The Experts below are selected from a list of 141 Experts worldwide ranked by ideXlab platform
Todd P Michael - One of the best experts on this subject based on the ideXlab platform.
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development of microsatellite markers for the carnivorous plant Genlisea aurea lentibulariaceae using genomics data of ngs
Molecular Biology Reports, 2018Co-Authors: Yani C Arangurendiaz, Alessandro M Varani, Todd P MichaelAbstract:Genlisea aurea A.St.-Hil. is a carnivorous plant endemic species to Brazil in the Lentibulariaceae family. Very few studies have addressed the genetic structure and conservation status of G. aurea and the Lentibulariaceae. Microsatellites markers are advantageous tools that can be employed to predict the vulnerability of Lentibulariaceae species. Therefore, the development of molecular markers focusing the population analyses of Genlisea for future genetic studies and conservation actions are essential. Thus, we developed simple sequence repeats (SSRs) based on in silico analyses of G. aurea draft genome assembly. We characterized 40 individuals from several populations and identified 12 loci that were polymorphic, with heterozygosity between 0.123 and 0.650. We demonstrated that the G. aurea SSR markers work cross-species in Genlisea filiformis, G. repens, G. tuberosa and G. violacea. These markers will be important for future population, phylogeographic and conservation studies in G. aurea and other Genlisea species.
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comparative genomic analysis of Genlisea corkscrew plants lentibulariaceae chloroplast genomes reveals an increasing loss of the ndh genes
PLOS ONE, 2018Co-Authors: Saura R Silva, Alessandro M Varani, Todd P Michael, Elliott J Meer, Daniel Guariz Pinheiro, Vitor F O MirandaAbstract: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.
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the complete chloroplast genome sequence of the leafy bladderwort utricularia foliosa l lentibulariaceae
Conservation Genetics Resources, 2017Co-Authors: Saura R Silva, Todd P Michael, Daniel G Pinheiro, Elliott J Meer, Alessandro M VaraniAbstract:Utricularia foliosa L., commonly known as leafy bladderwort, is a widespread aquatic carnivorous plant from the Lentibulariaceae family. The species of the Utricularia and Genlisea genera are known to possess the smallest nuclear genomes across angiosperms. This study reveals that U. foliosa have a typical chloroplast genome of 150,851 bp in length, comprised of a large single-copy region (LSC) of 82,720 bp, a small single-copy region (SSC) of 17,481 bp, and inverted repeat regions (IRs) of 25,325 bp. A total of 139 genes, 88 of which are protein coding genes, 37 tRNA genes, eight rRNA genes and six pseudogenes were identified. All plastid NAD(P)H-dehydrogenase genes are present as intact copies. Phylogenetic analyses indicate that U. foliosa is closely related to other suspended or affixed aquatic species belonging to the Utricularia sect. Utricularia.
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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, 2016Co-Authors: Saura R Silva, Vitor F O Miranda, Todd P Michael, Daniel G Pinheiro, Yani C A Diaz, Helen A Penha, Camila C Fernandes, Alessandro M VaraniAbstract: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.
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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, 2014Co-Authors: Andreas Fleischmann, Fernando Rivadavia, Kai F Muller, Todd P Michael, Johann Greilhuber, Aretuza Sousa, Wenqin Wang, Eva M Temsch, Gunther HeublAbstract: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.
Bartosz J Plachno - One of the best experts on this subject based on the ideXlab platform.
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structural features of carnivorous plant Genlisea utricularia tubers as abiotic stress resistance organs
International Journal of Molecular Sciences, 2020Co-Authors: Bartosz J Plachno, Piotr świątek, Saura R Silva, Kingsley W Dixon, Krzystof Lustofin, Guilherme C SeberAbstract:Carnivorous plants from the Lentibulariaceae form a variety of standard and novel vegetative organs and survive unfavorable environmental conditions. Within Genlisea, only G. tuberosa, from the Brazilian Cerrado, formed tubers, while Utricularia menziesii is the only member of the genus to form seasonally dormant tubers. We aimed to examine and compare the tuber structure of two taxonomically and phylogenetically divergent terrestrial carnivorous plants: Genlisea tuberosa and Utricularia menziesii. Additionally, we analyzed tubers of U. mannii. We constructed phylogenetic trees using chloroplast genes matK/trnK and rbcL and used studied characters for ancestral state reconstruction. All examined species contained mainly starch as histologically observable reserves. The ancestral state reconstruction showed that specialized organs such as turions evolved once and tubers at least 12 times from stolons in Lentibulariaceae. Different from other clades, tubers probably evolved from thick stolons for sect. Orchidioides and both structures are primarily water storage structures. In contrast to species from section Orchidioides, G. tuberosa, U. menziesii and U. mannii form starchy tubers. In G. tuberosa and U. menziesii, underground tubers provide a perennating bud bank that protects the species in their fire-prone and seasonally desiccating environments.
