Botany and Plant Science (Scholarly Articles)

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  • Publication
    Bumblebee colony development following chronic exposure to field-realistic levels of the neonicotinoid pesticide thiamethoxam under laboratory conditions
    (Nature Publishing Group, 2017-08-20) Stanley, Dara A.; Raine, Nigel E.; |~|
    Neonicotinoid pesticides are used in agriculture to reduce damage from crop pests. However, beneficial insects such as bees can come into contact with these pesticides when foraging in treated areas, with potential consequences for bee declines and pollination service delivery. Honeybees are typically used as a model organism to investigate insecticide impacts on bees, but relatively little is known about impacts on other taxa such as bumblebees. In this experiment, we chronically exposed whole mature bumblebee (Bombus terrestris) colonies to field-realistic levels of the neonicotinoid thiamethoxam (2.4ppb & 10ppb) over four weeks, and compared colony growth under laboratory conditions. We found no impact of insecticide exposure on colony weight gain, or the number or mass of sexuals produced, although colonies exposed to 2.4ppb produced larger males. As previous studies have reported pesticide effects on bumblebee colony growth, this may suggest that impacts on bumblebee colonies are more pronounced for colonies at an earlier stage in the reproductive cycle. Alternatively, it may also indicate that thiamethoxam differs in toxicity compared to previously tested neonicotinoids in terms of reproductive effects. In either case, assessing bumblebee colony development under field conditions is likely more informative for real world scenarios than tests conducted in laboratory conditions.
  • Publication
    Evolution and diversity of plant cell walls: from algae to flowering plants
    (Annual Reviews, 2011-02-22) Popper, Zoë A.; Gurvan, Michel; Hervé, Cécile; Domozych, David S.; Willats, William G.T.; Tuohy, Maria G.; Kloareg, Bernard; Stengel, Dagmar B.; |~|
    All photosynthetic multicellular Eukaryotes, including land plants and algae, have cells that are surrounded by a dynamic, complex, carbohydrate-rich cell wall. The cell wall exerts considerable biological and biomechanical control over individual cells and organisms, thus playing a key role in their environmental interactions. This has resulted in compositional variation that is dependent on developmental stage, cell type, and season. Further variation is evident that has a phylogenetic basis. Plants and algae have a complex phylogenetic history, including acquisition of genes responsible for carbohydrate synthesis and modification through a series of primary (leading to red algae, green algae, and land plants) and secondary (generating brown algae, diatoms, and dinoflagellates) endosymbiotic events. Therefore, organisms that have the shared features of photosynthesis and possession of a cell wall do not form a monophyletic group. Yet they contain some common wall components that can be explained increasingly by genetic and biochemical evidence.
  • Publication
    Ecological variation in response to mass-flowering oilseed rape and surrounding landscape composition by members of a cryptic bumblebee complex
    (Public Library of Science, 2013-06-19) Stanley, Dara A.; Knight, Mairi E.; Stout, Jane C.; |~|
    The Bombus sensu stricto species complex is a widespread group of cryptic bumblebee species which are important pollinators of many crops and wild plants. These cryptic species have, until now, largely been grouped together in ecological studies, and so little is known about their individual colony densities, foraging ranges or habitat requirements, which can be influenced by land use at a landscape scale. We used mass-flowering oilseed rape fields as locations to sample bees of this complex, as well as the second most common visitor to oilseed rape B. lapidarius, and molecular RFLP methods to distinguish between the cryptic species. We then used microsatellite genotyping to identify sisters and estimate colony densities, and related both proportions of cryptic species and their colony densities to the composition of the landscape surrounding the fields. We found B. lucorum was the most common member of the complex present in oilseed rape followed by B. terrestris. B. cryptarum was also present in all but one site, with higher proportions found in the east of the study area. High numbers of bumblebee colonies were estimated to be using oilseed rape fields as a forage resource, with B. terrestris colony numbers higher than previous estimates from non-mass-flowering fields. We also found that the cryptic species responded differently to surrounding landscape composition: both relative proportions of B. cryptarum in samples and colony densities of B. lucorum were negatively associated with the amount of arable land in the landscape, while proportions and colony densities of other species did not respond to landscape variables at the scale measured. This suggests that the cryptic species have different ecological requirements (which may be scale-dependent) and that oilseed rape can be an important forage resource for many colonies of bumblebees. Given this, we recommend sustainable management of this crop to benefit bumblebees.
  • Publication
    Response of farmland biodiversity to the introduction of bioenergy crops: effects of local factors and surrounding landscape context
    (Wiley Open Access, 2013-07-19) Bourke, David; Stanley, Dara; O'Rourke, Erin; Thompson, Rosalyn; Carnus, Tim; Dauber, Jens; Emmerson, Mark; Whelan, Pádraig; Hecq, Florence; Flynn, Evelyn; Dolan, Lisa; Stout, Jane; |~|
    The recent growth in bioenergy crop cultivation, stimulated by the need to implement measures to reduce net CO2 emissions, is driving major land-use changes with consequences for biodiversity and ecosystem service provision. Although the type of bioenergy crop and its associated management is likely to affect biodiversity at the local (field) scale, landscape context and its interaction with crop type may also influence biodiversity on farms. In this study, we assessed the impact of replacing conventional agricultural crops with two model bioenergy crops (either oilseed rape Brassica napus or Miscanthus à  giganteus) on vascular plant, bumblebee, solitary bee, hoverfly and carabid beetle richness, diversity and abundance in 50 sites in Ireland. We assessed whether within-field biodiversity was also related to surrounding landscape structure. We found that local- and landscape-scale variables correlated with biodiversity in these agricultural landscapes. Overall, the differences between the bioenergy crops and the conventional crops on farmland biodiversity were mostly positive (e.g. higher vascular plant richness in Miscanthus planted on former conventional tillage, higher solitary bee abundance and richness in Miscanthus and oilseed rape compared with conventional crops) or neutral (e.g. no differences between crop types for hoverflies and bumblebees). We showed that these crop type effects were independent of (i.e. no interactions with) the surrounding landscape composition and configuration. However, surrounding landscape context did relate to biodiversity in these farms, negatively for carabid beetles and positively for hoverflies. Although we conclude that the bioenergy crops compared favourably with conventional crops in terms of biodiversity of the taxa studied at the field scale, the effects of large-scale planting in these landscapes could result in very different impacts. Maintaining ecosystem functioning and the delivery of ecosystem services will require a greater understanding of impacts at the landscape scale to ensure the sustainable development of climate change mitigation measures.
  • Publication
    Bumblebee learning and memory is impaired by chronic exposure to a neonicotinoid pesticide.
    (Nature Publishing Group, 2015-11-16) Stanley, Dara A.; Smith, Karen E.; Raine, Nigel E.; |~|
    Bumblebees are exposed to pesticides applied for crop protection while foraging on treated plants, with increasing evidence suggesting that this sublethal exposure has implications for pollinator declines. The challenges of navigating and learning to manipulate many different flowers underline the critical role learning plays for the foraging success and survival of bees. We assessed the impacts of both acute and chronic exposure to field-realistic levels of a widely applied neonicotinoid insecticide, thiamethoxam, on bumblebee odour learning and memory. Although bees exposed to acute doses showed conditioned responses less frequently than controls, we found no difference in the number of individuals able to learn at field-realistic exposure levels. However, following chronic pesticide exposure, bees exposed to field-realistic levels learnt more slowly and their short-term memory was significantly impaired following exposure to 2.4¿ppb pesticide. These results indicate that field-realistic pesticide exposure can have appreciable impacts on learning and memory, with potential implications for essential individual behaviour and colony fitness.
  • Publication
    Pollination ecology of Desmodium setigerum (Fabaceae) in Uganda; do big bees do it better?
