Publications by authors named "Ian Small"

147 Publications

A synthetic RNA editing factor edits its target site in chloroplasts and bacteria.

Commun Biol 2021 May 10;4(1):545. Epub 2021 May 10.

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.

Members of the pentatricopeptide repeat (PPR) protein family act as specificity factors in C-to-U RNA editing. The expansion of the PPR superfamily in plants provides the sequence variation required for design of consensus-based RNA-binding proteins. We used this approach to design a synthetic RNA editing factor to target one of the sites in the Arabidopsis chloroplast transcriptome recognised by the natural editing factor CHLOROPLAST BIOGENESIS 19 (CLB19). We show that our synthetic editing factor specifically recognises the target sequence in in vitro binding assays. The designed factor is equally specific for the target rpoA site when expressed in chloroplasts and in the bacterium E. coli. This study serves as a successful pilot into the design and application of programmable RNA editing factors based on plant PPR proteins.
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http://dx.doi.org/10.1038/s42003-021-02062-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8110955PMC
May 2021

Peanut disease epidemiology under dynamic microclimate conditions and management practices in North Florida.

Plant Dis 2021 Mar 23. Epub 2021 Mar 23.

North Florida Research & Education Center, University of Florida, Plant Pathology, Quincy, Florida, United States;

Diverse field characteristics, weather patterns, and management practices can result in variable microclimates. The objective was to relate in-field microclimate conditions with peanut diseases and yield and determine the effect of irrigation and fungicides within these environments. Irrigation did not have a major impact on disease and yield. Stem rot () and early () and late () leaf spot were most affected by changes in environmental patterns across seasons. Average non-treated stem rot was 12.9% in 2017 which dropped considerably in 2018 to 0.2% but emerged again in 2019 to 3.2%. Stem rot incidence varied across the field, and the response to fungicides depended on management zone. Leaf spot defoliation in non-treated plots was severe in 2019 reaching an average of 73% at 126 days after planting but only reached 15% in 2017 and 35% in 2019 at the same stage. A low-input fungicide schedule was able to reduce foliar disease in all zones and seasons, but the microclimatic conditions in the low-lying area favored leaf spot in 2017 and 2018 although not in the dryer 2019 season. Seasonal differences in disease and plant growth affected the level of protection against average yield loss using a standard low-input program which in 2017 (527 kg/ha) was not as great as 2018 (2,235 kg/ha) or 2019 (1,763 kg/ha). Disease prediction models built on dynamic environmental factors in the context of multiple pathogens and natural field conditions could be developed to improve within-season management decisions for more efficient fungicide inputs.
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http://dx.doi.org/10.1094/PDIS-11-20-2390-REDOI Listing
March 2021

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Nat Genet 2021 04 18;53(4):564-573. Epub 2021 Mar 18.

Aquatic and Crop Resource Development, National Research Council, Saskatoon, Saskatchewan, Canada.

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.
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http://dx.doi.org/10.1038/s41588-021-00807-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8035072PMC
April 2021

The Pentatricopeptide Repeat Protein MEF100 Is Required for the Editing of Four Mitochondrial Editing Sites in .

Cells 2021 Feb 22;10(2). Epub 2021 Feb 22.

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia.

In there are more than 600 C-to-U RNA editing events in the mitochondria and at least 44 in the chloroplasts. Pentatricopeptide repeat (PPR) proteins provide the specificity for these reactions. They recognize RNA sequences in a partially predictable fashion via key amino acids at the fifth and last position in each PPR motif that bind to individual ribonucleotides. A combined approach of RNA-Seq, mutant complementation, electrophoresis of mitochondrial protein complexes and Western blotting allowed us to show that MEF100, a PPR protein identified in a genetic screen for mutants resistant to an inhibitor of γ -glutamylcysteine synthetase, is required for the editing of -493, -403, -698 and -356 sites in Arabidopsis mitochondria. The absence of editing in leads to a decrease in mitochondrial Complex I activity, which probably explains the physiological phenotype. Some plants have lost the requirement for MEF100 at one or more of these sites through mutations in the mitochondrial genome. We show that loss of the requirement for MEF100 editing leads to divergence in the MEF100 binding site.
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http://dx.doi.org/10.3390/cells10020468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7926422PMC
February 2021

The genetic basis of cytoplasmic male sterility and fertility restoration in wheat.

