Browsing by Author "Batista, Dora"
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- 4Pipe4 – A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain informationPublication . Pina-Martins, Francisco; Vieira, Bruno M.; Seabra, Sofia G.; Batista, Dora; Paulo, Octávio S.Next-generation sequencing datasets are becoming more frequent, and their use in population studies is becoming widespread. For non-model species, without a reference genome, it is possible from a panel of individuals to identify a set of SNPs that can be used for further population genotyping. However the lack of a reference genome to which the sequenced data could be compared makes the finding of SNPs more troublesome. Additionally when the data sources (strains) are not identified (e.g. in datasets of pooled individuals), the problem of finding reliable variation in these datasets can become much more difficult due to the lack of specialized software for this specific task.
- Biochemical and Molecular Profiling of Wild Edible Mushrooms from Huila, AngolaPublication . Kissanga, Raquel; Liberal, Ângela; Diniz, Inês; Rodrigues, Ana S.B.; Baptista-Ferreira, João L.; Batista, Dora; Ivanov, Marija; Sokovic, Marina; Ferreira, Isabel C.F.R.; Fernandes, ÂngelaThe harvesting, processing, and sale of wild edible mushrooms (WEM) is a relevant economic activity in Angola and a good example of the use of non-wood forest products for food. Although there is deep traditional knowledge about the general properties of WEMs, a huge gap remains in detailed scientific knowledge. Thus, this study aimed to investigate the socio-economic importance of the species sold at local markets in Huila, Angola, from their molecular identification to the assessment of their nutritional, chemical, and bioactive profiles. From the eight WEM morphotypes studied, five were identified based on phenotypical and molecular approaches (four Russula spp., and Amanita loosei). The studied mushrooms proved to be a rich source of carbohydrates, proteins, and ashes, also presenting low amounts of fat. Chemical analyses further revealed mannitol as the main free sugar in all samples, and organic acids, namely, oxalic, quinic, malic, citric, and fumaric acids in low amounts. Additionally, the -tocopherol isoform and monounsaturated fatty acids were predominant. Regarding phenolic acids, protocatechuic, p-hydroxybenzoic, p-coumaric, and cinnamic acids were detected in all mushroom hydroethanolic extracts, being responsible for their antioxidant, antibacterial, and antifungal activities. Our investigation contributes to the identification and knowledge of WEMs as important complementary food sources in Angola, some of which were reported for the first time, promoting their utilization as a basis of nutritional and functional ingredients, as being able to be part of a balanced diet and to be used in new bio-based formulations
- Biochemical and Molecular Profiling of Wild Edible Mushrooms from Huila, AngolaPublication . Kissanga, Raquel; Liberal, Ângela; Diniz, Inês; Rodrigues, Ana S. B.; Baptista-Ferreira, João L.; Batista, Dora; Ivanov, Marija; Soković, Marina; Ferreira, Isabel C. F. R.; Fernandes, Ângela; Barros, Lillian; Catarino, LuísThe harvesting, processing, and sale of wild edible mushrooms (WEM) is a relevant economic activity in Angola and a good example of the use of non-wood forest products for food. Although there is deep traditional knowledge about the general properties of WEMs, a huge gap remains in detailed scientific knowledge. Thus, this study aimed to investigate the socio-economic importance of the species sold at local markets in Huila, Angola, from their molecular identification to the assessment of their nutritional, chemical, and bioactive profiles. From the eight WEM morphotypes studied, five were identified based on phenotypical and molecular approaches (four Russula spp., and Amanita loosei). The studied mushrooms proved to be a rich source of carbohydrates, proteins, and ashes, also presenting low amounts of fat. Chemical analyses further revealed mannitol as the main free sugar in all samples, and organic acids, namely, oxalic, quinic, malic, citric, and fumaric acids in low amounts. Additionally, the α-tocopherol isoform and monounsaturated fatty acids were predominant. Regarding phenolic acids, protocatechuic, p-hydroxybenzoic, p-coumaric, and cinnamic acids were detected in all mushroom hydroethanolic extracts, being responsible for their antioxidant, antibacterial, and antifungal activities. Our investigation contributes to the identification and knowledge of WEMs as important complementary food sources in Angola, some of which were reported for the first time, promoting their utilization as a basis of nutritional and functional ingredients, as being able to be part of a balanced diet and to be used in new bio-based formulations.
