aquatic carnivorous genus, we analyzed the transcriptome of Utricularia vulgaris, a temperate species with well characterized physiology and ecology. We compared its transcriptome, namely gene content and overall transcript profile, with a previously described transcriptome of Utricularia gibba, a congener possessing one of the smallest angiosperm genomes. RESULTS We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. 454 pyrosequencing resulted in more than 1,400,000 reads which were assembled into 41,407 isotigs in 19,522 isogroups. We observed high transcript variation in several isogroups explained by multiple loci and/or alternative splicing. The comparison of U. vulgaris and U. gibba transcriptomes revealed a similar distribution of GO categories among expressed genes, despite the differences in transcriptome preparation. We also found a strong correspondence in the presence or absence of root-associated genes between the U. vulgaris transcriptome and U. gibba genome, which indicated that the loss of some root-specific genes had occurred before the divergence of the two rootless species. CONCLUSIONS The species-rich genus Utricularia offers a unique opportunity to study adaptations related to the environment and carnivorous habit and also evolutionary processes responsible for considerable genome reduction. We show that a transcriptome may approximate the genome for gene content or gene duplication estimation. Our study is the first comparison of two global sequence data sets in Utricularia.
Collapse
Affiliation(s)
- Jiří Bárta
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - James D Stone
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
- />Institute of Botany CAS, Zámek 1, Průhonice, 25243 Czech Republic
| | - Jiří Pech
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Dagmara Sirová
- />Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 37005 Czech Republic
| | - Lubomír Adamec
- />Institute of Botany CAS, Section of Plant Ecology, Dukelská 135, Treboň, 37982 Czech Republic
| | - Matthew A Campbell
- />Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North, 4442 New Zealand
| | - Helena Štorchová
- />Institute of Experimental Botany CAS, Rozvojová 263 6- Lysolaje, Praha, 16502 Czech Republic
| |
Collapse
|
28
|
Carretero-Paulet L, Chang TH, Librado P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA. Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biol Evol 2015; 7:444-56. [PMID: 25577200 PMCID: PMC4350169 DOI: 10.1093/gbe/evu288] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2014] [Indexed: 11/18/2022] Open
Abstract
The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.
Collapse
Affiliation(s)
- Lorenzo Carretero-Paulet
- Department of Biological Sciences, University at Buffalo Department of Biological Sciences, University at Buffalo
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo
| | - Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Guanajuato, México Present address: Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, Irapuato, Guanajuato, México
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | | |
Collapse
|
29
|
Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. ANNALS OF BOTANY 2014; 114:1651-63. [PMID: 25274549 PMCID: PMC4649684 DOI: 10.1093/aob/mcu189] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/07/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. METHODS Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. KEY RESULTS Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). CONCLUSIONS Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.
Collapse
Affiliation(s)
- Andreas Fleischmann
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Todd P Michael
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | | | - Aretuza Sousa
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Johann Greilhuber
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Kai F Müller
- Institute for Evolution and Biodiversity, University of Muenster, Hüfferstrasse 1, D 48149 Münster, Germany
| | - Günther Heubl
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| |
Collapse
|
30
|
Yang N, Hu F, Zhou L, Tang J. Reconstruction of ancestral gene orders using probabilistic and gene encoding approaches. PLoS One 2014; 9:e108796. [PMID: 25302942 PMCID: PMC4193752 DOI: 10.1371/journal.pone.0108796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 09/03/2014] [Indexed: 11/24/2022] Open
Abstract
Current tools used in the reconstruction of ancestral gene orders often fall into event-based and adjacency-based methods according to the principles they follow. Event-based methods such as GRAPPA are very accurate but with extremely high complexity, while more recent methods based on gene adjacencies such as InferCARsPro is relatively faster, but often produces an excessive number of chromosomes. This issue is mitigated by newer methods such as GapAdj, however it sacrifices a considerable portion of accuracy. We recently developed an adjacency-based method in the probabilistic framework called PMAG to infer ancestral gene orders. PMAG relies on calculating the conditional probabilities of gene adjacencies that are found in the leaf genomes using the Bayes' theorem. It uses a novel transition model which accounts for adjacency changes along the tree branches as well as a re-rooting procedure to prevent any information loss. In this paper, we improved PMAG with a new method to assemble gene adjacencies into valid gene orders, using an exact solver for traveling salesman problem (TSP) to maximize the overall conditional probabilities. We conducted a series of simulation experiments using a wide range of configurations. The first set of experiments was to verify the effectiveness of our strategy of using the better transition model and re-rooting the tree under the targeted ancestral genome. PMAG was then thoroughly compared in terms of three measurements with its four major competitors including InferCARsPro, GapAdj, GASTS and SCJ in order to assess their performances. According to the results, PMAG demonstrates superior performance in terms of adjacency, distance and assembly accuracies, and yet achieves comparable running time, even all TSP instances were solved exactly. PMAG is available for free at http://phylo.cse.sc.edu.