Nat Commun 2021 02 15;12(1):1036. Epub 2021 Feb 15.

ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.

Hybrid wheat varieties give higher yields than conventional lines but are difficult to produce due to a lack of effective control of male fertility in breeding lines. One promising system involves the Rf1 and Rf3 genes that restore fertility of wheat plants carrying Triticum timopheevii-type cytoplasmic male sterility (T-CMS). Here, by genetic mapping and comparative sequence analyses, we identify Rf1 and Rf3 candidates that can restore normal pollen production in transgenic wheat plants carrying T-CMS. We show that Rf1 and Rf3 bind to the mitochondrial orf279 transcript and induce cleavage, preventing expression of the CMS trait. The identification of restorer genes in wheat is an important step towards the development of hybrid wheat varieties based on a CMS-Rf system. The characterisation of their mode of action brings insights into the molecular basis of CMS and fertility restoration in plants.
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http://dx.doi.org/10.1038/s41467-021-21225-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884431PMC
February 2021

Predictive Modeling of Brown Rust of Sugarcane Based on Temperature and Relative Humidity in Florida.

Phytopathology 2021 Jan 20. Epub 2021 Jan 20.

University of Florida, Plant Pathology, Belle Glade, Florida, United States.

Logistic regression models were developed from five years (2014-2018) of disease severity and weather data in an attempt to predict brown rust of sugarcane at the Everglades Research and Education Center (EREC) in Belle Glade, Florida. Disease severity (percentage area of the top visible dewlap leaf covered by rust) was visually assessed in the field every two weeks for two varieties susceptible to brown rust. Two hundred fifty variables were derived from weather data for 10 to 40-day periods before each brown rust assessment day. A subset of these variables were then evaluated as potential predictors of severity of brown rust based on their individual correlation and/or their biological meaningfulness. Analyses of correlation and stepwise logistic regression allowed us to identify afternoon humid thermal ratio (AHTR), temperature-based duration variables, and their interaction terms as the most significant variables associated with brown rust epidemics of sugarcane in Florida. The nine best predictive models were identified based on model accuracy, sensitivity, specificity and estimates of the prediction error. The prediction accuracy of these models ranged from 73-85%. Single variable model BR2 (based on AHTR) classified 89% of the epidemic and 81% of the non-epidemic status of the disease. Greater than 83% of the epidemics and 81% of the non-epidemic status of sugarcane brown rust was correctly classified using multiple variable models. These models can potentially be used as components of a rust disease warning system to assist in the management of brown rust epidemics of sugarcane in south Florida.
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http://dx.doi.org/10.1094/PHYTO-02-20-0060-RDOI Listing
January 2021

Multiple wheat genomes reveal global variation in modern breeding.

Nature 2020 12 25;588(7837):277-283. Epub 2020 Nov 25.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome, and the lack of genome-assembly data for multiple wheat lines. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.
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http://dx.doi.org/10.1038/s41586-020-2961-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759465PMC
December 2020

Sixty-One Years Following Registration, Phorate Applied In-Furrow at Planting Suppresses Development of Late Leaf Spot on Peanut.

Plant Dis 2020 Sep 8:PDIS03200547RE. Epub 2020 Sep 8.

North Florida Research and Education Center, University of Florida, Quincy, FL 32351.