- Cashew as a high agricultural commodity in West Africa: insights towards sustainable production in Guinea-BissauPublication . Monteiro, Filipa; Catarino, Luís; Batista, Dora; Indjai, Bucar; Duarte, Maria Cristina; Romeiras, MariaIn Sub-Saharan Africa, the West African region has highly diverse agro-climatic conditions, which grant the potential for a remarkable agricultural production of a great diversity of crops. Since the 1980s, the production volumes of most crops have grown vigorously for both domestic and export markets. Traditional food crops—such as rice, groundnuts and sorghum—have been replaced by cash crops, namely cashew. Among the main cashew production areas, West Africa is the most recent and dynamic in the world, accounting for 45% of the worldwide production of cashew nuts in 2015. In consequence, cashew cultivation has acquired an important position in West African smallholder farming, providing positive economic and social effects. In this paper, we provide an overview of the cashew production system in the West African region, using Guinea-Bissau as a case study. In particular, we present some viewpoints concerning the impact of cashew production and discuss how the strong dependence on a single cash crop can compromise the local livelihoods and food security. Finally, some insights are given towards the sustainable production of cashew in the face of the recent risks affecting the agricultural sector in West Africa
- Characterization of the transcriptional signatures associated with resistance and susceptibility to Hemileia vastatrix in the Kawisari coffee hybridPublication . Azevedo, Herlander; Diniz, Inês; Figueiredo, Andreia; Guedes, Fernanda Alves Freitas; Sebastiana, Mónica Guita; Azinheira, Helena Gil; Barros, Danielle; Castro, Pedro Humberto; Freitas, Sara; Loureiro, Andreia; Muñoz-Pajares, Antonio Jesus; Pereira, Ana Paula; Sottomayor, Mariana; Tavares, Sílvia; Varzea, Vitor; Guerra-Guimarães, Leonor; Batista, Dora; Silva, Maria do CéuCoffee leaf rust (CLR), a disease caused by the biotrophic fungus Hemileia vastatrix (Hv), is the main threat to the worldwide production of Arabica coffee. The gradual breakdown of resistance in coffee varieties in the last years has highlighted the need for novel sources of resistance to CLR. This work aimed to unveil the cellular and molecular resistance profile of the Kawisari hybrid (C. arabica x C. liberica), a genotype used as a resistance donor in Arabica breeding programs in India. This coffee genotype was inoculated with two Hv races that triggered either resistance or susceptibility. Progress of infection was monitored using light microscopy. Simultaneously, we conducted a time-course RNA-seq characterization of the transcriptional responses. The microscopic studies showed that the post-haustorial resistance of Kawisari was associated with the hypersensitive response, accumulation of phenolic-like compounds and haustorium encasement with callose. The transcriptomic analysis suggest the downregulation of host primary metabolism genes at the early onset of infection, followed later by activation of genes functionally associated with multiple plant defense responses, including salicylic acid and jasmonate hormonal signaling. Resistance was also accompanied by the differential regulation of genes associated with phenylpropanoid metabolism and lignin biosynthesis. Our results, further validated by qPCR, provide important new insight into the molecular mechanisms underpinning resistance against CLR in this coffee genotype.
- A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrixPublication . Peri, Tobias; Edwards, Richard; Surana, Priyanka; Mangelson, Hayley; Inácio, Vera; Silva, Maria do Céu; Guerra-Guimarães, Leonor; Park, Obert; Varzea, Vitor; Batista, Dora
- A chromosome-level genome resource for studying virulence mechanisms and evolution of the coffee rust pathogen Hemileia vastatrixPublication . Tobias, Peri A; Edwards, Richard J.; Surana, Priyanka; Mangelson, Hayley; Inácio, Vera; Silva, Maria do Céu; Varzea, Vitor; Park, Robert F.; Batista, DoraRecurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained the sustainable production of Arabica coffee for over 150 years. The ability of H. vastatrix to overcome resistance in coffee cultivars and evolve new races is inexplicable for a pathogen that supposedly only utilizes clonal reproduction. Understanding the evolutionary complexity between H. vastatrix and its only known host, including determining how the pathogen evolves virulence so rapidly is crucial for disease management. Achieving such goals relies on the availability of a comprehensive and high-quality genome reference assembly. To date, two reference genomes have been assembled and published for H. vastatrix that, while useful, remain fragmented and do not represent chromosomal scaffolds. Here, we present a complete scaffolded pseudochromosome-level genome resource for H. vastatrix strain 178a (Hv178a). Our initial assembly revealed an unusually high degree of gene duplication (over 50% BUSCO basidiomycota_odb10 genes). Upon inspection, this was predominantly due to a single scaffold that itself showed 91.9% BUSCO Completeness. Taxonomic analysis of predicted BUSCO genes placed this scaffold in Exobasidiomycetes and suggests it is a distinct genome, which we have named Hv178a associated fungal genome (Hv178a AFG). The high depth of coverage and close association with Hv178a raises the prospect of symbiosis, although we cannot completely rule out contamination at this time. The main Ca. 546 Mbp Hv178a genome was primarily (97.7%) localised to 11 pseudochromosomes (51.5 Mb N50), building the foundation for future advanced studies of genome structure and organization.