Collapse
Affiliation(s)
- Ning Yang
- School of Automation, Northwestern Polytechnical University, Xi'an, shaanxi, China
| | - Fei Hu
- Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, China
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
| | - Lingxi Zhou
- Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, China
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
| | - Jijun Tang
- Tianjin Key Laboratory of Cognitive Computing and Application, Tianjin University, Tianjin, China
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail:
| |
Collapse
|
31
|
Veleba A, Bureš P, Adamec L, Šmarda P, Lipnerová I, Horová L. Genome size and genomic GC content evolution in the miniature genome-sized family Lentibulariaceae. THE NEW PHYTOLOGIST 2014; 203:22-8. [PMID: 24661198 DOI: 10.1111/nph.12790] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Adam Veleba
- Department of Botany and Zoology, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | | | | | | | | | | |
Collapse
|
32
|
Oliver KR, McComb JA, Greene WK. Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol Evol 2014; 5:1886-901. [PMID: 24065734 PMCID: PMC3814199 DOI: 10.1093/gbe/evt141] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin's "abominable mystery": the spectacular success of the angiosperms.
Collapse
Affiliation(s)
- Keith R Oliver
- School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia, Australia
| | | | | |
Collapse
|
33
|
Abstract
PREMISE OF THE STUDY The Lamiidae, a clade composed of approximately 15% of all flowering plants, consists of five orders: Boraginales, Gentianales, Garryales, Lamiales, and Solanales; and four families unplaced in an order: Icacinaceae, Metteniusiaceae, Oncothecaceae, and Vahliaceae. Our understanding of the phylogenetic relationships of Lamiidae has improved significantly in recent years, however, relationships among the orders and unplaced families of the clade remain partly unresolved. Here, we present a phylogenetic analysis of the Lamiidae based on an expanded sampling, including all families together, for the first time, in a single phylogenetic analyses. METHODS Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood, and Bayesian approaches. Analyses included nine plastid regions (atpB, matK, ndhF, psbBTNH, rbcL, rps4, rps16, trnL-F, and trnV-atpE) and the mitochondrial rps3 region, and 129 samples representing all orders and unplaced families of Lamiidae. KEY RESULTS Maximum Likelihood (ML) and Bayesian trees provide good support for Boraginales sister to Lamiales, with successive outgroups (Solanales + Vahlia) and Gentianales, together comprising the core Lamiidae. Early branching patterns are less well supported, with Garryales only poorly supported as sister to the above 'core' and a weakly supported clade composed of Icacinaceae, Metteniusaceae, and Oncothecaceae sister to all other Lamiidae. CONCLUSIONS Our phylogeny of Lamiidae reveals increased resolution and support for internal relationships that have remained elusive. Within Lamiales, greater resolution also is obtained, but some family interrelationships remain a challenge.