Late and early leaf spot are caused by and , respectively, and are damaging diseases of peanut ( L.) capable of defoliation and yield loss. Management of these diseases is most effective through the integration of tactics that reduce starting inoculum and prevent infection. The insecticide phorate was first registered in 1959 and has been used in peanut production for decades in-furrow at planting to suppress thrips. Phorate further provides significant suppression of infection beyond suppression of its thrips vector alone by activating defense-related responses in the peanut plant. From six experiments conducted from 2017 to 2019 in Blackville, SC, Reddick, FL, and Quincy, FL, significantly less leaf spot defoliation was exhibited on peanuts treated with phorate in-furrow at planting (26%) compared with nontreated checks (48%). In-season fungicides were excluded from five of the experiments, whereas the 2018 Quincy, FL, experiment included eight applications on a 15-day interval. Across individual experiments, significant suppression of defoliation caused by late leaf spot was observed from 64 to 147 days after planting. Although more variable within location-years, pod yield following phorate treatment was overall significantly greater than for nontreated peanut (2,330 compared with 2,030 kg/ha; = 0.0794). The consistent defoliation suppression potential was estimated to confer an average potential net economic yield savings of $90 to $120 per hectare under analogous leaf spot defoliation. To our knowledge, these are the first data in the 61 years since its registration demonstrating significant suppression of leaf spot on peanut following application of phorate in-furrow at planting. Results support phorate use in peanut as an effective and economical tactic to incorporate to manage late and early leaf spot infections and development of fungicide resistance.
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http://dx.doi.org/10.1094/PDIS-03-20-0547-REDOI Listing
September 2020

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic.

Nucleic Acids Res 2020 09;48(15):8812-8813

Institut de biologie moléculaire des plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France.

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http://dx.doi.org/10.1093/nar/gkaa651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7470981PMC
September 2020

Nematicide influence on cotton yield and plant-parasitic nematodes in conventional and sod-based crop rotation.

J Nematol 2020 ;52:1-14

North Florida Research and Education Center, University of Florida , Quincy, FL, 32351.

Plant-parasitic nematodes ( (reniform, RN), (spiral), and (ring)) and yield were investigated in cotton phases of conventional (peanut-cotton-cotton) and sod-based (bahiagrass-bahiagrass-peanut-cotton) rotations with or without irrigation and fluopyram nematicide at a long-term research site, established in 2000, in Quincy, Florida, USA. Objectives were to determine impacts of nematicide application on cotton yield and evaluate effects of nematicide on plant-parasitic nematodes in these rotations in 2017 and 2018. Reniform nematode population densities were greater in conventional cotton than sod-based cotton. Ring and spiral nematode population densities were greater in sod-based cotton than conventional cotton. Plots receiving nematicide had increased RN population densities in preplant 2018 soil samples and spiral nematode population densities in preplant 2017, harvest 2017, preplant 2018, and harvest 2018 soil samples compared to untreated plots. Cotton seed yield in conventional rotation was increased by 18% following nematicide application in 2017 but decreased by 10% in sod-based rotation in 2018, relative to the untreated control. Sod-based rotation had greater cotton yield than conventional rotation in 2017 and 2018. Nematicide application did not improve cotton yield in sod-based rotation and was inconsistent in conventional rotation.

Plant-parasitic nematodes ( (reniform, RN), (spiral), and (ring)) and yield were investigated in cotton phases of conventional (peanut–cotton–cotton) and sod-based (bahiagrass–bahiagrass–peanut–cotton) rotations with or without irrigation and fluopyram nematicide at a long-term research site, established in 2000, in Quincy, Florida, USA. Objectives were to determine impacts of nematicide application on cotton yield and evaluate effects of nematicide on plant-parasitic nematodes in these rotations in 2017 and 2018. Reniform nematode population densities were greater in conventional cotton than sod-based cotton. Ring and spiral nematode population densities were greater in sod-based cotton than conventional cotton. Plots receiving nematicide had increased RN population densities in preplant 2018 soil samples and spiral nematode population densities in preplant 2017, harvest 2017, preplant 2018, and harvest 2018 soil samples compared to untreated plots. Cotton seed yield in conventional rotation was increased by 18% following nematicide application in 2017 but decreased by 10% in sod-based rotation in 2018, relative to the untreated control. Sod-based rotation had greater cotton yield than conventional rotation in 2017 and 2018. Nematicide application did not improve cotton yield in sod-based rotation and was inconsistent in conventional rotation.
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http://dx.doi.org/10.21307/jofnem-2020-034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7266013PMC
January 2020

Peanut Yield Loss in the Presence of Defoliation Caused by Late or Early Leaf Spot.

Plant Dis 2020 May 30;104(5):1390-1399. Epub 2020 Mar 30.

Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849.

Late and early leaf spot, respectively caused by and , are damaging diseases of peanut () capable of defoliating canopies and reducing yield. Although one of these diseases may be more predominant in a given area, both are important on a global scale. To assist informed management decisions and quantify relationships between end-of-season defoliation and yield loss, meta-analyses were conducted over 140 datasets meeting established criteria. Slopes of proportion yield loss with increasing defoliation were estimated separately for Virginia and runner market type cultivars. Yield loss for Virginia types was described by an exponential function over the range of defoliation levels, with a loss increase of 1.2 to 2.2% relative to current loss levels per additional percent defoliation. Results for runner market type cultivars showed yield loss to linearly increase 2.2 to 2.8% per 10% increase in defoliation for levels up to approximately 95% defoliation, after which the rate of yield loss was exponential. Defoliation thresholds to prevent economic yield loss for Virginia and runner types were estimated at 40 and 50%, respectively. Although numerous factors remain important in mitigating overall yield losses, the integration of these findings should aid recommendations about digging under varying defoliation intensities and peanut maturities to assist in minimizing yield losses.
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http://dx.doi.org/10.1094/PDIS-11-19-2286-REDOI Listing
May 2020

Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics.

Plant Methods 2020 4;16. Epub 2020 Jan 4.

4Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia.

Background: Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara.

Results: Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions and from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (, , , , ) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA > rDNA >  > 

Conclusions: We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.
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http://dx.doi.org/10.1186/s13007-019-0534-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6942304PMC
January 2020

The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants.

Mol Plant 2020 02 21;13(2):215-230. Epub 2019 Nov 21.

Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, WA, Australia; School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, WA, Australia. Electronic address:

The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.
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http://dx.doi.org/10.1016/j.molp.2019.11.002DOI Listing
February 2020

Towards a plant model for enigmatic U-to-C RNA editing: the organelle genomes, transcriptomes, editomes and candidate RNA editing factors in the hornwort Anthoceros agrestis.

New Phytol 2020 03 14;225(5):1974-1992. Epub 2019 Dec 14.

Institut für Zelluläre und Molekulare Botanik (IZMB), University of Bonn, Kirschallee 1, 53115, Bonn, Germany.

Hornworts are crucial to understand the phylogeny of early land plants. The emergence of 'reverse' U-to-C RNA editing accompanying the widespread C-to-U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort-tracheophyte clade. C-to-U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U-to-C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C-to-U and 1300 sites of U-to-C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the 'classic' DYW domain, in the meantime confirmed as the cytidine deaminase for C-to-U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U-to-C editing targets according to the PPR-RNA binding code.
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http://dx.doi.org/10.1111/nph.16297DOI Listing
March 2020

Weather-Based Predictive Modeling of Orange Rust of Sugarcane in Florida.

Phytopathology 2020 Mar 28;110(3):626-632. Epub 2020 Jan 28.

Everglades Research and Education Center, Plant Pathology Department, University of Florida, Belle Glade 33430, FL, U.S.A.

Epidemics of sugarcane orange rust (caused by ) in Florida are largely influenced by prevailing weather conditions. In this study, we attempted to model the relationship between weather conditions and rust epidemics as a first step toward development of a decision aid for disease management. For this purpose, rust severity data were collected from 2014 through 2016 at the Everglades Research and Education Center, Belle Glade, Florida, by recording percentage of rust-affected area of the top visible dewlap leaf every 2 weeks from three orange rust susceptible cultivars. Hourly weather data for 10- to 40-day periods prior to each orange rust assessment were evaluated as potential predictors of rust severity under field conditions. Correlation and stepwise regression analyses resulted in the identification of nighttime (8 PM to 8 AM) accumulation of hours with average temperature 20 to 22°C as a key predictor explaining orange rust severity. The five best regression models for a 30-day period prior to disease assessment explained 65.3 to 76.2% of variation of orange rust severity. Prediction accuracy of these models was tested using a case control approach with disease observations collected in 2017 and 2018. Based on receiver operator characteristic curve analysis of these two seasons of test data, a single-variable model with the nighttime temperature predictor mentioned above gave the highest prediction accuracy of disease severity. These models have potential for use in quantitative risk assessment of sugarcane rust epidemics.
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http://dx.doi.org/10.1094/PHYTO-06-19-0211-RDOI Listing
March 2020

Plant organellar RNA editing: what 30 years of research has revealed.

Plant J 2020 03 12;101(5):1040-1056. Epub 2019 Dec 12.

Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel.

The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.
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http://dx.doi.org/10.1111/tpj.14578DOI Listing
March 2020

The coordinated action of PPR4 and EMB2654 on each intron half mediates trans-splicing of rps12 transcripts in plant chloroplasts.

Plant J 2019 12 25;100(6):1193-1207. Epub 2019 Sep 25.

Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea.

The pentatricopeptide repeat proteins PPR4 and EMB2654 have been shown to be required for the trans-splicing of plastid rps12 transcripts in Zea mays (maize) and Arabidopsis, respectively, but their roles in this process are not well understood. We investigated the functions of the Arabidopsis and Oryza sativa (rice) orthologs of PPR4, designated AtPPR4 (At5g04810) and OsPPR4 (Os4g58780). Arabidopsis atppr4 and rice osppr4 mutants are embryo-lethal and seedling-lethal 3 weeks after germination, respectively, showing that PPR4 is essential in the development of both dicot and monocot plants. Artificial microRNA-mediated mutants of AtPPR4 displayed a specific defect in rps12 trans-splicing, with pale-green, yellowish or albino phenotypes, according to the degree of knock-down of AtPPR4 expression. Comparison of RNA footprints in atppr4 and emb2654 mutants showed a similar concordant loss of extensive footprints at the 3' end of intron 1a and at the 5' end of intron 1b in both cases. EMB2654 is known to bind within the footprint region in intron 1a and we show that AtPPR4 binds to the footprint region in intron 1b, via its PPR motifs. Binding of both PPR4 and EMB2654 is essential to juxtapose the two intron halves and to maintain the RNAs in a splicing-competent structure for the efficient trans-splicing of rps12 intron 1, which is crucial for chloroplast biogenesis and plant development. The similarity of EMB2654 and PPR4 orthologs and their respective binding sites across land plant phylogeny indicates that their coordinate function in rps12 trans-splicing has probably been conserved for 500 million years.
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http://dx.doi.org/10.1111/tpj.14509DOI Listing
December 2019

Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants.

NPJ Syst Biol Appl 2019 18;5:24. Epub 2019 Jul 18.

1Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia.

Heterosis, or hybrid vigour, is said to occur when F1 individuals exhibit increased performance for a number of traits compared to their parental lines. Improved traits can include increased size, better yield, faster development and a higher tolerance to pathogens or adverse conditions. The molecular basis for the phenomenon remains disputed, despite many decades of theorising and experimentation. In this study, we add a genetics layer to a constraint-based model of plant () primary metabolism and show that we can realistically reproduce and quantify heterosis in a highly complex trait (the rate of biomass production). The results demonstrate that additive effects coupled to the complex patterns of epistasis generated by a large metabolic network are sufficient to explain most or all the heterosis seen in typical F1 hybrids. Such models provide a simple approach to exploring and understanding heterosis and should assist in designing breeding strategies to exploit this phenomenon in the future.
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http://dx.doi.org/10.1038/s41540-019-0101-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639380PMC
April 2020

Evolutionary Model of Plastidial RNA Editing in Angiosperms Presumed from Genome-Wide Analysis of Amborella trichopoda.

Plant Cell Physiol 2019 Oct;60(10):2141-2151

Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, Japan.

Amborella trichopoda is placed close to the base of the angiosperm lineage (basal angiosperm). By genome-wide RNA sequencing, we identified 184C-to-U RNA editing sites in the plastid genome of Amborella. This number is much higher than that observed in other angiosperms including maize (44 sites), rice (39 sites) and grape (115 sites). Despite the high frequency of RNA editing, the biased distribution of RNA editing sites in the genome, target codon preference and nucleotide preference adjacent to the edited cytidine are similar to that in other angiosperms, suggesting a common editing machinery. Consistent with this idea, the Amborella nuclear genome encodes 2-3 times more of the E- and DYW-subclass members of pentatricopeptide repeat proteins responsible for RNA editing site recognition in plant organelles. Among 165 editing sites in plastid protein coding sequences in Amborella, 100 sites were conserved at least in one out of 38 species selected to represent key branching points of the angiosperm phylogenetic tree. We assume these 100 sites represent at least a subset of the sites in the plastid editotype of ancestral angiosperms. We then mapped the loss and gain of editing sites on the phylogenetic tree of angiosperms. Our results support the idea that the evolution of angiosperms has led to the loss of RNA editing sites in plastids.
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http://dx.doi.org/10.1093/pcp/pcz111DOI Listing
October 2019

Recent range expansion in Australian hummock grasses () inferred using genotyping-by-sequencing.

AoB Plants 2019 Apr 28;11(2):plz017. Epub 2019 Mar 28.

School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia.

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for , originating in central or eastern Australia. Divergence time estimation indicates that began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.
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http://dx.doi.org/10.1093/aobpla/plz017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6481909PMC
April 2019

Transplastomic Arabidopsis plants at last.

Authors:
Ian Small

Nat Plants 2019 03;5(3):249-250

ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Western Australia, Australia.

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http://dx.doi.org/10.1038/s41477-019-0388-xDOI Listing
March 2019

Comparison of Progress of Brown Rust and Orange Rust and Conditions Conducive for Severe Epidemic Development During the Sugarcane Crop Season in Florida.

Plant Dis 2019 May 25;103(5):825-831. Epub 2019 Feb 25.

1 Everglades Research and Education Center, Plant Pathology Department, University of Florida, Belle Glade, FL 33430.

Brown rust (caused by ) and orange rust (caused by ) are two major diseases of sugarcane in Florida. To better understand the epidemiology of these two rusts, disease severity and weather variables were monitored for two seasons in cultivars CL90-4725 (susceptible to brown rust and resistant to orange rust) and CL85-1040 (susceptible to orange rust and resistant to brown rust). Brown rust was most severe during mid-May to mid-July, whereas orange rust severity peaked during two periods: mid-May to early August and then November to December. Overall, disease severity was higher for orange rust than for brown rust. Maximum disease severity was correlated with the number of hours at night with an average temperature of 20 to 22.2°C for brown rust one season and orange rust both seasons. Slightly higher correlation was obtained when relative humidity above 90% was included in the number of hours at night with an average temperature of 20 to 22.2°C for brown rust but not orange rust, suggesting that leaf wetness is not a limiting factor for either disease in Florida. Epidemics of brown rust began at lower night temperatures (16.7 to 22.2°C) in one season, but epidemics of orange rust lasted longer under higher temperatures. The correlation of rust severity on recently emerged leaves with conducive temperatures recorded in 10-, 20-, or 30-day windows starting 7 days before disease assessment suggested that earlier inoculum production is needed to create severe epidemics that result in yield loss.
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http://dx.doi.org/10.1094/PDIS-05-18-0862-REDOI Listing
May 2019

Plastome-Wide Rearrangements and Gene Losses in Carnivorous Droseraceae.

Genome Biol Evol 2019 02;11(2):472-485

Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia, Australia.

The plastid genomes of four related carnivorous plants (Drosera regia, Drosera erythrorhiza, Aldrovanda vesiculosa, and Dionaea muscipula) were sequenced to examine changes potentially induced by the transition to carnivory. The plastid genomes of the Droseraceae show multiple rearrangements, gene losses, and large expansions or contractions of the inverted repeat. All the ndh genes are lost or nonfunctional, as well as in some of the species, clpP1, ycf1, ycf2 and some tRNA genes. Uniquely, among land plants, the trnK gene has no intron. Carnivory in the Droseraceae coincides with changes in plastid gene content similar to those induced by parasitism and mycoheterotrophy, suggesting parallel changes in chloroplast function due to the similar switch from autotrophy to (mixo-) heterotrophy. A molecular phylogeny of the taxa based on all shared plastid genes indicates that the "snap-traps" of Aldrovanda and Dionaea have a common origin.
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http://dx.doi.org/10.1093/gbe/evz005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380313PMC
February 2019

Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae).