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Genlisea hawkingii lentibulariaceae a new species from serra da canastra minas gerais brazil
PLOS ONE, 2020Co-Authors: Saura R Silva, Bartosz J Plachno, Samanta Gabriela Medeiros Carvalho, Vitor F O MirandaAbstract:Genlisea hawkingii, which is a new species of Genlisea subgen. Tayloria (Lentibulariaceae) from cerrado in southwest Brazil, is described and illustrated. This species has been found in only one locality thus far, in the Serra da Canastra, which is located in the Delfinopolis municipality in Minas Gerais, Brazil. The new species is morphologically similar to Genlisea violacea and G. flexuosa, but differs from them in having a corolla with a conical and curved spur along with sepals with an acute apex and reproductive organs that only have glandular hairs. Moreover, it is similar to G. uncinata’s curved spur. G. hawkingii is nested within the subgen. Tayloria clade as a sister group to all the other species of this subgenus. Therefore, both morphological and phylogenetic results strongly support G. hawkingii as a new species in the subgen. Tayloria.
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vascular tissue in traps of australian carnivorous bladderworts utricularia of the subgenus polypompholyx
Aquatic Botany, 2017Co-Authors: Bartosz J Plachno, Lubomír Adamec, Iwona Kaminska, Piotr świątekAbstract:Abstract Utricularia (bladderworts) are rootless carnivorous plants forming small suction traps which are hollow discoid bladders. There is some controversy surrounding the understanding of trap vascularization in Utricularia species and most of the knowledge in the literature is based on aquatic Utricularia from section Utricularia . In this study, we investigated trap vascularization in 9 Utricularia species or clones from the subgenus Polypompholyx using several light microscopy staining techniques. Both xylem and phloem elements were found in the traps of all investigated species or clones. The pattern of trap vascular bundles from the subgenus Polypompholyx was similar to that reported for subgenus Bivalvaria, but different from that of aquatic U. vulgaris from the subgenus Utricularia . The system of trap vascularization in the members of the subgenus Polypompholyx was different from that found in the traps of Genlisea , which is a closely related genus (both Lentibulariaceae). The structure of trap vascular bundles was, however, similar in Genlisea and Polypompholyx . Possible utilization of xylem elements in Utricularia traps is discussed.
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female germ unit in Genlisea and utricularia with remarks about the evolution of the extra ovular female gametophyte in members of lentibulariaceae
Protoplasma, 2011Co-Authors: Bartosz J PlachnoAbstract: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.
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algae commensal community in Genlisea traps
Acta Societatis Botanicorum Poloniae, 2011Co-Authors: Konrad Wolowski, Bartosz J PlachnoAbstract:The community of algae occurring in Genlisea traps and on the external traps surface in laboratory conditions were studied. A total of 29 taxa were found inside the traps, with abundant diatoms, green algae ( Chlamydophyceae ) and four morphotypes of chrysophytes stomatocysts. One morphotype is described as new for science. There are two ways of algae getting into Genlisea traps. The majority of those recorded inside the traps, are mobile; swimming freely by flagella or moving exuding mucilage like diatoms being ablate to colonize the traps themselves. Another possibility is transport of algae by invertebrates such as mites and crustaceans. In any case algae in the Genlisea traps come from the surrounding environment. Two dominant groups of algae ( Chladymonas div. and diatoms) in the trap environment, show ability to hydrolyze phosphomonoseters. We suggest that algae in carnivorous plant traps can compete with plant (host) for organic phosphate (phosphomonoseters). From the spectrum and ecological requirements of algal species found in the traps, environment inside the traps seems to be acidic. However, further studies are needed to test the relations between algae and carnivorous plants both in laboratory conditions and in the natural environment. All the reported taxa are described briefly and documented with 74 LM and SEM micrographs.
Kai F Muller - One of the best experts on this subject based on the ideXlab platform.
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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, 2014Co-Authors: Andreas Fleischmann, Fernando Rivadavia, Kai F Muller, Todd P Michael, Johann Greilhuber, Aretuza Sousa, Wenqin Wang, Eva M Temsch, Gunther HeublAbstract: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.
