"Agave" gene expression for bioenergy

Orientador: Gonçalo Amarante Guimarães PereiraDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de BiologiaResumo: Muito têm-se especulado sobre a utilização dos agaves para a produção de biomassa em áreas marginais, principalmente, por sua alta produtividade em áreas de baixa pluviosidade, tolerância a seca e baixos teores de lignina. A agaveicultura brasileira ocupa uma extensa área de solos pobres em nutrientes na região semiárida do Nordeste, onde, muitas vezes, é a única alternativa de cultivo com resultados econômicos satisfatórios. Os agaves oferecem uma oportunidade para o estudo de um largo espectro de mecanismos de resistência à seca e altas temperaturas, que incluem desde adaptações nas raízes até o seu Metabolismo Ácido Crassuláceo (CAM), o mecanismo fotossintético mais eficiente em uso de água; e aparecem como um importante modelo para a criação de soluções agronômicas associadas às mudanças climáticas e bioenergia. Neste contexto, o presente trabalho gerou atlas transcriptômicos de folha, caule e raiz de "Agave sisalana", "Agave fourcroydes" e do Híbrido 11648 ("A. amaniensis" x "A. angustifolia") em condições de campo, identificando, pela primeira vez, os genes relacionados a parede celular e mecanismos comuns de tolerância a seca através da comparação entre análises químicas e expressão gênica. Os dados levantados contribuem para o entendimento da biologia molecular de espécies CAM de alta produtividade e poderão auxiliar o melhoramento genético desta tão importante cultura do semiáridoAbstract: A lot of speculation has been made about the use of agaves for biomass production in marginal areas, mainly because of its high productivity in low rainfall areas, drought tolerance and low lignin content. Brazilian agave-culture occupies a large area of nutrient-poor soils in the Northeast's semiarid region, where it often shows itself as the only growing crop alternative with satisfactory economic results. Agaves provide an opportunity for the study of a broad spectrum of resistance mechanisms to drought and high temperatures, ranging from adaptations in the roots to the crassulacean acid metabolism (CAM), a highly water-use efficient photosynthetic mechanism; and appear as an important model for the creation of agronomic solutions associated with climate change and bioenergy. In this context, the present work generated transcriptomics atlases of "Agave sisalana", "Agave fourcroydes" and Hybrid 11648 ("A. amaniensis" x "A. angustifolia") under field conditions, identifying, for the first time, the genes related to cell wall and common mechanisms of drought tolerance through the comparison between chemical analysis and gene expression. The data collected contribute to the understanding of the molecular biology of high-yielding CAM species and may help the breeding process of this important semiarid cultureMestradoGenetica Vegetal e MelhoramentoMestre em Genética e Biologia Molecular2016/05396-8 ; 2017/04900-7CAPESFAPES

Molecular epidemiology of sisal bole rot disease suggests a potential phytosanitary crisis in Brazilian production areas

Sisal bole rot disease is the major phytosanitary problem of Agave plantations in Brazil. The disease is caused by a cryptic species of Aspergillus: A. welwitschiae. To date, the only way to diagnose the disease was to observe external symptoms, visible only when the plant is already compromised, or through the isolation and sequencing of the pathogen, which requires cutting the entire plant for bole tissue sampling. We developed a new primer set based on a unique gene region of A. welwitschiae, which can detect the phytopathogenic strains through PCR directly from sisal leaves. Using the new marker to study the main sisal-producing areas in Brazil, we discovered a troublesome situation. The main producing areas of this crop had a pathogen incidence of 78%–88%. The dispersion index indicates a regular spatial pattern for disease distribution, suggesting that the use of contaminated suckers to establish new fields may be the main disease-spreading mechanism. Altogether, the high incidence of the pathogen, the unavailability of clean plants, the unpredictability of disease progression, and the low investment capacity of farmers reveal the vulnerability of this sector to a potential phytosanitary crisis. By correlating the disease symptomatology with soil nutritional traits, we suggest that higher potassium availability might decrease visual symptoms, while phosphorus may have the opposite effect. Also, we observe a potential cultivar effect, suggesting that common sisal may be more susceptible than hybrid cultivars (especially H400). This new molecular tool is a significant advance for understanding the disease, enabling the implementation of a monitoring program and studies that may lead to pathogen control strategies and changes in the Brazilian production model

The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses

Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes