Aspectos biológicos y epidemiológicos de enfermedades del tabaco causadas por Rhizoctonia solani, en el noroeste argentino

Las enfermedades en tabaco (Nicotiana tabacum L.), causadas por Rhizoctonia solani Künh, y en importancia de prevalencia la podredumbre radicular, son las enfermedades que causan mayores pérdidas en la producción. Cuanto mayor es el conocimiento de todas las características de una epidemia, más completa es la visión de la estructura del comportamiento del patosistema para poder desarrollar estrategias de manejo de la enfermedad. Por ello este trabajo de tesis se planteó diferentes objetivos, determinar la modelización espacial de la enfermedad en las provincias de Salta y Jujuy, obteniendo por geoestadística una distribución agregada en el inicio de la epidemia y aleatoria en con el avance temporal, ajustándose al modelo exponencial, asociado a factores de manejo y ambientales. Asimismo se realizó un análisis de las secuencias de ADNr-ITS, morfología y pruebas de patogenicidad que permitieron la identificación de R. solani AG 4 HG-I, AG 2-1 y AG 4 HG-III como causantes de enfermedad en tabaco en el NOA. En los aislamientos determinados como R.solani, los marcadores ISSR permitieron detectar gran variabilidad genética, la cual estaría influenciada por la existencia de diferentes factores como ser el flujo génico por dispersión de propagulos y las prácticas de manejo. Finalmente el análisis de la dinámica temporal de epidemias permitió interpretar y entender el comportamiento de la enfermedad en diferentes materiales genéticos de tabaco, generando una importante base de información para la toma de decisiones en la generación de una estrategia de manejo de la patología. La información generada contribuye al conocimiento del sistema epidemiológico y recalca la necesidad de encarar estudios que integren a la unidad de producción a un contexto regional, teniendo en cuenta que el patosistema debe ser abordado como parte reconocida de una complejidad biológica intrínseca a la sanidad.

Análise filogenética e funcional de dois genes de reparo homólogos a AP endonuclease em cana-de-açúcar: ScARP1 e ScARP3

The genome of all organisms constantly suffers the influence of mutagenic factors from endogenous and/or exogenous origin, which may result in damage for the genome. In order to keep the genome integrity there are different DNA repair pathway to detect and correct these lesions. In relation to the plants as being sessile organisms, they are exposed to this damage frequently. The Base Excision DNA Repair (BER) is responsible to detect and repair oxidative lesions. Previous work in sugarcane identified two sequences that were homologous to Arabidopsis thaliana: ScARP1 ScARP3. These two sequences were homologous to AP endonuclease from BER pathway. Then, the aim of this work was to characterize these two sequence using different approaches: phylogenetic analysis, in silico protein organelle localization and by Nicotiana tabacum transgenic plants with overexpression cassette. The in silico data obtained showed a duplication of this sequence in sugarcane and Poaceae probably by a WGD event. Furthermore, in silico analysis showed a new localization in nuclei for ScARP1 protein. The data obtained with transgenic plants showed a change in development and morphology. Transgenic plants had slow development when compared to plants not transformed. Then, these results allowed us to understand better the potential role of this sequence in sugarcane and in plants in general. More work is important to be done in order to confirm the protein localization and protein characterization for ScARP1 and ScARP3

Posibles funciones de la familia génica de la glutamato descarboxilasa en Populus

Aunque hace más de 50 años que se describió que la glutamato descarboxilasa (GAD) lleva a cabo la descarboxilación del glutamato para producir GABA, y en animales ha sido muy estudiada debido al papel del GABA como neurotransmisor, la información disponible sobre las GADs de plantas es aún limitada, conociéndose sólo algunos aspectos de la regulación por calcio de su actividad enzimática o de expresión de algunos de los genes de su familia génica. El GABA es un metabolito que tradicionalmente se ha asociado a estrés, pero su papel en plantas todavía no está claro. En las últimas dos décadas los resultados experimentales obtenidos sobre la GAD y el GABA, destacando las alteraciones fenotípicas mostradas por plantas tratadas con GABA y por plantas transgénicas para GAD, han generado preguntas interesantes sobre el posible papel de este metabolito y la enzima en señalización en plantas. En plantas, son varios los papeles que se han propuesto para el metabolismo del GABA tales como su participación como componente del metabolismo del carbono y del nitrógeno (Fait y col., 2008), protección frente especies reactivas de oxigeno (Liu y col., 2011), regulación de la expresión génica incluyendo la regulación de genes implicados en la síntesis de hormonas (Khatiresan y col., 1997; Shi y col., 2010; Lancien y Roberts, 2006) y señalización a larga distancia (Beuve y col., 2004) y en gradiente guiando el crecimiento del tubo polínico (Palanivelu y col., 2013). Nuestro grupo de investigación ha sugerido un papel novedoso para la producción de GABA durante la xilogénesis en pino (Molina-Rueda y col., 2010, 2015). En base a estos antecedentes, los objetivos planteados para este trabajo han sido: la asignación de posibles funciones a las GADs de Populus en condiciones normales de crecimiento y en estrés abióticos, estudiar la adquisición del dominio de unión a calmodulina (CaMBD) de las GADs de plantas vasculares y analizar el efecto del GABA y del glutamato en las raíces de Populus. Las conclusiones que se derivan de los resultados de este trabajo se detallan a continuación. El dominio de unión a calmodulina de la GAD de plantas esta conservado en GADs de plantas consideradas ancestros de plantas vasculares y ausente en plantas no vasculares, lo que sitúa juntos en la evolución los eventos de adquisición del dominio de unión a CaM y el desarrollo del tejido vascular de plantas. Los resultados similares de la localización de GABA en xilema y una expresión GAD asociada a la formación de madera de reacción tanto en pino como en chopo apuntan a un papel relevante de la producción de GABA durante la xilogénesis en leñosas. La familia génica GAD posee seis genes codificando todos ellos para proteínas aparentemente funcionales y susceptibles de ser reguladas por calcio. Esta familia génica ha sufrido duplicaciones y eventos de especialización durante la evolución de Populus. Este trabajo ha posibilitado la asociación entre papeles específicos y los diferentes genes de esta familia. Beuvé N, Rispail N, Laine P, Cliquet J-B, Ourry A, Deunff F (2004) Putative role of Υ-aminobutyric acid as a long-distance signal in up-regulation of nitrate uptake in Brassica napus L. Plant Cell Environ. 27: 1035-1046 Fait A, Fromm H, Walter D, Galili G, Fernie AR (2008) Highway or byway: the metabolic role of the GABA shunt in plants. Trends in plant science 13: 14-19 Kathiresan A, Tung P, Chinnappa CC, Reid DM (1997) gamma-Aminobutyric acid stimulates ethylene biosynthesis in sunflower. Plant Physiol. 115: 129-135 Lancien M, Roberts MR (2006) Regulation of Arabidopsis thaliana 14-3-3 gene expression by ϒ-aminobutyric acid. Plant Cell Environ. 29: 1430-1436 Liu C, Zhao L, Yu G (2011) The dominant glutamic acid metabolic flux to produce gamma-amino butyric acid over proline in Nicotiana tabacum leaves under water stress relates to its significant role in antioxidant activity. Journal of integrative plant biology 53: 608-618 Molina-Rueda JJ, Pascual MB, Canovas FM, Gallardo F (2010) Characterization and developmental expression of a glutamate decarboxylase from maritime pine. Planta 232: 1471-1483 Molina-Rueda, J.J. y col., 2015. A putative role for γ-aminobutyric acid (GABA) in vascular development in pine seedlings. Planta 241: 257-267 Palanivelu R, Brass L, Edlund AF, D P (2003) Pollen tube growth and guidance is regulated by POP2, an Arabidopsis gene that controls GABA levels. Cell 114: 47-59 Shi SQ, Shi Z, Jiang ZP, Qi LW, Sun XM, Li CX, Liu JF, Xiao WF, Zhang SG (2010) Effects of exogenous GABA on gene expression of Caragana intermedia roots under NaCl stress: regulatory roles for H2O2 and ethylene production. Plant, cell & environment 33: 149-162

Experiências com métodos alternativos de controle de pragas e doenças no município de Igarapé-Açu, Pará.