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phylogenetics and character evolution in the carnivorous plant genus Genlisea a st hil lentibulariaceae
Molecular Phylogenetics and Evolution, 2010Co-Authors: Andreas Fleischmann, Fernando Rivadavia, Bastian Schaferhoff, Gunther Heubl, Wilhelm Barthlott, Kai F MullerAbstract:The carnivorous plant genus Genlisea A. St.-Hil. (Lentibulariaceae) comprises at least 22 species distributed in South and Central America as well as in Africa (including Madagascar). It has only recently been shown to be a true carnivore, specialized in protozoa and other small soil organisms. Here we present a statistically highly supported phylogeny of Genlisea based on three chloroplast loci. The most recent common ancestor of Genlisea most likely was of Neotropical origin and characterized by pedicels that are recurved in fruit, a strongly glandular inflorescence, and bivalvate capsule dehiscence. The further evolution of various morphological characters during the diversification of the genus is discussed. The two previously suggested subgenera Tayloria and Genlisea correspond to the two major clades found in our analyses. In subgenus Genlisea, three clades can be clearly distinguished based on molecular and morphological characters and on biogeographic patterns, which led us to propose a new sectional classification.
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smallest angiosperm genomes found in lentibulariaceae with chromosomes of bacterial size
Plant Biology, 2006Co-Authors: Johann Greilhuber, Stefan Porembski, Kai F Muller, Thomas Borsch, Andreas Worberg, Wilhelm BarthlottAbstract:Abstract: Nuclear holoploid genome sizes (C-values) have been estimated to vary about 800-fold in angiosperms, with the smallest established 1C-value of 157 Mbp recorded in Arabidopsis thaliana. In the highly specialized carnivorous family Lentibulariaceae now three taxa have been found that exhibit significantly lower values: Genlisea margaretae with 63 Mbp, G. aurea with 64 Mbp, and Utricularia gibba with 88 Mbp. The smallest mitotic anaphase chromatids in G. aurea have 2.1 Mbp and are thus of bacterial size (NB: E. coli has ca. 4 Mbp). Several Utricularia species range somewhat lower than A. thaliana or are similar in genome size. The highest 1C-value known from species of Lentibulariaceae was found in Genlisea hispidula with 1510 Mbp, and results in about 24-fold variation for Genlisea and the Lentibulariaceae. Taking into account these new measurements, genome size variation in angiosperms is now almost 2000-fold. Genlisea and Utricularia are plants with terminal positions in the phylogeny of the eudicots, so that the findings are relevant for the understanding of genome miniaturization. Moreover, the Genlisea-Utricularia clade exhibits one of the highest mutational rates in several genomic regions in angiosperms, what may be linked to specialized patterns of genome evolution. Ultrasmall genomes have not been found in Pinguicula, which is the sister group of the Genlisea-Utricularia clade, and which does not show accelerated mutational rates. C-values in Pinguicula varied only 1.7-fold from 487 to 829 Mbp.
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recent progress in understanding the evolution of carnivorous lentibulariaceae lamiales
Plant Biology, 2006Co-Authors: Kai F Muller, Stefan Porembski, Thomas Borsch, Laurent Legendre, Wilhelm BarthlottAbstract:: Carnivorous plants have emerged as model systems for addressing many ecological and evolutionary questions, and since Lentibulariaceae comprise more than half of all known carnivorous species (325 spp.), they are of particular interest. Studies using various molecular markers have established that Lentibulariaceae and their three genera are monophyletic with Pinguicula being sister to a Genlisea-Utricularia-clade, while the closest relatives of the family remain uncertain. Character states of the carnivorous syndrome in related proto-carnivorous lamialean families apparently emerged independently. In Utricularia, the terrestrial habit has been reconstructed as plesiomorphic, and an extension of subgenus Polypompholyx is warranted. In the protozoan-attracting Genlisea, subgenus Tayloria is revealed as basal lineage. In Pinguicula, the six major lineages found reflect radiations in clearly defined geographic regions, whereas most previously recognized subgeneric taxa are non-monophyletic. Genlisea and Utricularia exhibit substitutional rates that rank among the highest in angiosperms for the molecular markers analyzed. One possible explanation for this lies in selective constraints on a wide range of genomic regions that may have been lowered due to the use of an alternative mode of acquiring nutrients.