    (2016-09) Stanley, Dara; Otieno, Mark; Syeijven, Karin; Berlin, Emma Sandler; Piironen, Tiina; Willmer, Pat; Nuttman, Clive; |~|1267880|~|
    Explosive pollen release is documented in many plant families, including the Fabaceae. Desmodium setigerum E. Mey (Fabaceae) is a perennial herb with single trip explosive pollen release found in eastern Africa, and the unique ability to reverse floral colour change if insufficient pollination has occurred. However, little else is known about the pollination ecology of this species, what visitors can trigger explosive pollen release, and whether bee body size is related to pollination efficiency. We investigated: 1) the breeding system of D. setigerum, and whether it is pollen limited; 2) whether flowers are visited early in the day allowing sufficient time for a second opportunity for pollination; and 3) what insect species visit D. setigerum and the relative efficacy of different flower visitors in relation to visitor size and pollination success. We found that although self-compatible, D. setigerum requires insect visitation to set seed as explosive pollen release is needed even for selfing. Most flowers are initially visited before 1400h, and by 1800h nearly all flowers have been tripped. Flowers were not pollen limited in this study, and were visited primarily by bees. We observed 16 visiting species, and there was a wide variation (0-404 grains) in the amount of pollen deposited on stigmas. Although almost all bees deposited some pollen, the mean number of pollen grains deposited in a single visit per species was negatively related to body size. However, one particular megachilid species deposited significantly more pollen grains than any other visitor and so is likely an important pollinator of this species. This provides insights into the pollination biology of this unique plant species, and adds to increasing literature on the relationships between bee body size, explosive pollen release and pollination effectiveness.
  • Publication
    The cell walls of pteridophytes and other green plants - a review
    (British Pteridological Society, 2006-12-22) Popper, Zoë A.; |~|
    The cell wall is one of the defining characteristics of plants and is a fundamental component in normal growth and development. Cell wall composition is a potentially valuable source of phylogenetic information as notable similarities and differences exist between and within major embryophyte groups. In particular, there is a pronounced chemical demarcation between the eusporangiate pteridophytes (high mannan, low tannin) and the leptosporangiate pteridophytes (low mannan, high tannin). The results of recent biochemical and immunocytochemical investigations have shown that changes in cell wall composition accompanied the bryophyte–lycopodiophyte and eusporangiate–leptosporangiate transitions.
  • Publication
    Beyond the green: understanding the evolutionary puzzle of plant and algal cell walls
    (American Society of Plant Biologists, 2010-04-26) Popper, Zoë A.; Tuohy, Maria G.; |~|
    Niklas (2000) defined plants as “photosynthetic eukaryotes,” thereby including brown, red, and green macroalgae and microalgae. These groups share several features, including the presence of a complex, dynamic, and polysaccharide-rich cell wall. Cell walls in eukaryotes are thought to have evolved by lateral transfer from cell wall-producing organisms (Niklas, 2004). Green and red algae originate from a primary endosymbiotic event with a cyanobacterium, which is thought to have occurred over 1,500 million years ago (Palmer et al., 2004). Even though extant cyanobacteria have cell walls that are based on a peptidoglycan-polysaccharide-lipopolysaccharide matrix and thus differ markedly from the polysaccharide-rich cell walls of plants, there is preliminary evidence that they may contain some similar polysaccharides (Hoiczyk and Hansel, 2000), and genes already involved in polysaccharide synthesis or those subsequently coopted into wall biosynthesis may have been transferred during endosymbiosis. Independent secondary endosymbiotic events subsequently gave rise to the Euglenozoa (which lack cell walls) and brown algae (which have cell walls; Palmer et al., 2004). Investigations of the diversity of wall composition, structure, and biosynthesis that include algae, therefore, may lend new insights into wall evolution (Niklas, 2004).
  • Publication
    Cell wall evolution and diversity
    (Frontiers Media, 2012-07-06) Fangel, Jonatan U.; Ulvskov, Peter; Knox, J. P.; Mikkelsen, Maria Dalgaard; Harholt, Jesper; Popper, Zoë A.; Willats, William G. T.; |~|
    Plant cell walls display a considerable degree of diversity in their compositions and molecular architectures. In some cases the functional significance of a particular cell wall type appears to be easy to discern: secondary cells walls are often reinforced with lignin that provides durability; the thin cell walls of pollen tubes have particular compositions that enable their tip growth; lupin seed cell walls are characteristically thickened with galactan used as a storage polysaccharide. However, more frequently the evolutionary mechanisms and selection pressures that underpin cell wall diversity and evolution are unclear. For diverse green plants (chlorophytes and streptophytes) the rapidly increasing availability of transcriptome and genome data sets, the development of methods for cell wall analyses which require less material for analysis, and expansion of molecular probe sets, are providing new insights into the diversity and occurrence of cell wall polysaccharides and associated biosynthetic genes. Such research is important for refining our understanding of some of the fundamental processes that enabled plants to colonize land and to subsequently radiate so comprehensively. The study of cell wall structural diversity is also an important aspect of the industrial utilization of global polysaccharide bio-resources.