Com o intuito de conhecer, caracterizar e sistematizar as decisões tomadas por agricultores familiares de Igarapé-Açu, Pará, no que diz respeito à utilização de métodos alternativos no controle de pragas e doenças, a presente pesquisa foi proposta. Utilizou-se a técnica de ?sistematização?. Conclui-se que, os agricultores familiares de Igarapé-Açu acreditam ser viável a utilização de produtos alternativos, para o controle de pragas e doenças. Os principais inseticidas botânicos utilizados são: fumo (Nicotiana tabacum), nim (Azadirachta indica) e o tucupi (extraído a partir do processamento da Manihot esculenta Crantz). E a participação dos agricultores nos treinamentos oferecidos pela Embrapa Amazônia Oriental não é fator determinante para a disseminação do uso de inseticidas botânicos na região.

New insights into plant salt acclimation: the roles of vesicle trafficking and reactive oxygen species signalling in mitochondria and the endomembrane system

In this study, we investigated the cellular and molecular mechanisms that regulate salt acclimation. The main objective was to obtain new insights into the molecular mechanisms that control salt acclimation. Therefore, we carried out a multidisciplinary study using proteomic, transcriptomic, subcellular and physiological techniques. We obtained a Nicotiana tabacum BY-2 cell line acclimated to be grown at 258 mM NaCl as a model for this study. The proteomic and transcriptomic data indicate that the molecular response to stress (chaperones, defence proteins, etc.) is highly induced in these salt-acclimated cells. The subcellular results show that salt induces sodium compartmentalization in the cell vacuoles and seems to be mediated by vesicle trafficking in tobacco salt-acclimated cells. Our results demonstrate that abscisic acid (ABA) and proline metabolism are crucial in the cellular signalling of salt acclimation, probably regulating reactive oxygen species (ROS) production in the mitochondria. ROS may act as a retrograde signal, regulating the cell response. The network of endoplasmic reticulum and Golgi apparatus is highly altered in salt-acclimated cells. The molecular and subcellular analysis suggests that the unfolded protein response is induced in salt-acclimated cells. Finally, we propose that this mechanism may mediate cell death in salt-acclimated cells.

Aspectos biológicos y epidemiológicos de enfermedades del tabaco causadas por Rhizoctonia solani, en el noroeste argentino

Las enfermedades en tabaco (Nicotiana tabacum L.), causadas por Rhizoctonia solani Künh, y en importancia de prevalencia la podredumbre radicular, son las enfermedades que causan mayores pérdidas en la producción. Cuanto mayor es el conocimiento de todas las características de una epidemia, más completa es la visión de la estructura del comportamiento del patosistema para poder desarrollar estrategias de manejo de la enfermedad. Por ello este trabajo de tesis se planteó diferentes objetivos, determinar la modelización espacial de la enfermedad en las provincias de Salta y Jujuy, obteniendo por geoestadística una distribución agregada en el inicio de la epidemia y aleatoria en con el avance temporal, ajustándose al modelo exponencial, asociado a factores de manejo y ambientales. Asimismo se realizó un análisis de las secuencias de ADNr-ITS, morfología y pruebas de patogenicidad que permitieron la identificación de R. solani AG 4 HG-I, AG 2-1 y AG 4 HG-III como causantes de enfermedad en tabaco en el NOA. En los aislamientos determinados como R.solani, los marcadores ISSR permitieron detectar gran variabilidad genética, la cual estaría influenciada por la existencia de diferentes factores como ser el flujo génico por dispersión de propagulos y las prácticas de manejo. Finalmente el análisis de la dinámica temporal de epidemias permitió interpretar y entender el comportamiento de la enfermedad en diferentes materiales genéticos de tabaco, generando una importante base de información para la toma de decisiones en la generación de una estrategia de manejo de la patología. La información generada contribuye al conocimiento del sistema epidemiológico y recalca la necesidad de encarar estudios que integren a la unidad de producción a un contexto regional, teniendo en cuenta que el patosistema debe ser abordado como parte reconocida de una complejidad biológica intrínseca a la sanidad.