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evolution of carnivory in lentibulariaceae and the lamiales
Plant Biology, 2004Co-Authors: Kai F Muller, Stefan Porembski, Inge Theisen, Thomas Borsch, Laurent Legendre, Wilhelm BarthlottAbstract:: As a basis for analysing the evolution of the carnivorous syndrome in Lentibulariaceae (Lamiales), phylogenetic reconstructions were conducted based on coding and non-coding chloroplast DNA (matK gene and flanking trnK intron sequences, totalling about 2.4 kb). A dense taxon sampling including all other major lineages of Lamiales was needed since the closest relatives of Lentibulariaceae and the position of “proto-carnivores” were unknown. Tree inference using maximum parsimony, maximum likelihood, and Bayesian approaches resulted in fully congruent topologies within Lentibulariaceae, whereas relationships among the different lineages of Lamiales were only congruent between likelihood and Bayesian optimizations. Lentibulariaceae and their three genera (Pinguicula, Genlisea, and Utricularia) are monophyletic, with Pinguicula being sister to a Genlisea-Utricularia clade. Likelihood and Bayesian trees converge on Bignoniaceae as sister to Lentibulariaceae, albeit lacking good support. The “proto-carnivores” (Byblidaceae, Martyniaceae) are found in different positions among other Lamiales but not as sister to the carnivorous Lentibulariaceae, which is also supported by Khishino-Hasegawa tests. This implies that carnivory and its preliminary stages (“proto-carnivores”) independently evolved more than once among Lamiales. Ancestral states of structural characters connected to the carnivorous syndrome are reconstructed using the molecular tree, and a hypothesis on the evolutionary pathway of the carnivorous syndrome in Lentibulariaceae is presented. Extreme DNA mutational rates found in Utricularia and Genlisea are shown to correspond to their unusual nutritional specialization, thereby hinting at a marked degree of carnivory in these two genera.
Ingo Schubert - One of the best experts on this subject based on the ideXlab platform.
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chromosome identification for the carnivorous plant Genlisea margaretae
Chromosoma, 2017Co-Authors: Trung Dinh Tran, Ingo Schubert, Hana Simkova, Renate Schmidt, Jaroslav Doležel, Jorg FuchsAbstract: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.
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centromere and telomere sequence alterations reflect the rapid genome evolution within the carnivorous plant genus Genlisea
Plant Journal, 2015Co-Authors: Trung D Tran, Hieu X Cao, Gabriele Jovtchev, Pavel Neumann, Petr Novak, Jiři Macas, Miloslava Fojtova, Jiři Fajkus, Ingo SchubertAbstract:Linear chromosomes of eukaryotic organisms invariably possess centromeres and telomeres to ensure proper chromosome segregation during nuclear divisions and to protect the chromosome ends from deterioration and fusion, respectively. While centromeric sequences may differ between species, with arrays of tandemly repeated sequences and retrotransposons being the most abundant sequence types in plant centromeres, telomeric sequences are usually highly conserved among plants and other organisms. The genome size of the carnivorous genus Genlisea (Lentibulariaceae) is highly variable. Here we study evolutionary sequence plasticity of these chromosomal domains at an intrageneric level. We show that Genlisea nigrocaulis (1C = 86 Mbp; 2n = 40) and G. hispidula (1C = 1550 Mbp; 2n = 40) differ as to their DNA composition at centromeres and telomeres. G. nigrocaulis and its close relative G. pygmaea revealed mainly 161 bp tandem repeats, while G. hispidula and its close relative G. subglabra displayed a combination of four retroelements at centromeric positions. G. nigrocaulis and G. pygmaea chromosome ends are characterized by the Arabidopsis-type telomeric repeats (TTTAGGG); G. hispidula and G. subglabra instead revealed two intermingled sequence variants (TTCAGG and TTTCAGG). These differences in centromeric and, surprisingly, also in telomeric DNA sequences, uncovered between groups with on average a > 9-fold genome size difference, emphasize the fast genome evolution within this genus. Such intrageneric evolutionary alteration of telomeric repeats with cytosine in the guanine-rich strand, not yet known for plants, might impact the epigenetic telomere chromatin modification.
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chromatin organization and cytological features of carnivorous Genlisea species with large genome size differences
Frontiers in Plant Science, 2015Co-Authors: Trung Dinh Tran, Hieu X Cao, Gabriele Jovtchev, Ingo Schubert, Petr Novak, Jiři Macas, Joerg FuchsAbstract: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.