  • Publication
    Ceratopteris richardii (C-Fern): a model for investigating adaptive modification of vascular plant cell walls
    (Frontiers Media, 2013-09-23) Leroux, Olivier; Eeckhout, Sharon; Viane, Ronald L. L.; Popper, Zoë A.; |~|
    Plant cell walls are essential for most aspects of plant growth, development, and survival, including cell division, expansive cell growth, cell-cell communication, biomechanical properties, and stress responses. Therefore, characterizing cell wall diversity contributes to our overall understanding of plant evolution and development. Recent biochemical analyses, concomitantly with whole genome sequencing of plants located at pivotal points in plant phylogeny, have helped distinguish between homologous characters and those which might be more derived. Most plant lineages now have at least one fully sequenced representative and although genome sequences for fern species are in progress they are not yet available for this group. Ferns offer key advantages for the study of developmental processes leading to vascularisation and complex organs as well as the specific differences between diploid sporophyte tissues and haploid gametophyte tissues and the interplay between them. Ceratopteris richardii has been well investigated building a body of knowledge which combined with the genomic and biochemical information available for other plants will progress our understanding of wall diversity and its impact on evolution and development.
  • Publication
    Pectin metabolism and assembly in the cell wall of the charophyte green alga penium margaritaceum
    (American Society of Plant Biologists, 2014-03-20) Domozych, David S.; Sørensen, Iben; Popper, Zoë A.; Ochs, Julie; Andreas, Amanda; Fangel, Jonatan U.; Pielach, Anna; Sacks, Carly; Brechka, Hannah; Ruisi-Besares, Pia; Willats, William G.T.; Rose, Jocelyn K.C.; |~|
    The pectin polymer homogalacturonan (HG) is a major component of land plant cell walls and is especially abundant in the middle lamella. Current models suggest that HG is deposited into the wall as a highly methylesterified polymer, demethylesterified by pectin methylesterase enzymes and cross-linked by calcium ions to form a gel. However, this idea is based largely on indirect evidence and in vitro studies. We took advantage of the wall architecture of the unicellular alga Penium margaritaceum, which forms an elaborate calcium cross-linked HG-rich lattice on its cell surface, to test this model and other aspects of pectin dynamics. Studies of live cells and microscopic imaging of wall domains confirmed that the degree of methylesterification and sufficient levels of calcium are critical for lattice formation in vivo. Pectinase treatments of live cells and immunological studies suggested the presence of another class of pectin polymer, rhamnogalacturonan I, and indicated its colocalization and structural association with HG. Carbohydrate microarray analysis of the walls of P. margaritaceum, Physcomitrella patens, and Arabidopsis (Arabidopsis thaliana) further suggested the conservation of pectin organization and interpolymer associations in the walls of green plants. The individual constituent HG polymers also have a similar size and branched structure to those of embryophytes. The HG-rich lattice of P. margaritaceum, a member of the charophyte green algae, the immediate ancestors of land plants, was shown to be important for cell adhesion. Therefore, the calcium-HG gel at the cell surface may represent an early evolutionary innovation that paved the way for an adhesive middle lamella in multicellular land plants.
  • Publication
    Bioinformatic identification and analysis of extensins in the plant kingdom
    (Public Library of Science, 2016-02-26) Liu, Xiao; Wolfe, Richard; Welch, Lonnie R.; Domozych, David S.; Popper, Zoë A.; Showalter, Allan M.; |~|
    Extensins (EXTs) are a family of plant cell wall hydroxyproline-rich glycoproteins (HRGPs) that are implicated to play important roles in plant growth, development, and defense. Structurally, EXTs are characterized by the repeated occurrence of serine (Ser) followed by three to five prolines (Pro) residues, which are hydroxylated as hydroxyproline (Hyp) and glycosylated. Some EXTs have Tyrosine (Tyr)-X-Tyr (where X can be any amino acid) motifs that are responsible for intramolecular or intermolecular cross-linkings. EXTs can be divided into several classes: classical EXTs, short EXTs, leucine-rich repeat extensins (LRXs), proline-rich extensin-like receptor kinases (PERKs), formin-homolog EXTs (FH EXTs), chimeric EXTs, and long chimeric EXTs. To guide future research on the EXTs and understand evolutionary history of EXTs in the plant kingdom, a bioinformatics study was conducted to identify and classify EXTs from 16 fully sequenced plant genomes, including Ostreococcus lucimarinus, Chlamydomonas reinhardtii, Volvox carteri, Klebsormidium flaccidum, Physcomitrella patens, Selaginella moellendorffii, Pinus taeda, Picea abies, Brachypodium distachyon, Zea mays, Oryza sativa, Glycine max, Medicago truncatula, Brassica rapa, Solanum lycopersicum, and Solanum tuberosum, to supplement data previously obtained from Arabidopsis thaliana and Populus trichocarpa. A total of 758 EXTs were newly identified, including 87 classical EXTs, 97 short EXTs, 61 LRXs, 75 PERKs, 54 FH EXTs, 38 long chimeric EXTs, and 346 other chimeric EXTs. Several notable findings were made: (1) classical EXTs were likely derived after the terrestrialization of plants; (2) LRXs, PERKs, and FHs were derived earlier than classical EXTs; (3) monocots have few classical EXTs; (4) Eudicots have the greatest number of classical EXTs and Tyr-X-Tyr cross-linking motifs are predominantly in classical EXTs; (5) green algae have no classical EXTs but have a number of long chimeric EXTs that are absent in embryophytes. Furthermore, phylogenetic analysis was conducted of LRXs, PERKs and FH EXTs, which shed light on the evolution of three EXT classes.
  • Publication
    Charophytes: evolutionary giants and emerging model organisms
    (Frontiers Media, 2016-10-10) Domozych, David S.; Popper, Zoë A.; Sørensen, Iben; |~|
    Charophytes are the group of green algae whose ancestral lineage gave rise to land plants in what resulted in a profoundly transformative event in the natural history of the planet. Extant charophytes exhibit many features that are similar to those found in land plants and their relatively simple phenotypes make them efficacious organisms for the study of many fundamental biological phenomena. Several taxa including Micrasterias, Penium, Chara, and Coleochaete are valuable model organisms for the study of cell biology, development, physiology and ecology of plants. New and rapidly expanding molecular studies are increasing the use of charophytes that in turn, will dramatically enhance our understanding of the evolution of plants and the adaptations that allowed for survival on land. The Frontiers in Plant Science series on "Charophytes" provides an assortment of new research reports and reviews on charophytes and their emerging significance as model plants.
  • Publication
    Variability of candidate genes, genetic structure and association with sugar accumulation and climacteric behavior in a broad germplasm collection of melon (Cucumis melo L.)
    (BioMed Central, 2015-03-19) Leida, Carmen; Moser, Claudio; Esteras, Cristina; Sulpice, Ronan; Lunn, John E.; de Langen, Frank; Monforte, Antonio J.; Picó, Belen; |~|
    Background: A collection of 175 melon (Cucumis melo L.) accessions (including wild relatives, feral types, landraces, breeding lines and commercial cultivars) from 50 countries was selected to study the phenotypic variability for ripening behavior and sugar accumulation. The variability of single nucleotide polymorphisms (SNPs) at 53 selected candidate genes involved in sugar accumulation and fruit ripening processes was studied, as well as their association with phenotypic variation of related traits.Results: The collection showed a strong genetic structure, defining seven groups plus a number of accessions that could not be associated to any of the groups (admixture), which fitted well with the botanical classification of melon varieties. The variability in candidate genes for ethylene, cell wall and sugar-related traits was high and similar to SNPs located in reference genes. Variability at ripening candidate genes had an important weight on the genetic stratification of melon germplasm, indicating that traditional farmers might have selected for ripening traits during cultivar diversification. A strong relationship was also found between the genetic structure and phenotypic diversity, which could hamper genetic association studies. Accessions belonging to the ameri group are the most appropriate for association analysis given the high phenotypic and molecular diversity within the group, and lack of genetic structure. The most remarkable association was found between sugar content and SNPs in LG III, where a hotspot of sugar content QTLs has previously been defined. By studying the differences in allelic variation of SNPs within horticultural groups with specific phenotypic features, we also detected differential variation in sugar-related candidates located in LGIX and LGX, and in ripening-related candidates located in LGII and X, all in regions with previously mapped QTLs for the corresponding traits.Conclusions: In the current study we have found an important variability at both the phenotypic and candidate gene levels for ripening behavior and sugar accumulation in melon fruit. By combination of differences in allelic diversity and association analysis, we have identified several candidate genes that may be involved in the melon phenotypic diversity.
