ORCID Profile
0000-0002-7564-0868
Current Organisation
University of Queensland
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Plant Cell and Molecular Biology | Plant Biology | Plant Developmental and Reproductive Biology | Plant Physiology |
Horticultural Crops not elsewhere classified | Expanding Knowledge in the Biological Sciences | Grain Legumes
Publisher: Springer Science and Business Media LLC
Date: 19-04-2015
Publisher: Proceedings of the National Academy of Sciences
Date: 25-03-2008
Abstract: Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis . There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of MSX, an inhibitor of glutamine synthetase, resulting in a block of Glu/Gln synthesis. Genes that responded to organic N were identified as those whose response to ammonium nitrate treatment was blocked in the presence of MSX. We showed that some genes previously identified to be regulated by nitrate are under the control of an organic N-metabolite. Using an integrated network model of molecular interactions, we uncovered a subnetwork regulated by organic N that included CCA1 and target genes involved in N-assimilation. We validated some of the predicted interactions and showed that regulation of the master clock control gene CCA1 by Glu or a Glu-derived metabolite in turn regulates the expression of key N-assimilatory genes. Phase response curve analysis shows that distinct N-metabolites can advance or delay the CCA1 phase. Regulation of CCA1 by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function.
Publisher: Wiley
Date: 14-12-2021
DOI: 10.1111/JEB.13746
Abstract: Non‐native species experience novel selection pressures in introduced environments and may interbreed with native lineages. Species introductions therefore provide opportunities to investigate repeated patterns of adaptation and introgression across replicated contact zones. Here, we investigate genetic parallelism between multiple introduced populations of the invasive marine mussel, Mytilus galloprovincialis , in the absence (South Africa and California) and presence of hybridization with a native congener ( Mytilus planulatus in Batemans Bay and Sydney Harbour, Australia). Repeatability in post‐introduction differentiation from native‐range populations varied between genetically distinct Atlantic and Mediterranean lineages, with Atlantic‐derived introductions displaying high differentiation (max F ST 0.4) and parallelism at outlier loci. Identification of long noncoding RNA transcripts (lncRNA) additionally allowed us to clarify that parallel responses are largely limited to protein‐coding loci, with lncRNAs likely evolving under evolutionary constraints. Comparisons of independent hybrid zones revealed differential introgression most strongly in Batemans Bay, with an excess of M. galloprovincialis ancestry and resistance to introgression at loci differentiating parental lineages ( M. planulatus and Atlantic M. galloprovincialis ). Additionally, contigs putatively introgressed with ergent alleles from a closely related species, Mytilus edulis, showed stronger introgression asymmetries compared with genome‐wide trends and also erged in parallel in both Atlantic‐derived introductions. These results suggest that ergent demographic histories experienced by introduced lineages, including pre‐introduction introgression, influence contemporary admixture dynamics. Our findings build on previous investigations reporting contributions of historical introgression to intrinsic reproductive architectures shared between marine lineages and illustrate that interspecific introgression history can shape differentiation between colonizing populations and their hybridization with native congeners.
Publisher: Springer Science and Business Media LLC
Date: 21-04-2017
DOI: 10.1038/SREP46567
Abstract: Virulence of Cryptococcus neoformans is regulated by a range of transcription factors, and is also influenced by the acquisition of adaptive mutations during infection. Beyond the temporal regulation of virulence factor production by transcription factors and these permanent microevolutionary changes, heritable epigenetic modifications such as histone deacetylation may also play a role during infection. Here we describe the first comprehensive analysis of the sirtuin class of NAD+ dependent histone deacetylases in the phylum Basidiomycota, identifying five sirtuins encoded in the C. neoformans genome. Each sirtuin gene was deleted and a wide range of phenotypic tests performed to gain insight into the potential roles they play. Given the pleiotropic nature of sirtuins in other species, it was surprising that only two of the five deletion strains revealed mutant phenotypes in vitro . However, cryptic consequences of the loss of each sirtuin were identified through whole cell proteomics, and mouse infections revealed a role in virulence for SIR2, HST3 and HST4 . The most intriguing phenotype was the repeated inability to complement mutant phenotypes through the reintroduction of the wild-type gene. These data support the model that regulation of sirtuin activity may be employed to enable a drastic alteration of the epigenetic landscape and virulence of C. neoformans .