Collapse
|
34
|
Hook I, Mills C, Sheridan H. Bioactive Naphthoquinones from Higher Plants. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2014. [DOI: 10.1016/b978-0-444-63294-4.00005-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
35
|
Wicke S, Schäferhoff B, dePamphilis CW, Müller KF. Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae. Mol Biol Evol 2013; 31:529-45. [PMID: 24344209 DOI: 10.1093/molbev/mst261] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carnivorous Lentibulariaceae exhibit the most sophisticated implementation of the carnivorous syndrome in plants. Their unusual lifestyle coincides with distinct genomic peculiarities such as the smallest angiosperm nuclear genomes and extremely high nucleotide substitution rates across all genomic compartments. Here, we report the complete plastid genomes from each of the three genera Pinguicula, Utricularia, and Genlisea, and investigate plastome-wide changes in their molecular evolution as the carnivorous syndrome unfolds. We observe a size reduction by up to 9% mostly due to the independent loss of genes for the plastid NAD(P)H dehydrogenase and altered proportions of plastid repeat DNA, as well as a significant plastome-wide increase of substitution rates and microstructural changes. Protein-coding genes across all gene classes show a disproportional elevation of nonsynonymous substitutions, particularly in Utricularia and Genlisea. Significant relaxation of purifying selection relative to noncarnivores occurs in the plastid-encoded fraction of the photosynthesis ATP synthase complex, the photosystem I, and in several other photosynthesis and metabolic genes. Shifts in selective regimes also affect housekeeping genes including the plastid-encoded polymerase, for which evidence for relaxed purifying selection was found once during the transition to carnivory, and a second time during the diversification of the family. Lentibulariaceae significantly exhibit enhanced rates of nucleotide substitution in most of the 130 noncoding regions. Various factors may underlie the observed patterns of relaxation of purifying selection and substitution rate increases, such as reduced net photosynthesis rates, alternative paths of nutrient uptake (including organic carbon), and impaired DNA repair mechanisms.
Collapse
Affiliation(s)
- Susann Wicke
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | | | | | | |
Collapse
|
36
|
Naumann J, Salomo K, Der JP, Wafula EK, Bolin JF, Maass E, Frenzke L, Samain MS, Neinhuis C, dePamphilis CW, Wanke S. Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages. PLoS One 2013; 8:e79204. [PMID: 24265760 PMCID: PMC3827129 DOI: 10.1371/journal.pone.0079204] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/20/2013] [Indexed: 11/19/2022] Open
Abstract
Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ∼15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ∼91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.
Collapse
Affiliation(s)
- Julia Naumann
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- * E-mail: (JN); (SW)
| | - Karsten Salomo
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Joshua P. Der
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Eric K. Wafula
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jay F. Bolin
- Department of Biology, Catawba College, Salisbury, North Carolina, United States of America
| | - Erika Maass
- Department of Biological Sciences, University of Namibia, Windhoek, Namibia
| | - Lena Frenzke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | | | | | - Claude W. dePamphilis
- Department of Biology and Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
- * E-mail: (JN); (SW)
| |
Collapse
|
37
|
Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD. The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics 2013; 14:476. [PMID: 23855885 PMCID: PMC3728226 DOI: 10.1186/1471-2164-14-476] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Accepted: 07/09/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Genlisea aurea (Lentibulariaceae) is a carnivorous plant with unusually small genome size - 63.6 Mb - one of the smallest known among higher plants. Data on the genome sizes and the phylogeny of Genlisea suggest that this is a derived state within the genus. Thus, G. aurea is an excellent model organism for studying evolutionary mechanisms of genome contraction. RESULTS Here we report sequencing and de novo draft assembly of G. aurea genome. The assembly consists of 10,687 contigs of the total length of 43.4 Mb and includes 17,755 complete and partial protein-coding genes. Its comparison with the genome of Mimulus guttatus, another representative of higher core Lamiales clade, reveals striking differences in gene content and length of non-coding regions. CONCLUSIONS Genome contraction was a complex process, which involved gene loss and reduction of lengths of introns and intergenic regions, but not intron loss. The gene loss is more frequent for the genes that belong to multigenic families indicating that genetic redundancy is an important prerequisite for genome size reduction.
