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- 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.
- First Report of Three Lasiodiplodia Species (L. theobromae, L. pseudotheobromae, and L. caatinguensis) Causing Cashew Gummosis in Guinea-Bissau (West Africa)Publication . Monteiro, Filipa; Diniz, Inês; Pena, Ana Rita; Baldé, Aladje; Catarino, Luís; Batista, Dora
- First Report of Dieback Caused by Neofusicoccum batangarum in Cashew in Guinea-BissauPublication . Diniz, Inês; Batista, Dora; Pena, Ana Rita; Rodrigues, Ana S. B.; Reis, Pedro; Baldé, Aladje; Bucar, Indjai; Catarino, Luís; Monteiro, Filipa
- 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.
- Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawaePublication . Cabral, Ana; Azinheira, Helena G.; Talhinhas, Pedro; Batista, Dora; Ramos, Ana Paula; Silva, Maria do Céu; Oliveira, Helena; Várzea, VítorThe genus Colletotrichum has witnessed tremendous variations over the years in the number of species recognized, ranging from 11 to several hundreds. Host-specific fungal species, once the rule, are now the exception, with polyphagous behavior regarded as normal in this genus. The species Colletotrichum kahawae was created to accommodate the pathogens that have the unique ability to infect green developing coffee berries causing the devastating Coffee Berry Disease in Africa, but its close phylogenetic relationship to a polyphagous group of fungi in the C. gloeosporioides species complex led some researchers to regard these pathogens as members of a wider species. In this work we combine pathological, morphological, cytogenomic, biochemical, and molecular data of a comprehensive set of phylogenetically-related isolates to show that the Coffee Berry Disease pathogen forms a separate species, C. kahawae, and also to assign the closely related fungi, previously in C. kahawae subsp. cigarro, to a new species, C. cigarro comb. et stat. nov. This taxonomic clarification provides an opportunity to link phylogeny and functional biology, and additionally enables a much-needed tool for plant pathology and agronomy, associating exclusively C. kahawae to the Coffee Berry Disease pathogen.
- Genome-Wide Signatures of Selection in Colletotrichum kahawae Reveal Candidate Genes Potentially Involved in Pathogenicity and AggressivenessPublication . Vieira, Ana; Silva, Diogo Nuno; Várzea, Vitor; Paulo, Octávio S.; Batista, DoraPlants and their pathogens are engaged in continuous evolutionary battles, with pathogens evolving to circumvent plant defense mechanisms and plants responding through enhanced protection to prevent or mitigate damage induced by pathogen attack. Managed ecosystems are composed of genetically identical populations of crop plants with few changes from year to year. These environments are highly conducive to the emergence and dissemination of pathogens and they exert selective pressure for both qualitative virulence factors responsible for fungal pathogenicity, and quantitative traits linked to pathogen fitness, such as aggressiveness. In this study, we used a comparative genome-wide approach to investigate the genomic basis underlying the pathogenicity and aggressiveness of the fungal coffee pathogen Colletotrichum kahawae infecting green coffee berries. The pathogenicity was investigated by comparing genomic variation between C. kahawae and its non-pathogenic sibling species, while the aggressiveness was studied by a genome-wide association approach with groups of isolates with different phenotypic profiles. High genetic differentiation was observed between C. kahawae and the most closely related species with 5,560 diagnostic SNPs identified, in which a significant enrichment of non-synonymous mutations was detected. Functional annotation of these non-synonymous mutations revealed a significant enrichment mainly in two gene ontology categories, “oxidation–reduction process” and “integral component of membrane.” Finally, the annotation of several genes potentially under-selection revealed that C. kahawae’s pathogenicity may be a complex biological process, in which important biological functions, such as, detoxification and transport, regulation of host and pathogen gene expression, and signaling are involved. On the other hand, the genome-wide association analyses for aggressiveness were able to identify 10 SNPs and 15 SNPs of small effect in single and multi-association analysis, respectively, from which 7 were common, giving in total 18 SNPs potentially associated. The annotation of these genomic regions allowed the identification of four candidate genes encoding F-box domain-containing, nitrosoguanidine resistance, Fungal specific transcription factor domain-containing and C6 transcription factor that could be associated with aggressiveness. This study shed light, for the first time, on the genetic mechanisms of C. kahawae host specialization.
- Using gradient Forest to predict climate response and adaptation in Cork oakPublication . Vanhove, Mathieu; Pina Martins, Francisco; Coelho, Ana Cristina; Branquinho, Cristina; Costa, Augusta; Batista, Dora; Príncipe, Adriana; Sousa, Paulo; Henriques, André; Marques, Isabel; Belkadi, Bouchra; Knowles, L. Lacey; Paulo, Octávio S.Climate change is impacting locally adapted species such as the keystone tree species cork oak (Quercus suber L.). Quantifying the importance of environmental variables in explaining the species distribution can help build resilient populations in restoration projects and design forest management strategies. Using landscape genomics, we investigated the population structure and ecological adaptation of this tree species across the Mediterranean Basin. We applied genotyping by sequencing and derived 2,583 single nucleotide polymorphism markers genotyped from 81 individuals across 17 sites in the studied region. We implemented an approach based on the nearest neighbour haplotype 'coancestry' and uncovered a weak population structure along an east-west climatic gradient across the Mediterranean region. We identified genomic regions potentially involved in local adaptation and predicted differences in the genetic composition across the landscape under current and future climates. Variants associated with temperature and precipitation variables were detected, and we applied a nonlinear multivariate association method, gradient forest, to project these gene-environment relationships across space. The model allowed the identification of geographic areas within the western Mediterranean region most sensitive to climate change: south-western Iberia and northern Morocco. Our findings provide a preliminary assessment towards a potential management strategy for the conservation of cork oak in the Mediterranean Basin.
- 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.