Fitoextracção de cádmio de solos contaminados, com plantas seleccionadas

A remediação de locais contaminados com metais pesados usando plantas hiperacumuladoras aparenta ser uma alternativa bastante viável. Neste trabalho comparou-se a acumulação e tolerância ao cádmio (Cd), ambas baseadas nas respostas ao stress oxidativo em três espécies de plantas diferentes: Brassica juncea (L.) Czem., Nicotiana tabacum L. e Solanum nigrum L., descritas na literatura como plantas bastante tolerantes ou até com características híper acumuladoras. As plantas cresceram num solo contaminado com diferentes concentrações de Cd (O- 35 mg kg-1) durante um período de 90 dias. O factor de translocação (FT), utilizado para medir a translocação efectiva do Cd da raiz para a parte aérea, variou consideravelmente entre as espécies desenvolvidas. A N. tabacum foi a planta que apresentou os maiores valores de FT. Neste trabalho foi a única planta que preencheu todas as condições para ser considerada hiperacumuladora para todos os níveis de contaminação do solo. Por outro lado, a S. nigrum apresentou os maiores valores de concentração de Cd nos tecidos, com um FT > 1, na presença de 5 mg Cd kg·1 de solo. Apesar da B. juncea ter apresentado um resultado de FT inferior às restantes, foi a única planta com valores crescentes de FT com o aumento da contaminação de Cd. O stress oxidativo nas plantas desenvolvidas foi avaliado pela peroxidação lipídica e pelas actividades da catalase (CAT), ascorbato peroxidase (APX), guaiacol peroxidase (GPX) e superóxido dismutase (SOO), quer na raiz quer na parte aérea. Foi observado um aumento significativo (versus controlo) na peroxidação lipídica e actividade enzimática da CATe APX na parte aérea da B. juncea, N. tabacum e S. nigrum para os níveis de contaminação mais elevados, 15 e/ou 35 mg Cd kg-1 A B. juncea apresentou maior sensibilidade na resposta da GPX, para todas as concentrações de Cd no solo. A peroxidação lipídica e a actividade da CAT foram superiores na parte aérea em relação à raiz para todas as plantas em todas as contaminações de Cd presentes no solo. A actividade da SOO não apresentou respostas consistentes para nenhuma das plantas. ABSTRACT: Remediation of sites contaminated with heavy metals using hyper accumulators seems a promising alternative to engineering approaches. ln this work, we compared cadmium (Cd) accumulation and tolerance (based on responses to oxidative stress) in three different species, Brassica juncea (L) Czem., Nicotiana tabacum L. and Solanum nigrum L., described in the literature as very tolerant or even as hyper accumulators. The plants were grown in soil spiked with different Cd concentrations (O- 35 mg kg- 1) over a period of 90 days. The translocation factor (TF), used to measure the effectiveness of translocating Cd from roots to shoots, depended greatly on the species. N. tabacum was the plant which exhibited the highest TF values. lt was the only plant under study that fulfilled the conditions of a hyper accumulator for all levels of soil contamination. On the other hand, S. nigrum presented the highest Cd concentration in plant tissues, with TF > 1 in the presence of 5 mg Cd kg-1 of soil. Although B. juncea had presented the lowest TF and Cd concentrations, it was the only plant with TF values increasing with the level of cadmium. Oxidative stress in plants was evaluated by lipid peroxidation and activities of catalase (CAT), ascorbate peroxidase (APX), guaiacol peroxidase (GPX) and superoxide dismutase (SOO), both in roots and shoots. A significant enhancement (versus control) on lipid peroxidation and enzymatic activity of CAT and APX in shoots of B. juncea, N. tabacum and S. nigrum was observed for the highest levels of Cd in soil, 15 and/or 35 mg Cd kg-1. B. juncea presented the most sensitive response of GPX, for all levels of Cd in soil. Lipid peroxidation and CAT activity were greater in shoots than in roots for all plants and soil Cd concentrations. SOO activity did not present consistent trends for any plant.

Os gêneros Nicotiana L., Bouchetia Dunal e Nierembergia Ruiz & Pav.(Solanaceae) no Rio Grande do Sul, Brasil

Os gêneros Nicotiana L., Bouchetia Dunal e Nierembergia Ruiz & Pav. da tribo Nicotianeae G.Don (Solanaceae), presentes no estado do Rio Grande do Sul, apresentam diversas características em comum, como o hábito predominantemente herbáceo, fruto seco, capsular, com numerosas sementes. Estes gêneros distinguem-se basicamente por Nicotiana apresentar prefloração geralmente contorcido-conduplicada ou conduplicada, corola infundibuliforme, tubular ou hipocrateriforme, anteras dorsifixas e um disco nectarífero presente, enquanto que Bouchetia e Nierembergia apresentam prefloração imbricadoconduplicada ou imbricada e anteras ventrifixas. Em Bouchetia a corola é campanulado-infundibuliforme e um disco nectarífero está presente, enquanto que em Nierembergia a corola é hipocrateriforme e o disco nectarífero está ausente. O gênero Nicotiana, da subtribo Nicotianineae, está representado no Estado por seis espécies nativas: N. alata Link & Otto, N. bonariensis Lehm., N. forgetiana Hemsl., N. langsdorffii Weinm., N. longiflora Cav. e N. mutabilis Stehmann & Semir. Duas outras espécies, provavelmente originárias da Argentina, são também encontradas no Estado: N. glauca Graham, que ocorre de forma ruderal ou cultivada e N. tabacum L., também cultivada, de importância econômica por ser fonte de matéria prima para a indústria do fumo. A única espécie do gênero Bouchetia, presente no Estado, é Bouchetia anomala (Miers) Britton & Rusby, endêmica da região sul do Brasil, Uruguai, Paraguai e nordeste da Argentina. Pertence à subtribo Nierembergiinae Hunz., junto com Nierembergia, com quem apresenta maior afinidade. Nierembergia está representado no Rio Grande do Sul por cinco espécies nativas: N. linariifolia Graham, N. micrantha Cabrera, N. pinifolia Miers, N. riograndensis Hunz. & A.A.Cocucci e N. scoparia Sendtn. Chaves analíticas para identificação dos gêneros da tribo Nicotianeae G.Don e para os da subtribo Nierembergiinae, assim como para as espécies de Nicotiana, Bouchetia e Nierembergia, são apresentadas. Descrições para os três gêneros e suas espécies, ilustrações, mapas de distribuição geográfica no Estado, considerações quanto ao hábitat, observações sobre a fenologia, variabilidade morfológica e outros comentários também são referidos.

Transient expression of Human papillomavirus type 16 L1 protein in Nicotiana benthamiana using an infectious tobamovirus vector

A Tobacco mosaic virus (TMV)-derived vector was used to express a native Human papillomavirus type 16 (HPV-16) L1 gene in Nicotiana benthamiana by means of infectious in vitro RNA transcripts inoculated onto N. benthamiana plants. HPV-16 L1 protein expression was quantitated by enzyme-linked immunosorbent assays (ELISA) after concentration of the plant extract. We estimated that the L1 product yield was 20-37 μg/kg of fresh leaf material. The L1 protein in the concentrated extract was antigenically characterised using the neutralising and conformation-specific Mabs H16:V5 and H16:E70, which bound to the plant-produced protein. Particles observed by transmission electron microscopy were mainly capsomers but virus-like particles (VLPs) similar to those produced in other systems were also present. Immunisation of rabbits with the concentrated plant extract induced a weak immune response. This is the first report of the successful expression of an HPV L1 gene in plants using a plant virus vector. © 2006 Elsevier B.V. All rights reserved.

Advanced Engineering of Lipid Metabolism in Nicotiana benthamiana Using a Draft Genome and the V2 Viral Silencing-Suppressor Protein

The transient leaf assay in Nicotiana benthamiana is widely used in plant sciences, with one application being the rapid assembly of complex multigene pathways that produce new fatty acid profiles. This rapid and facile assay would be further improved if it were possible to simultaneously overexpress transgenes while accurately silencing endogenes. Here, we report a draft genome resource for N. benthamiana spanning over 75% of the 3.1 Gb haploid genome. This resource revealed a two-member NbFAD2 family, NbFAD2.1 and NbFAD2.2, and quantitative RT-PCR (qRT-PCR) confirmed their expression in leaves. FAD2 activities were silenced using hairpin RNAi as monitored by qRT-PCR and biochemical assays. Silencing of endogenous FAD2 activities was combined with overexpression of transgenes via the use of the alternative viral silencing-suppressor protein, V2, from Tomato yellow leaf curl virus. We show that V2 permits maximal overexpression of transgenes but, crucially, also allows hairpin RNAi to operate unimpeded. To illustrate the efficacy of the V2-based leaf assay system, endogenous lipids were shunted from the desaturation of 18:1 to elongation reactions beginning with 18:1 as substrate. These V2-based leaf assays produced ~50% more elongated fatty acid products than p19-based assays. Analyses of small RNA populations generated from hairpin RNAi against NbFAD2 confirm that the siRNA population is dominated by 21 and 22 nt species derived from the hairpin. Collectively, these new tools expand the range of uses and possibilities for metabolic engineering in transient leaf assays. © 2012 Naim et al.