Publisher: Cold Spring Harbor Laboratory
Date: 20-03-2020
DOI: 10.1101/2020.03.19.999581
Abstract: The plant hormone strigolactone (SL) inhibits shoot branching by suppressing the growth of axillary buds. This is thought to occur largely via regulation of the transcription factor BRANCHED1 (BRC1). Here, we clarify the central role of BRC1 and identify additional transcriptional responses by which SL might regulate axillary bud outgrowth in garden pea ( Pisum sativum ). We used a transcriptomic approach to identify differentially expressed transcripts in pea axillary buds in response to a synthetic SL, rac -GR24. Changes in transcript abundance were confirmed by measuring their response to GR24 5DS . BRC1 was required for the regulation of over half of the fourteen GR24 5DS -regulated genes, confirming its role as a mediator of SL transcriptional responses in axillary buds. All, but one, of the BRC1-dependent GR24 5DS -regulated genes were also regulated by branch-promoting treatments cytokinin (CK) and/or decapitation in an opposing manner to SL. This suggests that SL, CK, and decapitation regulate shoot branching via a common pathway. We used correlational analyses of gene co-expression data to infer a gene regulatory network consisting of nine key co-expression modules correlated with rac -GR24 treatment. Enrichment of GO terms such as cell proliferation, carbohydrate responses, and abscisic acid and jasmonic acid hormone pathways suggest a role for these in SL-mediated inhibition of shoot branching. In summary, we have shown that BRC1 is indeed a key transcriptional regulator of the SL signalling pathway in pea buds as well as a focal point of the SL, CK and decapitation signalling pathways to coordinate shoot branching in pea buds. Identification of genes that are strigolactone-responsive and BRC1-dependent in pea buds reveals a high degree of overlap among strigolactone, cytokinin and decapitation response pathways.
Publisher: Springer Science and Business Media LLC
Date: 14-06-2005
Abstract: The lycophytes are an ancient lineage of vascular plants that erged from the seed plant lineage about 400 Myr ago. Although the lycophytes occupy an important phylogenetic position for understanding the evolution of plants and their genomes, no genomic resources exist for this group of plants. Here we describe the construction of a large-insert bacterial artificial chromosome (BAC) library from the lycophyte Selaginella moellendorffii . Based on cell flow cytometry, this species has the smallest genome size among the different lycophytes tested, including Huperzia lucidula , Diphaiastrum digita , Isoetes engelmanii and S. kraussiana . The arrayed BAC library consists of 9126 clones the average insert size is estimated to be 122 kb. Inserts of chloroplast origin account for 2.3% of the clones. The BAC library contains an estimated ten genome-equivalents based on DNA hybridizations using five single-copy and two duplicated S. moellendorffii genes as probes. The S. moellenforffii BAC library, the first to be constructed from a lycophyte, will be useful to the scientific community as a resource for comparative plant genomics and evolution.
Publisher: Elsevier BV
Date: 12-2005
DOI: 10.1016/J.DEVCEL.2005.11.011
Abstract: In a recent issue of Current Biology, Kapoor et al. (2005) and Elmayan et al. (2005) illuminate the linkage between DNA replication and repair and transcriptional gene silencing in plants by showing that mutants in RPA2, a homolog of yeast and mammalian replication protein A, exhibit loss of silencing at transgene loci as well as some transposable elements. This is accompanied by a shift in histone H3 methylation modifications at these loci from a heterochromatic to a euchromatic pattern. Intriguingly, cytosine methylation is unaffected at the reactivated loci, indicating that transmission of DNA methylation and histone modification status can be uncoupled.
Publisher: Springer Science and Business Media LLC
Date: 20-12-2017
DOI: 10.1038/S41598-017-18106-2
Abstract: Reference strains are a key component of laboratory research, providing a common background allowing for comparisons across a community of researchers. However, laboratory passage of these strains has been shown to lead to reduced fitness and the attenuation of virulence in some species. In this study we show the opposite in the fungal pathogen Cryptococcus neoformans , with analysis of a collection of type strain H99 subcultures revealing that the most commonly used laboratory subcultures belong to a mutant lineage of the type strain that is hypervirulent. The pleiotropic mutant phenotypes in this H99L (for “Laboratory”) lineage are the result of a deletion in the gene encoding the SAGA Associated Factor Sgf29, a mutation that is also present in the widely-used H99L-derived KN99 a /α congenic pair. At a molecular level, loss of this gene results in a reduction in histone H3K9 acetylation. Remarkably, analysis of clinical isolates identified loss of function SGF29 mutations in C. neoformans strains infecting two of fourteen patients, demonstrating not only the first ex le of hypervirulence in clinical C. neoformans s les, but also parallels between in vitro and in vivo microevolution for hypervirulence in this important pathogen.