Collapse
Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow 119992, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow 127994, Russia
| | - Roman A Sutormin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow 119992, Russia
| | - Elena R Nabieva
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow 119992, Russia
| | - Aleksey A Penin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow 119992, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow 127994, Russia
- Department of Genetics, Lomonosov Moscow State University, Moscow 119992, Russia
| | - Alexey S Kondrashov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow 119992, Russia
- Department of Ecology and Evolutionary Biology and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maria D Logacheva
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow 119992, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
38
|
Reconstructing Ancestral Genomic Orders Using Binary Encoding and Probabilistic Models. BIOINFORMATICS RESEARCH AND APPLICATIONS 2013. [DOI: 10.1007/978-3-642-38036-5_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
39
|
Hidden genetic diversity in the green alga Spirogyra (Zygnematophyceae, Streptophyta). BMC Evol Biol 2012; 12:77. [PMID: 22655677 PMCID: PMC3527229 DOI: 10.1186/1471-2148-12-77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/07/2012] [Indexed: 11/10/2022] Open
Abstract
Background The unbranched filamentous green alga Spirogyra (Streptophyta, Zygnemataceae) is easily recognizable based on its vegetative morphology, which shows one to several spiral chloroplasts. This simple structure falsely points to a low genetic diversity: Spirogyra is commonly excluded from phylogenetic analyses because the genus is known as a long-branch taxon caused by a high evolutionary rate. Results We focused on this genetic diversity and sequenced 130 Spirogyra small subunit nuclear ribosomal DNA (SSU rDNA) strands of different origin. The resulting SSU rDNA sequences were used for phylogenetic analyses using complex evolutionary models (posterior probability, maximum likelihood, neighbor joining, and maximum parsimony methods). The sequences were between 1672 and 1779 nucleotides long. Sequence comparisons revealed 53 individual clones, but our results still support monophyly of the genus. Our data set did not contain a single slow-evolving taxon that would have been placed on a shorter branch compared to the remaining sequences. Out of 130 accessions analyzed, 72 showed a secondary loss of the 1506 group I intron, which formed a long-branched group within the genus. The phylogenetic relationship to the genus Spirotaenia was not resolved satisfactorily. The genetic distance within the genus Spirogyra exceeded the distances measured within any other genus of the remaining Zygnemataceae included in this study. Conclusion Overall, we define eight distinct clades of Spirogyra, one of them including the genus Sirogonium. A large number of non-homoplasious synapomorphies (NHS; 114 NHS in total) was found for Spirogyra (41 NHS) and for each clade (totaling 73 NHS). This emphasizes the high genetic diversity of this genus and the distance to the remaining Zygnematophyceae.
Collapse
|
40
|
Płachno BJ, Swiątek P, Kozieradzka-Kiszkurno M. The F-actin cytoskeleton in syncytia from non-clonal progenitor cells. PROTOPLASMA 2011; 248:623-9. [PMID: 20878195 PMCID: PMC3135821 DOI: 10.1007/s00709-010-0209-6] [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: 07/02/2010] [Accepted: 09/01/2010] [Indexed: 05/10/2023]
Abstract
The actin cytoskeleton of plant syncytia (a multinucleate cell arising through fusion) is poorly known: to date, there have only been reports about F-actin organization in plant syncytia induced by parasitic nematodes. To broaden knowledge regarding this issue, we analyzed F-actin organization in special heterokaryotic Utricularia syncytia, which arise from maternal sporophytic tissues and endosperm haustoria. In contrast to plant syncytia induced by parasitic nematodes, the syncytia of Utricularia have an extensive F-actin network. Abundant F-actin cytoskeleton occurs both in the region where cell walls are digested and the protoplast of nutritive tissue cells fuse with the syncytium and also near a giant amoeboid in the shape nuclei in the central part of the syncytium. An explanation for the presence of an extensive F-actin network and especially F-actin bundles in the syncytia is probably that it is involved in the movement of nuclei and other organelles and also the transport of nutrients in these physiological activity organs which are necessary for the development of embryos in these unique carnivorous plants. We observed that in Utricularia nutritive tissue cells, actin forms a randomly arranged network of F-actin, and later in syncytium, two patterns of F-actin were observed, one characteristic for nutritive cells and second-actin bundles-characteristic for haustoria and suspensors, thus syncytia inherit their F-actin patterns from their progenitors.