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metatranscriptome analysis reveals host microbiome interactions in traps of carnivorous Genlisea species
Frontiers in Microbiology, 2015Co-Authors: Hieu X Cao, Thomas Schmutzer, Ales Pecinka, Uwe Scholz, Ingo SchubertAbstract:In the carnivorous plant genus Genlisea a unique lobster pot trapping mechanism supplements nutrition in nutrient-poor habitats. A wide spectrum of microbes frequently occurs in Genlisea's leaf-derived traps without clear relevance for Genlisea carnivory. We sequenced the metatranscriptomes of subterrestrial traps vs. the aerial chlorophyll-containing leaves of G. nigrocaulis and of G. hispidula. Ribosomal RNA assignment revealed soil-borne microbial diversity in Genlisea traps, with 92 genera of 19 phyla present in more than one sample. Microbes from 16 of these phyla including proteobacteria, green algae, amoebozoa, fungi, ciliates and metazoans, contributed additionally short-lived mRNA to the metatranscriptome. Furthermore, transcripts of 438 members of hydrolases (e.g., proteases, phosphatases, lipases), mainly resembling those of metazoans, ciliates and green algae, were found. Compared to aerial leaves, Genlisea traps displayed a transcriptional up-regulation of endogenous NADH oxidases generating reactive oxygen species as well as of acid phosphatases for prey digestion. A leaf-vs.-trap transcriptome comparison reflects that carnivory provides inorganic P- and different forms of N-compounds (ammonium, nitrate, amino acid, oligopeptides) and implies the need to protect trap cells against oxidative stress. The analysis elucidates a complex food web inside the Genlisea traps, and suggests ecological relationships between this plant genus and its entrapped microbiome.
Vitor F O Miranda - One of the best experts on this subject based on the ideXlab platform.
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Genlisea hawkingii lentibulariaceae a new species from serra da canastra minas gerais brazil
PLOS ONE, 2020Co-Authors: Saura R Silva, Bartosz J Plachno, Samanta Gabriela Medeiros Carvalho, Vitor F O MirandaAbstract:Genlisea hawkingii, which is a new species of Genlisea subgen. Tayloria (Lentibulariaceae) from cerrado in southwest Brazil, is described and illustrated. This species has been found in only one locality thus far, in the Serra da Canastra, which is located in the Delfinopolis municipality in Minas Gerais, Brazil. The new species is morphologically similar to Genlisea violacea and G. flexuosa, but differs from them in having a corolla with a conical and curved spur along with sepals with an acute apex and reproductive organs that only have glandular hairs. Moreover, it is similar to G. uncinata’s curved spur. G. hawkingii is nested within the subgen. Tayloria clade as a sister group to all the other species of this subgenus. Therefore, both morphological and phylogenetic results strongly support G. hawkingii as a new species in the subgen. Tayloria.
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comparative genomic analysis of Genlisea corkscrew plants lentibulariaceae chloroplast genomes reveals an increasing loss of the ndh genes
PLOS ONE, 2018Co-Authors: Saura R Silva, Alessandro M Varani, Todd P Michael, Elliott J Meer, Daniel Guariz Pinheiro, Vitor F O MirandaAbstract: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.
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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, 2016Co-Authors: Saura R Silva, Vitor F O Miranda, Todd P Michael, Daniel G Pinheiro, Yani C A Diaz, Helen A Penha, Camila C Fernandes, Alessandro M VaraniAbstract: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.
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Bacterial community associated with traps of the carnivorous plants Utricularia hydrocarpa and Genlisea filiformis
Aquatic Botany, 2014Co-Authors: Fernanda A. Caravieri, Vitor F O Miranda, Almir José Ferreira, Anderson Ferreira, Débora Clivati, Welington Luiz AraújoAbstract:The species of bacteria associated with the traps of the carnivorous plants Utricularia hydrocarpa Vahl and Genlisea filiformis A. St.-Hil. were identified by analysing 16S rRNA gene libraries. We observed larger bacterial diversity inside the traps of U. hydrocarpa than in G. filiformis. The Clostridium genus (Firmicutes) was the dominant group in G. filiformis, while Aeromonas (γ-Proteobacteria) and Acidobacterium (Acidobacteria) were the dominant genera in U. hydrocarpa. In general, the microbial community observed in these carnivorous plants was composed of Firmicutes (46.8%), Proteobacteria (33.9%), Acidobacteria (9.3%), Actinobacteria (4.4%), Bacteroidetes (0.8%), Chloroflexi (0.4%), Gemmatimonadetes (0.4%), Cyanobacteria (0.4%), Chlamydiae (0.4%) and Tenericutes (0.4%). Only 1.2% of the observed operational taxonomic units (OTU0.03) were shared by U. hydrocarpa and G. filiformis. The present study describes the dominant bacterial species associated with the traps of the carnivorous plant G. filiformis and U. hydrocarpa and briefly discusses the possible role of bacteria in plant prey utilisation.