Publisher: Cold Spring Harbor Laboratory
Date: 2008
Abstract: Plants and fission yeast exhibit a wealth of epigenetic phenomena, including transposon regulation, heterochromatic silencing, and gene imprinting. They provide excellent model organisms to address the question of how epigenetic information is propagated to daughter cells. We have addressed the questions of establishment, maintenance, and inheritance of heterochromatic silencing using the fission yeast Schizosaccharomyces pombe and the plant Arabidopsis thaliana by using a variety of genetic and genomic approaches. We present here results showing the cell cycle dependence of RNA in fission yeast RNA interference (RNAi), which is required for proper transcriptional silencing of the centromeric heterochromatin, and that this process occurs during S phase, allowing for precise copying and reestablishment of heterochromatic histone modifications following DNA replication and cell ision. We also show that in plants, cells in culture and male germ-line cells undergo massive epigenomic changes correlated with the appearance of a novel class of 21-nucleotide small interfering RNA (siRNA) from transcriptionally reactivated transposable elements (TEs) following loss of heterochromatic DNA and histone methylation. We propose a model for the role of deliberate TE reactivation in germ-line companion cells as part of a developmental mechanism for first revealing and then silencing TEs via small RNA, which may contribute to reprogramming during early development in plants and animals.
Publisher: Public Library of Science (PLoS)
Date: 09-12-2008
Publisher: Cold Spring Harbor Laboratory
Date: 15-02-2019
DOI: 10.1101/551069
Abstract: Nitrate (N) and phosphate (P) levels are sensed by plant cells and signaled via local and systemic signaling pathways to modulate plant growth and development. Understanding the genetic basis of these signaling mechanisms is key to future improvement of nutrient use efficiency. While major progress has been made in understanding N and P signaling pathways and their interaction in the model plant Arabidopsis, understanding of transcriptional responses to N and P in a major monocot crop wheat is lacking. Therefore, we investigated gene expression dynamics of wheat roots in response to N and/or P provision using RNA-Seq. We found that nitrate presence is the major trigger for most of the transcriptional response to occur within 24 h, however, we also identified a large array of synergistic transcriptional responses to concomitant supply of N and P. Through gene co-expression analysis, we identified gene co-expression modules prominent in nitrate signaling and metabolism in wheat. Importantly, we identified likely instances of functional ergence in major N-responsive transcription factors families HRS1/HHO and TGA of wheat from their rice/Arabidopsis homologues. Our work broadens the understanding of wheat N and P transcriptional responses and aids in prioritizing gene candidates for production of wheat varieties that are efficient in nitrogen usage.
Publisher: Springer New York
Date: 2019
DOI: 10.1007/978-1-4939-9045-0_16
Abstract: The ability to identify and quantify transcribed sequences from a multitude of organisms using high-throughput RNA sequencing has revolutionized our understanding of genetics and plant biology. However, a number of computational tools used in these analyses still require a reference genome sequence, something that is seldom available for non-model organisms. Computational tools employing de Bruijn graphs to reconstruct full-length transcripts from short sequence reads allow for de novo transcriptome assembly. Here we provide detailed methods for generating and annotating de novo transcriptome assembly from plant RNA-seq data.
Publisher: Springer Science and Business Media LLC
Date: 02-07-2012
Abstract: MicroRNA-regulation of gene expression plays a key role in the development and response to biotic and abiotic stresses. Deep sequencing analyses accelerate the process of small RNA discovery in many plants and expand our understanding of miRNA-regulated processes. We therefore undertook small RNA sequencing of sugarcane miRNAs in order to understand their complexity and to explore their role in sugarcane biology. A bioinformatics search was carried out to discover novel miRNAs that can be regulated in sugarcane plants submitted to drought and salt stresses, and under pathogen infection. By means of the presence of miRNA precursors in the related sorghum genome, we identified 623 candidates of new mature miRNAs in sugarcane. Of these, 44 were classified as high confidence miRNAs. The biological function of the new miRNAs candidates was assessed by analyzing their putative targets. The set of bona fide sugarcane miRNA includes those likely targeting serine/threonine kinases, Myb and zinc finger proteins. Additionally, a MADS-box transcription factor and an RPP2B protein, which act in development and disease resistant processes, could be regulated by cleavage (21-nt-species) and DNA methylation (24-nt-species), respectively. A large scale investigation of sRNA in sugarcane using a computational approach has identified a substantial number of new miRNAs and provides detailed genotype-tissue-culture miRNA expression profiles. Comparative analysis between monocots was valuable to clarify aspects about conservation of miRNA and their targets in a plant whose genome has not yet been sequenced. Our findings contribute to knowledge of miRNA roles in regulatory pathways in the complex, polyploidy sugarcane genome.