Mol Phylogenet Evol 2019 03 7;132:243-250. Epub 2018 Dec 7.

ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia (M316), 35 Stirling Highway, 6009 Crawley, Australia.

Angiosperm mitochondrial horizontal gene transfer (HGT) has been widely reported during the past decades. With a few exceptions, foreign sequences are mitochondrial genes or intronic regions from other plants, indicating that HGT has played a major role in shaping mitochondrial genome evolution. Host-parasite relationships are a valuable system to study this phenomenon due to the high frequency of HGT. In particular, the interaction between mimosoid legumes and holoparasites of the genus Lophophytum represents an outstanding opportunity to discern HGT events. The mitochondrial genome of the holoparasite L. mirabile has remarkable properties, the most extraordinary of which is the presence of 34 out of 43 mitochondrial protein genes acquired from its legume host, with the stunning replacement of up to 26 native homologs. However, the origin of the intergenic sequences that represent the majority (>90%) of the L. mirabile mtDNA remains largely unknown. The lack of mitochondrial sequences available from the donor angiosperm lineage (mimosoid legumes) precluded a large-scale evolutionary study. We sequenced and assembled the mitochondrial genome of the mimosoid Acacia ligulata and performed genome wide comparisons with L. mirabile. The A. ligulata mitochondrial genome is almost 700 kb in size, encoding 60 genes. About 60% of the L. mirabile mtDNA had greatest affinity to members of the family Fabaceae (∼49% to mimosoids in particular) with an average sequence identity of ∼96%, including genes but mostly intergenic regions. These findings strengthen the mitochondrial fusion compatibility model for angiosperm mitochondrion-to-mitochondrion HGT.
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http://dx.doi.org/10.1016/j.ympev.2018.12.006DOI Listing
March 2019

The E domain of CRR2 participates in sequence-specific recognition of RNA in plastids.

New Phytol 2019 04 6;222(1):218-229. Epub 2018 Dec 6.

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.

Pentatricopeptide repeat (PPR) proteins are modular RNA-binding proteins involved in different aspects of RNA metabolism in organelles. PPR proteins of the PLS subclass often contain C-terminal domains that are important for their function, but the role of one of these domains, the E domain, is far from resolved. Here, we elucidate the role of the E domain in CRR2 in plastids. We identified a surprisingly large number of small RNAs that represent in vivo footprints of the Arabidopsis PLS-class PPR protein CRR2. An unexpectedly strong base conservation was found in the nucleotides aligned to the E domain. We used both in vitro and in vivo experiments to reveal the role of the E domain of CRR2. The E domain of CRR2 can be predictably altered to prefer different nucleotides in its RNA ligand, and position 5 of the E1-motif is biologically important for the PPR-RNA interaction. The 'code' of the E domain PPR motifs is different from that of P- and S-motifs. The findings presented here show that the E domain of CRR2 is involved in sequence-specific interaction with its RNA ligand and have implications for our ability to predict RNA targets for PLS-PPRs and their use as biotechnological tools to manipulate specific RNAs in vivo.
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http://dx.doi.org/10.1111/nph.15578DOI Listing
April 2019

Targeted cleavage of mRNA induced by a modified pentatricopeptide repeat protein in plant mitochondria.

Commun Biol 2018 11;1:166. Epub 2018 Oct 11.

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, 6009, Australia.

Mitochondrial genes encode key components of the cellular energy machinery, but their genetic analysis is difficult or impossible in most organisms (including plants) because of the lack of viable transformation approaches. We report here a method to block the expression of the mitochondrial gene encoding a subunit of respiratory complex I in , via the modification of the specificity of the RNA-binding protein RNA PROCESSING FACTOR 2 (RPF2). We show that the modified RPF2 binds and specifically induces cleavage of RNA, almost eliminating expression of the Nad6 protein and consequently complex I accumulation and activity. To our knowledge, this is the first example of a targeted block in expression of a specific mitochondrial transcript by a custom-designed RNA-binding protein. This opens the path to reverse genetics studies on mitochondrial gene functions and leads to potential applications in agriculture.
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http://dx.doi.org/10.1038/s42003-018-0166-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6181959PMC
October 2018

High intraspecific diversity of Restorer-of-fertility-like genes in barley.