- Coffee Leaf Rust Resistance: An OverviewPublication . Guerra-Guimarães, Leonor; Diniz, Inês; Azinheira, Helena Gil; Loureiro, Andreia; Pereira, Ana Paula; Tavares, Sílvia; Batista, Dora; Varzea, Vitor; Silva, Maria do Céu Lavado daCoffee is one of the most important cash crops and beverages. Several diseases caused by fungi, bacteria, and viruses can affect coffee plantations and compromise production. Coffee leaf rust (CLR), caused by the biotrophic fungus Hemileia vastatrix is the top fungal disease, representing a permanent threat to sustainable Arabica coffee production for more than a century. This review provides a comprehensive survey of the most common coffee diseases, their importance, and geographic distribution, with an emphasis on coffee leaf rust. Summing up the progress obtained so far from different research fields on the coffee–H. vastatrix interaction, we revisited the pathogen genetic diversity and population dynamics, and the complex mechanisms underlying plant resistance/immunity. We also highlight how new advanced technologies can provide avenues for a deeper understanding of this pathosystem, which is crucial for devising more reliable and long-term strategies for disease control.
- Disease-Causing Agents in Cashew: A Review in a Tropical Cash CropPublication . Monteiro, Filipa; Romeiras, Maria M.; Barnabé, João; Catarino, Silvia; Batista, Dora; Sebastiana, MónicaDue to the high market value of cashew nut, cashew became a significantly important cash crop in many countries. Originating from Brazil, the plant was introduced into Africa, India, and Southeast Asia and is nowadays found across most of the tropical regions. However, the diseases that threaten and compromise crop production have not yet been comprehensively documented. The aim of this study was to examine the published scientific data on cashew diseases, to identify current knowledge gaps, and to present a review of the most important diseases and pathogens affecting cashew productivity. The most described diseases are caused by fungi genera—mainly Colletotrichum, Lasiodiplodia, and Erysiphe (worldwide); Cryptosporiopsis (East Africa); and recently Fusarium in Tanzania. Other fungal genera (e.g., Septoria, Pilgeriella, and Pestalotia) may correspond to emerging local cashew diseases that have not yet expanded to other geographic regions or for which records are lacking. Gummosis (Lasiodiplodia spp.), which is considered the most prevalent and damaging disease of cashew, has a pantropical distribution. There is large discrepancy concerning the causal agents of cashew diseases that might be explained by the lack of proper species identification through morpho-cultural and molecular approaches. This, in turn, can easily lead to misdiagnoses that have serious negative consequences for the implementation of specific control actions. It is important to establish a standardized identification workflow that will allow a reliable identification of the disease-causing agent and to determine the occurrence and/or expansion of a given pathogen across cashew-producing regions
- Disease-Causing Agents in Cashew: A Review in a Tropical Cash CropPublication . Monteiro, Filipa; Romeiras, Maria M.; Barnabé, João; Catarino, Silvia; Batista, Dora; Sebastiana, MónicaDue to the high market value of cashew nut, cashew became a significantly important cash crop in many countries. Originating from Brazil, the plant was introduced into Africa, India, and Southeast Asia and is nowadays found across most of the tropical regions. However, the diseases that threaten and compromise crop production have not yet been comprehensively documented. The aim of this study was to examine the published scientific data on cashew diseases, to identify current knowledge gaps, and to present a review of the most important diseases and pathogens affecting cashew productivity. The most described diseases are caused by fungi genera—mainly Colletotrichum, Lasiodiplodia, and Erysiphe (worldwide); Cryptosporiopsis (East Africa); and recently Fusarium in Tanzania. Other fungal genera (e.g., Septoria, Pilgeriella, and Pestalotia) may correspond to emerging local cashew diseases that have not yet expanded to other geographic regions or for which records are lacking. Gummosis (Lasiodiplodia spp.), which is considered the most prevalent and damaging disease of cashew, has a pantropical distribution. There is large discrepancy concerning the causal agents of cashew diseases that might be explained by the lack of proper species identification through morpho-cultural and molecular approaches. This, in turn, can easily lead to misdiagnoses that have serious negative consequences for the implementation of specific control actions. It is important to establish a standardized identification workflow that will allow a reliable identification of the disease-causing agent and to determine the occurrence and/or expansion of a given pathogen across cashew-producing regions.