Publisher: Springer Science and Business Media LLC
Date: 05-06-2019
Publisher: Springer Science and Business Media LLC
Date: 2004
Publisher: MDPI AG
Date: 07-03-2018
DOI: 10.3390/NCRNA4010006
Publisher: Elsevier BV
Date: 02-2009
Publisher: Oxford University Press (OUP)
Date: 14-03-2019
DOI: 10.1105/TPC.18.00656
Publisher: Public Library of Science (PLoS)
Date: 02-04-2014
Publisher: Springer Berlin Heidelberg
Date: 2012
Publisher: Oxford University Press (OUP)
Date: 22-10-2019
DOI: 10.1104/PP.19.00682
Publisher: Apple Academic Press
Date: 15-12-2011
DOI: 10.1201/B12226-6
Publisher: Public Library of Science (PLoS)
Date: 19-06-2007
Publisher: Oxford University Press (OUP)
Date: 07-2018
Abstract: The fern Ceratopteris richardii is an important model for studies of sex determination and gamete differentiation in homosporous plants. Here we use RNA-seq to de novo assemble a transcriptome and identify genes differentially expressed in young gametophytes as their sex is determined by the presence or absence of the male-inducing pheromone called antheridiogen. Of the 1,163 consensus differentially expressed genes identified, the vast majority (1,030) are up-regulated in gametophytes treated with antheridiogen. GO term enrichment analyses of these DEGs reveals that a large number of genes involved in epigenetic reprogramming of the gametophyte genome are up-regulated by the pheromone. Additional hormone response and development genes are also up-regulated by the pheromone. This C. richardii gametophyte transcriptome and gene expression dataset will prove useful for studies focusing on sex determination and differentiation in plants.
Publisher: Oxford University Press (OUP)
Date: 12-03-2004
DOI: 10.1105/TPC.016667
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.YDBIO.2016.11.013
Abstract: Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa. High-throughput next-generation sequencing, largely in bilaterian model species, has led to the discovery of tens of thousands of non-coding RNA genes (ncRNAs), including short, long and circular forms, and uncovered the central roles they play in development. Based on the analysis of non-bilaterian metazoan, unicellular holozoan and fungal genomes, the evolution of some ncRNAs, such as Piwi-interacting RNAs, correlates with the emergence of metazoan multicellularity, while others, including microRNAs, long non-coding RNAs and circular RNAs, appear to be more ancient. Analysis of non-coding regulatory DNA and histone post-translational modifications have revealed that some cis-regulatory mechanisms, such as those associated with proximal promoters, are present in non-animal holozoans, while others appear to be metazoan innovations, most notably distal enhancers. In contrast, the cohesin-CTCF system for regulating higher-order chromatin structure and enhancer-promoter long-range interactions appears to be restricted to bilaterians. Taken together, most bilaterian non-coding regulatory mechanisms appear to have originated before the ergence of crown metazoans. However, differential expansion of non-coding RNA and cis-regulatory DNA repertoires in bilaterians may account for their increased regulatory and morphological complexity relative to non-bilaterians.
Publisher: Portland Press Ltd.
Date: 24-01-2022
DOI: 10.1042/ETLS20210258
Abstract: Epigenomics encompasses a broad field of study, including the investigation of chromatin states, chromatin modifications and their impact on gene regulation as well as the phenomena of epigenetic inheritance. The epigenome is a multi-modal layer of information superimposed on DNA sequences, instructing their usage in gene expression. As such, it is an emerging focus of efforts to improve crop performance. Broadly, this might be ided into avenues that leverage chromatin information to better annotate and decode plant genomes, and into complementary strategies that aim to identify and select for heritable epialleles that control crop traits independent of underlying genotype. In this review, we focus on the first approach, which we term ‘epigenome guided’ improvement. This encompasses the use of chromatin profiles to enhance our understanding of the composition and structure of complex crop genomes. We discuss the current progress and future prospects towards integrating this epigenomic information into crop improvement strategies in particular for CRISPR/Cas9 gene editing and precision genome engineering. We also highlight some specific opportunities and challenges for grain and horticultural crops.