  • Publication
    Projected Range Contractions of European Protected Oceanic Montane Plant Communities: Focus on Climate Change Impacts Is Essential for Their Future Conservation
    (PlosOne, 2014-04-21) Hodd, Rory L.; Bourke, David; Sheehy-Skeffington, Micheline; |~|IRCSET|~|Other|~|Other Government|~|
    Global climate is rapidly changing and while many studies have investigated the potential impacts of this on the distribution of montane plant species and communities, few have focused on those with oceanic montane affinities. In Europe, highly sensitive bryophyte species reach their optimum occurrence, highest diversity and abundance in the north-west hyperoceanic regions, while a number of montane vascular plant species occur here at the edge of their range. This study evaluates the potential impact of climate change on the distribution of these species and assesses the implications for EU Habitats Directive-protected oceanic montane plant communities. We applied an ensemble of species distribution modelling techniques, using atlas data of 30 vascular plant and bryophyte species, to calculate range changes under projected future climate change. The future effectiveness of the protected area network to conserve these species was evaluated using gap analysis. We found that the majority of these montane species are projected to lose suitable climate space, primarily at lower altitudes, or that areas of suitable climate will principally shift northwards. In particular, rare oceanic montane bryophytes have poor dispersal capacity and are likely to be especially vulnerable to contractions in their current climate space. Significantly different projected range change responses were found between 1) oceanic montane bryophytes and vascular plants; 2) species belonging to different montane plant communities; 3) species categorised according to different biomes and eastern limit classifications. The inclusion of topographical variables in addition to climate, significantly improved the statistical and spatial performance of models. The current protected area network is projected to become less effective, especially for specialised arctic-montane species, posing a challenge to conserving oceanic montane plant communities. Conservation management plans need significantly greater focus on potential climate change impacts, including models with higher-resolution species distribution and environmental data, to aid these communities' long-term survival.
  • Publication
    Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds
    (2011) McKeown, Peter C.; Laouielle-Duprat, Sylvia; Donoghue, Mark T.A.; Fort, Antoine; Duszynska, Dorota; Aurélie, Comte; Lao, Nga T.; Spillane, Charles; |~|SFI|~|
    Background: Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants.Results: cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to ATCDC48 and PDE120, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are MET1-dependent, while their uniparental maternal expression in the seed is not dependent on MET1.Conclusions: Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, ATCDC48, PDE120 and MS5-like which represent novel maternally expressed imprinted genes in the Arabidopsis thaliana seed. The extent of overlap between our cDNA-AFLP screen for maternally expressed imprinted genes, and other screens for imprinted and endosperm-expressed genes is discussed.
  • Publication
    High-resolution analysis of parent-of-origin allelic expression in the Arabidopsis endosperm.
    (2011) Donoghue, Mark T. A.; Spillane, Charles; |~|
    Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal crosses of Arabidopsis Col-0 and Bur-0 accessions. Using polymorphic sites to quantify allele-specific expression levels, we could identify more than 60 genes with potential parent-of-origin specific expression. By analyzing the distribution of DNA methylation and epigenetic marks established by Polycomb group (PcG) proteins using publicly available datasets, we suggest that for maternally expressed genes (MEGs) repression of the paternally inherited alleles largely depends on DNA methylation or PcG-mediated repression, whereas repression of the maternal alleles of paternally expressed genes (PEGs) predominantly depends on PcG proteins. While maternal alleles of MEGs are also targeted by PcG proteins, such targeting does not cause complete repression. Candidate MEGs and PEGs are enriched for cis-proximal transposons, suggesting that transposons might be a driving force for the evolution of imprinted genes in Arabidopsis. In addition, we find that MEGs and PEGs are significantly faster evolving when compared to other genes in the genome. In contrast to the predominant location of mammalian imprinted genes in clusters, cluster formation was only detected for few MEGs and PEGs, suggesting that clustering is not a major requirement for imprinted gene regulation in Arabidopsis.