Collapse
Affiliation(s)
- Bartosz Jan Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University, Cracow, Poland.
| | | | | |
Collapse
|
41
|
Ibarra-Laclette E, Albert VA, Pérez-Torres CA, Zamudio-Hernández F, Ortega-Estrada MDJ, Herrera-Estrella A, Herrera-Estrella L. Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome. BMC PLANT BIOLOGY 2011; 11:101. [PMID: 21639913 PMCID: PMC3141634 DOI: 10.1186/1471-2229-11-101] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 06/03/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The carnivorous plant Utricularia gibba (bladderwort) is remarkable in having a minute genome, which at ca. 80 megabases is approximately half that of Arabidopsis. Bladderworts show an incredible diversity of forms surrounding a defined theme: tiny, bladder-like suction traps on terrestrial, epiphytic, or aquatic plants with a diversity of unusual vegetative forms. Utricularia plants, which are rootless, are also anomalous in physiological features (respiration and carbon distribution), and highly enhanced molecular evolutionary rates in chloroplast, mitochondrial and nuclear ribosomal sequences. Despite great interest in the genus, no genomic resources exist for Utricularia, and the substitution rate increase has received limited study. RESULTS Here we describe the sequencing and analysis of the Utricularia gibba transcriptome. Three different organs were surveyed, the traps, the vegetative shoot bodies, and the inflorescence stems. We also examined the bladderwort transcriptome under diverse stress conditions. We detail aspects of functional classification, tissue similarity, nitrogen and phosphorus metabolism, respiration, DNA repair, and detoxification of reactive oxygen species (ROS). Long contigs of plastid and mitochondrial genomes, as well as sequences for 100 individual nuclear genes, were compared with those of other plants to better establish information on molecular evolutionary rates. CONCLUSION The Utricularia transcriptome provides a detailed genomic window into processes occurring in a carnivorous plant. It contains a deep representation of the complex metabolic pathways that characterize a putative minimal plant genome, permitting its use as a source of genomic information to explore the structural, functional, and evolutionary diversity of the genus. Vegetative shoots and traps are the most similar organs by functional classification of their transcriptome, the traps expressing hydrolytic enzymes for prey digestion that were previously thought to be encoded by bacteria. Supporting physiological data, global gene expression analysis shows that traps significantly over-express genes involved in respiration and that phosphate uptake might occur mainly in traps, whereas nitrogen uptake could in part take place in vegetative parts. Expression of DNA repair and ROS detoxification enzymes may be indicative of a response to increased respiration. Finally, evidence from the bladderwort transcriptome, direct measurement of ROS in situ, and cross-species comparisons of organellar genomes and multiple nuclear genes supports the hypothesis that increased nucleotide substitution rates throughout the plant may be due to the mutagenic action of amplified ROS production.