Plant J 2019 01 9;97(2):281-295. Epub 2018 Nov 9.

ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.

Nuclear restorer of fertility (Rf) genes suppress the effects of mitochondrial genes causing cytoplasmic male sterility (CMS), a condition in which plants fail to produce viable pollen. Rf genes, many of which encode RNA-binding pentatricopeptide repeat (PPR) proteins, are applied in hybrid breeding to overcome CMS used to block self-pollination of the seed parent. Here, we characterise the repertoire of restorer-of-fertility-like (RFL) PPR genes in barley (Hordeum vulgare). We found 26 RFL genes in the reference genome ('Morex') and an additional 51 putative orthogroups (POGs) in a re-sequencing data set from 262 barley genotypes and landraces. Whereas the sequences of some POGs are highly conserved across hundreds of barley accessions, the sequences of others are much more variable. High sequence variation strongly correlates with genomic location - the most variable genes are found in a cluster on chromosome 1H. A much higher likelihood of diversifying selection was found for genes within this cluster than for genes present as singlets. This work includes a comprehensive analysis of the patterns of intraspecific variation of RFL genes. The RFL sequences characterised in this study will be useful for the development of new markers for fertility restoration loci.
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http://dx.doi.org/10.1111/tpj.14115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7380019PMC
January 2019

Shifting the limits in wheat research and breeding using a fully annotated reference genome.

Science 2018 08 16;361(6403). Epub 2018 Aug 16.

GDEC (Genetics, Diversity and Ecophysiology of Cereals), INRA, Université Clermont Auvergne (UCA), 5 chemin de Beaulieu, 63039 Clermont-Ferrand, France.

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
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http://dx.doi.org/10.1126/science.aar7191DOI Listing
August 2018

Editing of Chloroplast by PPR Editing Factor EMB2261 Is Essential for Development.

Front Plant Sci 2018 20;9:841. Epub 2018 Jun 20.

Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia.

RNA editing in plastids is known to be required for embryogenesis, but no single editing event had been shown to be essential. We show that the mutation is lethal through a failure to express an editing factor that specifically recognizes the site. EMB2261 was predicted to bind the -element upstream of the site and genetic complementation with promoters of different strength followed by RNA-seq analysis was conducted to test the correlation between editing and expression. is the only editing event in chloroplasts that correlates with expression. Sequence divergence between the -element and the EMB2261 protein sequence in plants where editing is not required adds support to the association between them. We conclude that EMB2261 is the specificity factor for editing. This editing event converts P51 in Rps14 to L51, which is conserved among species lacking RNA editing, implying the importance of the editing event to Rps14 function. Rps14 is an essential ribosomal subunit for plastid translation, which, in turn, is essential for embryogenesis.
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http://dx.doi.org/10.3389/fpls.2018.00841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6019781PMC
June 2018

Fern genomes elucidate land plant evolution and cyanobacterial symbioses.

Nat Plants 2018 07 2;4(7):460-472. Epub 2018 Jul 2.

University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA.

Ferns are the closest sister group to all seed plants, yet little is known about their genomes other than that they are generally colossal. Here, we report on the genomes of Azolla filiculoides and Salvinia cucullata (Salviniales) and present evidence for episodic whole-genome duplication in ferns-one at the base of 'core leptosporangiates' and one specific to Azolla. One fern-specific gene that we identified, recently shown to confer high insect resistance, seems to have been derived from bacteria through horizontal gene transfer. Azolla coexists in a unique symbiosis with N-fixing cyanobacteria, and we demonstrate a clear pattern of cospeciation between the two partners. Furthermore, the Azolla genome lacks genes that are common to arbuscular mycorrhizal and root nodule symbioses, and we identify several putative transporter genes specific to Azolla-cyanobacterial symbiosis. These genomic resources will help in exploring the biotechnological potential of Azolla and address fundamental questions in the evolution of plant life.
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http://dx.doi.org/10.1038/s41477-018-0188-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786969PMC
July 2018