Publisher: Springer Science and Business Media LLC
Date: 31-05-2021
Publisher: Public Library of Science (PLoS)
Date: 10-06-2010
Publisher: eLife Sciences Publications, Ltd
Date: 02-03-2017
Publisher: New Prairie Press
Date: 29-04-2001
Publisher: Springer Science and Business Media LLC
Date: 11-10-2013
Abstract: Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out. In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A + enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3. Sequencing of small RNAs and mRNAs uncovered new genes, and enabled us to develop new hypotheses for nitrate regulation and coordination of carbon and nitrogen metabolism.
Publisher: Springer Science and Business Media LLC
Date: 06-06-2005
Abstract: The lycophyte Selaginella moellendorffii is a member of one of the oldest lineages of vascular plants on Earth. Fossil records show that the lycophyte clade arose 400 million years ago, 150–200 million years earlier than angiosperms, a group of plants that includes the well-studied flowering plant Arabidopsis thaliana . S. moellendorffii has a genome size of approximately 100 Mbp, as small or smaller than that of A. thaliana . S. moellendorffii has the potential to provide significant comparative information to better understand the evolution of vascular plants. We sequenced 2181 Expressed Sequence Tags (ESTs) from a S. moellendorffii cDNA library. One thousand three hundred and one non-redundant sequences were assembled, containing 291 contigs and 1010 singletons. Approximately 75% of the ESTs matched proteins in the non-redundant protein database. Among 1301 clusters, 343 were categorized according to Gene Ontology (GO) hierarchy and were compared to the GO mapping of A. thaliana tentative consensus sequences. We compared S. moellendorffii ESTs to the A. thaliana and Physcomitrella patens EST databases, using the tBLASTX algorithm. Approximately 60% of the ESTs exhibited similarity with both A. thaliana and P. patens ESTs whereas, 13% and 1% of the ESTs had exclusive similarity with A. thaliana and P. patens ESTs, respectively. A substantial proportion of the ESTs (26%) had no match with A. thaliana or P. patens ESTs. We discovered 1301 putative unigenes in S. moellendorffii . These results give an initial insight into its transcriptome that will aid in the study of the S. moellendorffii genome in the near future.
Publisher: eLife Sciences Publications, Ltd
Date: 11-04-2017
DOI: 10.7554/ELIFE.22194
Abstract: Combinatorial patterns of histone modifications regulate developmental and cell type-specific gene expression and underpin animal complexity, but it is unclear when this regulatory system evolved. By analysing histone modifications in a morphologically-simple, early branching animal, the sponge Amphimedonqueenslandica, we show that the regulatory landscape used by complex bilaterians was already in place at the dawn of animal multicellularity. This includes distal enhancers, repressive chromatin and transcriptional units marked by H3K4me3 that vary with levels of developmental regulation. Strikingly, Amphimedon enhancers are enriched in metazoan-specific microsyntenic units, suggesting that their genomic location is extremely ancient and likely to place constraints on the evolution of surrounding genes. These results suggest that the regulatory foundation for spatiotemporal gene expression evolved prior to the ergence of sponges and eumetazoans, and was necessary for the evolution of animal multicellularity.
Publisher: Springer Science and Business Media LLC
Date: 02-03-2017
Publisher: Oxford University Press (OUP)
Date: 14-05-2015
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 11-2021
Publisher: Springer Science and Business Media LLC
Date: 08-01-2020
DOI: 10.1038/S41597-019-0350-9
Abstract: Avocado ( Persea americana Mill.), macadamia ( Macadamia integrifolia L.) and mango ( Mangifera indica L.) are important subtropical tree species grown for their edible fruits and nuts. Despite their commercial and nutritional importance, the genomic information for these species is largely lacking. Here we report the generation of avocado, macadamia and mango transcriptome assemblies from pooled leaf, stem, bud, root, floral and fruit/nut tissue. Using normalized cDNA libraries, we generated comprehensive RNA-Seq datasets from which we assembled 63420, 78871 and 82198 unigenes of avocado, macadamia and mango, respectively using a combination of de novo transcriptome assembly and redundancy reduction. These unigenes were functionally annotated using Basic Local Alignment Search Tool (BLAST) to query the Universal Protein Resource Knowledgebase (UniProtKB). A workflow encompassing RNA extraction, library preparation, transcriptome assembly, redundancy reduction, assembly validation and annotation is provided. This study provides avocado, macadamia and mango transcriptome and annotation data, which is valuable for gene discovery and gene expression profiling experiments as well as ongoing and future genome annotation and marker development applications.
Publisher: Informa UK Limited
Date: 25-05-2018
Publisher: Wiley
Date: 25-09-2008
Start Date: 2015
End Date: 12-2017
Amount: $386,700.00
Funder: Australian Research Council
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