Collapse
Affiliation(s)
- Enrique Ibarra-Laclette
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Guanajuato, México
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260, USA
| | - Claudia A Pérez-Torres
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Guanajuato, México
| | - Flor Zamudio-Hernández
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Guanajuato, México
| | - María de J Ortega-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Guanajuato, México
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Guanajuato, México
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Guanajuato, México
| |
Collapse
|
42
|
Płachno BJ, Swiątek P. Syncytia in plants: cell fusion in endosperm-placental syncytium formation in Utricularia (Lentibulariaceae). PROTOPLASMA 2011; 248:425-35. [PMID: 20567861 DOI: 10.1007/s00709-010-0173-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/08/2010] [Indexed: 05/22/2023]
Abstract
The syncytium formed by Utricularia is extremely unusual and perhaps unique among angiosperm syncytia. All typical plant syncytia (articulated laticifers, amoeboid tapetum, the nucellar plasmodium of river weeds) are formed only by fusion of sporophytic cells which possess the same genetic material, unlike Utricularia in which the syncytium possesses nuclei from two different sources: cells of maternal sporophytic nutritive tissue and endosperm haustorium (both maternal and paternal genetic material). How is this kind of syncytium formed and organized and is it similar to other plant syncytial structures? We used light and electron microscopy to reconstruct the step-by-step development of the Utricularia syncytia. The syncytia of Utricularia developed through heterotypic cell fusion involving the digestion of the cell wall, and finally, heterokaryotic multinucleate structures were formed, which possessed different-sized nuclei that were not regularly arranged in the cytoplasm. We showed that these syncytia were characterized by hypertrophy of nuclei, abundant endoplasmic reticulum and organelles, and the occurrence of wall ingrowths. All these characters testify to high activity and may confirm the nutritive and transport functions of the syncytium for the developing embryo. In Utricularia, the formation of the syncytium provides an economical way to redistribute cell components and release nutrients from the digested cell walls, which can now be used for the embryo, and finally to create a large surface for the exchange of nutrients between the placenta and endosperm.
Collapse
Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University, 52 Grodzka st, 31-044, Cracow, Poland.
| | | |
Collapse
|
43
|
Płachno BJ. Female germ unit in Genlisea and Utricularia, with remarks about the evolution of the extra-ovular female gametophyte in members of Lentibulariaceae. PROTOPLASMA 2011; 248:391-404. [PMID: 20689973 PMCID: PMC3066386 DOI: 10.1007/s00709-010-0185-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 07/14/2010] [Indexed: 05/22/2023]
Abstract
Lentibulariaceae is the largest family among carnivorous plants which displays not only an unusual morphology and anatomy but also the special evolution of its embryological characteristics. It has previously been reported by authors that Utricularia species lack a filiform apparatus in the synergids. The main purposes of this study were to determine whether a filiform apparatus occurs in the synergids of Utricularia and its sister genus Genlisea, and to compare the female germ unit in these genera. The present studies clearly show that synergids in both genera possess a filiform apparatus; however, it seems that Utricularia quelchii synergids have a simpler structure compared to Genlisea aurea and other typical angiosperms. The synergids are located at the terminal position in the embryo sacs of Pinguicula, Genlisea and were probably also located in that position in common Utricularia ancestor. This ancestral characteristic still occurs in some species from the Bivalvaria subgenus. An embryo sac, which grows out beyond the limit of the integument and has contact with nutritive tissue, appeared independently in different Utricularia lineages and as a consequence of this, the egg apparatus changes position from apical to lateral.
Collapse
Affiliation(s)
- Bartosz Jan Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University, 52 Grodzka st., 31-044, Cracow, Poland.
| |
Collapse
|
44
|
Fukushima K, Imamura K, Nagano K, Hoshi Y. Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae). JOURNAL OF PLANT RESEARCH 2011; 124:231-44. [PMID: 20623155 PMCID: PMC3040357 DOI: 10.1007/s10265-010-0366-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 06/11/2010] [Indexed: 05/07/2023]
Abstract
To clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.
Collapse
Affiliation(s)
- Kenji Fukushima
- Department of Basic Biology, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193 Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585 Japan
| | - Kaori Imamura
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
- Japan Software Management Co. Ltd., 5-32 KinKou-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0056 Japan
| | - Katsuya Nagano
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
| |
Collapse
|
45
|
Schäferhoff B, Fleischmann A, Fischer E, Albach DC, Borsch T, Heubl G, Müller KF. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC Evol Biol 2010; 10:352. [PMID: 21073690 PMCID: PMC2992528 DOI: 10.1186/1471-2148-10-352] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 11/12/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past. RESULTS Our analysis of the rapidly evolving trnK/matK, trnL-F and rps16 chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position. CONCLUSIONS Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a fully resolved plastid tree of Lamiales.
Collapse
Affiliation(s)
- Bastian Schäferhoff
- Institute for Evolution and Biodiversity, University of Muenster, Hüfferstraße 1, 48149 Münster, Germany
| | | | | | | | | | | | | |
Collapse
|
46
|
Fleischmann A, Schäferhoff B, Heubl G, Rivadavia F, Barthlott W, Müller KF. Phylogenetics and character evolution in the carnivorous plant genus Genlisea A. St.-Hil. (Lentibulariaceae). Mol Phylogenet Evol 2010; 56:768-83. [DOI: 10.1016/j.ympev.2010.03.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Revised: 03/01/2010] [Accepted: 03/07/2010] [Indexed: 10/19/2022]
|
47
|
Płachno BJ, Swiatek P. Unusual embryo structure in viviparous Utricularia nelumbifolia, with remarks on embryo evolution in genus Utricularia. PROTOPLASMA 2010; 239:69-80. [PMID: 19921393 DOI: 10.1007/s00709-009-0084-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 10/22/2009] [Indexed: 05/21/2023]
Abstract
In most species of the Genlisea-Utricularia sister lineage, the organs arising directly after germination comprise a single leaf-like structure, followed by a bladder-trap/stolon, with the lack of an embryonic primary root considered a synapomorphic character. Previous anatomical work suggests that the most common recent ancestor of Utricularia possessed an embryo comprising storage tissue and a meristematic apical region minus lateral organs. Studies of embryogenesis across the Utricularia lineage suggest that multiple primary organs have only evolved in the viviparous Utricularia nelumbifolia, Utricularia reniformis, and Utricularia humboldtii within the derived Iperua/Orchidioides clade. All three of these species are specialized for growth as "aquatic epiphytes" in the tanks of bromeliads, with recent phylogenetic evidence suggesting the possibility that multiple primary organs may have evolved twice independently within this clade. The primary organs of viviparous Utricularia also possess epidermal surface glands, and our study suggests that these may function as root hairs for uptake of solutes from the external environment--a possible adaptation for the "aquatic-epiphytic" habitat.
Collapse
Affiliation(s)
- Bartosz J Płachno
- Department of Plant Cytology and Embryology, Jagiellonian University, Krakow, Poland.
| | | |
Collapse
|
48
|
Alcalá RE, Mariano NA, Osuna F, Abarca CA. An experimental test of the defensive role of sticky traps in the carnivorous plantPinguicula moranensis(Lentibulariaceae). OIKOS 2010. [DOI: 10.1111/j.1600-0706.2009.18110.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
49
|
Albert VA, Jobson RW, Michael TP, Taylor DJ. The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:5-9. [PMID: 20007200 DOI: 10.1093/jxb/erp349] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Carnivorous plants inhabit nutrient-poor environments, where prominent targets of prey capture are organic nitrogen and phosphorus. Some carnivorous plants also acquire carbon from their victims. A new report focusing on Utricularia, the bladderwort, demonstrates that carbon assimilated from photosynthesis is paradoxically secreted into the trapping environment, where it may help to support a mutualistic bacterial community. This bacterial community may also secrete allelochemicals that attract microcrustaceans which bear a strong overt resemblance to bladderwort traps. Furthermore, Utricularia and its sister genus Genlisea share anomalous molecular evolutionary features, such as highly increased rates of nucleotide substitution and dynamic evolution of genome size, from approximately 60-1500 megabases depending on the species or even population. A mechanistic hypothesis, based on the mutagenic action of reactive oxygen species (ROS) is proposed to underlie these phenomena, involving error-prone repair at the level of DNA bases and double-strand breaks. It is argued that these plants are prime candidates for further research on the complexities of plant physiology associated with carnivory, metagenomic surveys of trap microbial communities, novel plant nitrogen/nutrient utilization pathways, the ecology of prey attraction, whole-plant and trap comparative development, and, finally, evolution of the minimal angiosperm genome.
Collapse
Affiliation(s)
- Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York 14260, USA.
| | | | | | | |
Collapse
|
50
|
Jürgens A, El-Sayed AM, Suckling DM. Do carnivorous plants use volatiles for attracting prey insects? Funct Ecol 2009. [DOI: 10.1111/j.1365-2435.2009.01626.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|