De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

Background: Nicotiana benthamiana has been widely used for transient gene expression assays and as a model plant in the study of plant-microbe interactions, lipid engineering and RNA silencing pathways. Assembling the sequence of its transcriptome provides information that, in conjunction with the genome sequence, will facilitate gaining insight into the plant's capacity for high-level transient transgene expression, generation of mobile gene silencing signals, and hyper-susceptibility to viral infection. Methodology/Results: RNA-seq libraries from 9 different tissues were deep sequenced and assembled, de novo, into a representation of the transcriptome. The assembly, of16GB of sequence, yielded 237,340 contigs, clustering into 119,014 transcripts (unigenes). Between 80 and 85% of reads from all tissues could be mapped back to the full transcriptome. Approximately 63% of the unigenes exhibited a match to the Solgenomics tomato predicted proteins database. Approximately 94% of the Solgenomics N. benthamiana unigene set (16,024 sequences) matched our unigene set (119,014 sequences). Using homology searches we identified 31 homologues that are involved in RNAi-associated pathways in Arabidopsis thaliana, and show that they possess the domains characteristic of these proteins. Of these genes, the RNA dependent RNA polymerase gene, Rdr1, is transcribed but has a 72 nt insertion in exon1 that would cause premature termination of translation. Dicer-like 3 (DCL3) appears to lack both the DEAD helicase motif and second dsRNA binding motif, and DCL2 and AGO4b have unexpectedly high levels of transcription. Conclusions: The assembled and annotated representation of the transcriptome and list of RNAi-associated sequences are accessible at www.benthgenome.com alongside a draft genome assembly. These genomic resources will be very useful for further study of the developmental, metabolic and defense pathways of N. benthamiana and in understanding the mechanisms behind the features which have made it such a well-used model plant. © 2013 Nakasugi et al.

The identification and rapid extraction of hydrocarbons from Nicotiana glauca : A potential advanced renewable biofuel source

Declining fossil fuels reserves, a need for increased energy security and concerns over carbon emissions from fossil fuel use are the global drivers for alternative, renewable, biosources of fuels and chemicals. In the present study the identification of long chain (C29–C33) saturated hydrocarbons from Nicotiana glauca leaves is reported. The occurrence of these hydrocarbons was detected by gas chromatography–mass spectrometry (GC–MS) and identification confirmed by comparison of physico-chemical properties displayed by the authentic standards available. A simple, robust procedure was developed to enable the generation of an extract containing a high percentage of hydrocarbons (6.3% by weight of dried leaf material) higher than previous reports in other higher plant species consequently, it is concluded that N. glauca could be a crop of greater importance than previously recognised for biofuel production. The plant can be grown on marginal lands, negating the need to compete with food crops or farmland, and the hydrocarbon extract can be produced in a non-invasive manner, leaving remaining biomass intact for bioethanol production and the generation of valuable co-products.

In vitro micro propagation of Nicotiana benthamiana via axillary shoots

Axillary shoots of Nicotiana benthamiana were regenerated from nodal explants in two weeks using MS media supplemented with the cytokinin, kinetin (0.5 mg/L), and the auxin, indole-3-butyric acid (IBA) (0.1 mg/L). Ninety two percent of shoots were 2.1-20 mm tall, a size ideal for root induction. After transfer to hormone-free MS they readily produced roots within seven days, with phenotypically normal, fully developed plants being obtained within four weeks. Leaf chlorosis due to iron deficiency was observed in plants over time, however, this was overcome by doubling the concentration of inorganic iron. This rapid micro-propagation system is particularly useful for the in vitro mass production of N. benthamiana plants for various biotechnological applications.

Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana

Background Nicotiana benthamiana is an allo-tetraploid plant, which can be challenging for de novo transcriptome assemblies due to homeologous and duplicated gene copies. Transcripts generated from such genes can be distinct yet highly similar in sequence, with markedly differing expression levels. This can lead to unassembled, partially assembled or mis-assembled contigs. Due to the different properties of de novo assemblers, no one assembler with any one given parameter space can re-assemble all possible transcripts from a transcriptome. Results In an effort to maximise the diversity and completeness of de novo assembled transcripts, we utilised four de novo transcriptome assemblers, TransAbyss, Trinity, SOAPdenovo-Trans, and Oases, using a range of k-mer sizes and different input RNA-seq read counts. We complemented the parameter space biologically by using RNA from 10 plant tissues. We then combined the output of all assemblies into a large super-set of sequences. Using a method from the EvidentialGene pipeline, the combined assembly was reduced from 9.9 million de novo assembled transcripts to about 235,000 of which about 50,000 were classified as primary. Metrics such as average bit-scores, feature response curves and the ability to distinguish paralogous or homeologous transcripts, indicated that the EvidentialGene processed assembly was of high quality. Of 35 RNA silencing gene transcripts, 34 were identified as assembled to full length, whereas in a previous assembly using only one assembler, 9 of these were partially assembled. Conclusions To achieve a high quality transcriptome, it is advantageous to implement and combine the output from as many different de novo assemblers as possible. We have in essence taking the ‘best’ output from each assembler while minimising sequence redundancy. We have also shown that simultaneous assessment of a variety of metrics, not just focused on contig length, is necessary to gauge the quality of assemblies.

Movement-associated proteins of Potato virus A: attachment to virus particles and phosphorylation

The particles of Potato virus A (PVA; genus Potyvirus) are helically constructed filaments that contain multiple copies of a single type of coat-protein (CP) subunit and a single copy of genome-linked protein (VPg), attached to one end of the virion. Examination of negatively-stained virions by electron microscopy revealed flexuous, rod-shaped particles with no obvious terminal structures. It is known that particles of several filamentous plant viruses incorporate additional minor protein components, forming stable complexes that mediate particle disassembly, movement or transmission by insect vectors. The first objective of this work was to study the interaction of PVA movement-associated proteins with virus particles and how these interactions contribute to the morphology and function of the virus particles. Purified particles of PVA were examined by atomic force microscopy (AFM) and immuno-gold electron microscopy. A protrusion was found at one end of some of the potyvirus particles, associated with the 5' end of the viral RNA. The tip contained two virus-encoded proteins, the genome-linked protein (VPg) and the helper-component proteinase (HC-Pro). Both are required for cell-to-cell movement of the virus. Biochemical and electron microscopy studies of purified PVA samples also revealed the presence of another protein required for cell-to-cell movement the cylindrical inclusion protein (CI), which is also an RNA helicase/ATPase. Centrifugation through a 5-40% sucrose gradient separated virus particles with no detectable CI to a fraction that remained in the gradient, from the CI-associated particles that went to the pellet. Both types of particles were infectious. AFM and translation experiments demonstrated that when the viral CI was not present in the sample, PVA virions had a beads-on-a-string phenotype, and RNA within the virus particles was more accessible to translation. The second objective of this work was to study phosphorylation of PVA movement-associated and structural proteins (CP and VPg) in vitro and, if possible, in vivo. PVA virion structural protein CP is necessary for virus cell-to-cell movement. The tobacco protein kinase CK2 was identified as a kinase phosphorylating PVA CP. A major site of CK2 phosphorylation in PVA CP was identified as a single threonine within a CK2 consensus sequence. Amino acid substitutions affecting the CK2 consensus sequence in CP resulted in viruses that were defective in cell-to-cell and long-distance movement. The CK2 regulation of virion assembly and cell-to-cell movement by phosphorylation of CP was possibly due to the inhibition of CP binding to viral RNA. Four putative phosphorylation sites were identified from an in vitro phosphorylated recombinant VPg. All four were mutated and the spread of mutant viruses in two different host plants was studied. Two putative phosphorylation site mutants (Thr45 and Thr49) had phenotypes identical to that of a wild type (WT) virus infection in both Nicotiana benthamiana and N. tabacum plants. The other two mutant viruses (Thr132/Ser133 and Thr168) showed different phenotypes with increased or decreased accumulation rates, respectively, in inoculated and the first two systemically infected leaves of N. benthamiana. The same mutants were occasionally restricted to single cells in N. tabacum plants, suggesting the importance of these amino acids in the PVA infection cycle in N. tabacum.