How sex led to wine: Genomic and post-transcriptional differences associated to sex in Vitis vinifera sylvestris

Doutoramento em Biologia / Instituto Superior de Agronomia. Universidade de LisboaThe interest in the study of Vitis is closely associated with the importance of wine and the economic impact of this species. Within this duality, two subspecies gain relevant attention: Vitis vinifera vinifera (vinifera) is the subspecies most used in viticulture, contains essentially hermaphroditic plants and results from a long process of domestication; and Vitis vinifera sylvestris (sylvestris), an essentially dioecious subspecies (with only a few hermaphroditic individuals per population), which has not been domesticated. The comparative study of both subspecies is important, as it increases the general knowledge in relation to Vitis genus, namely, to clarify which genes are associated with its sexual determination. In order to deepen the knowledge regarding the sexual determination of Vitis, studies were performed in the areas of transcritomics, genomics and bioinformatics. One of the main conclusions of this work is the possible involvement of posttranscriptional regulators, such as micro RNAs, and RNA editing in nuclear transcripts, in a systematic and constant manner. The extensive validation of these results showed an association between these posttranscriptional players and the flower developmental stage, as well as the flower type (male or female), with consistent results in consecutive years analysed. It should also be emphasized that some of the processes studied, namely the RNA editing, can be transversal to other species and organs and so, the results found here can enhance knowledge in other systemsN/

A qualidade da cortiça e a sua relação com a expressão génica no felogénio de Quercus suber

Mestrado em Biologia Funcional - Instituto Superior de AgronomiaThe cork oak (Quercus suber) is an important species in Portugal, mainly due to the economic value of the cork it produces. Cork is produced by phellogen. In cork oaks, this meristematic tissue has few discontinuities and has a peak of activity in the spring. Every phellogen discontinuity will degenerate into cork defects, being pores and nail inclusions the most common and relevant to cork’s industry. Acknowledging that epigenetic processes are critical for plant development, their study in phellogen is essential. For this purpose, DNA methyltransferases were studied, by means of isolating sequences of each of its classes (MET, DRM and CMT) and one protein associated to MET1 (DMAP1). The analysis of its gene expression was performed in trees’ phellogens of both good and bad cork quality producers, after the evaluation of their quality by image analysis methods. Studies performed showed de novo methylation as the most significant in this tissue and a correlation was established between the QsMET2 and QsDMAP1 genes expressions and the defects’ coefficient measured, which revealed that these genes are important for the cork’s quality processe

Flower development and sex specification in wild grapevine

Background: Wild plants of Vitis closely related to the cultivated grapevine (V. v. vinifera) are believed to have been first domesticated 10,000 years BC around the Caspian Sea. V. v. vinifera is hermaphrodite whereas V. v. sylvestris is a dioecious species. Male flowers show a reduced pistil without style or stigma and female flowers present reflexed stamens with infertile pollen. V. vinifera produce perfect flowers with all functional structures. The mechanism for flower sex determination and specification in grapevine is still unknown.Results: To understand which genes are involved during the establishment of male, female and complete flowers, we analysed and compared the transcription profiles of four developmental stages of the three genders. We showed that sex determination is a late event during flower development and that the expression of genes from the ABCDE model is not directly correlated with the establishment of sexual dimorphism. We propose a temporal comprehensive model in which two mutations in two linked genes could be players in sex determination and indirectly establish the Vitis domestication process. Additionally, we also found clusters of genes differentially expressed between genders and between developmental stages that suggest a role involved in sex differentiation. Also, the detection of differentially transcribed regions that extended existing gene models (intergenic regions) between sexes suggests that they may account for some of the variation between the subspecies.Conclusions: There is no evidence of differences of expression levels in genes from the ABCDE model that could explain the shift from hermaphroditism to dioecy. We propose that sex specification occurs after floral organ identity has been established and therefore, sex determination genes might be having an effect downstream of the ABCDE model genes. For the first time a full transcriptomic analysis was performed in different flower developmental stages in the same individual. Our experimental approach enabled us to create a comprehensive catalogue of transcribed genes across developmental stages and genders that will contribute for future work in sex determination in seed plants.This work was supported by the funded project PTDC/AGR-GPL/119298/2010 from Fundacao para a Ciencia e Tecnologia and MRocheta, JLCoito and JCunha by the fellowships FRH/BPD/64905/2009, SFRH/BD/85824/2012 and SFRH/BPD/74895/2010, respectively. We are also grateful to Eng. Eiras- Dias, curator from Portuguese Ampelographic Collection (property of Instituto Nacional de Investigacao Agraria e Veterinaria, Dois Portos), for the collaboration in this work allowing the access to the Vitis collection

Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae

Epigenetic regulators are proteins involved in controlling gene expression. Informationabout the epigenetic regulators within the Fagaceae, a relevant family of trees andshrubs of the northern hemisphere ecosystems, is scarce. With the intent to character-ize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases(DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation(HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) inFagus,Quercus,andCastaneagenera. Blast searches were performed in the availablegenomes, and freely available RNA-seq data were used to de novo assemble transcrip-tomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs,32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them havethe putative characteristic domains found in these protein families, which suggeststheir conserved function. Additionally, to elucidate the evolutionary history of thesegenes within Fagaceae, paralogs were identified, and phylogenetic analyses were per-formed with DNA and histone modifiers. We detected duplication events in all speciesanalyzed with higher frequency inQuercusandCastaneaand discuss the evidence oftransposable elements adjacent to paralogs and their involvement in gene duplication.The knowledge gathered from this work is a steppingstone to upcoming studies con-cerning epigenetic regulation in this economically important family of Fagaceaeinfo:eu-repo/semantics/publishedVersio

The dynamics of flower development in Castanea sativa Mill

The sweet chestnut tree (Castanea sativa Mill.) is one of the most significant Mediterranean tree species, being an important natural resource for the wood and fruit industries. It is a monoecious species, presenting unisexual male catkins and bisexual catkins, with the latter having distinct male and female flowers. Despite the importance of the sweet chestnut tree, little is known regarding the molecular mechanisms involved in the determination of sexual organ identity. Thus, the study of how the different flowers of C. sativa develop is fundamental to understand the reproductive success of this species and the impact of flower phenology on its productivity. In this study, a C. sativa de novo transcriptome was assembled and the homologous genes to those of the ABCDE model for floral organ identity were identified. Expression analysis showed that the C. sativa B- and C-class genes are differentially expressed in the male flowers and female flowers. Yeast two-hybrid analysis also suggested that changes in the canonical ABCDE protein–protein interactions may underlie the mechanisms necessary to the development of separate male and female flowers, as reported for the monoecious Fagaceae Quercus suber. The results here depicted constitute a step towards the understanding of the molecular mechanisms involved in unisexual flower development in C. sativa, also suggesting that the ABCDE model for flower organ identity may be molecularly conserved in the predominantly monoecious Fagaceae family.This work was funded by FCT/COMPETE/FEDER with the project grant POCI-01-0145- FEDER-027980/PTDC/ASP-SIL/27980/2017—“FlowerCAST—Characterisation of genetic and environmental determinants involved in reproductive development of Castanea sativa”. A.T.A. and S.A. were supported by FCT with PhD grants (ref. SFRH/BD/136834/2018 and SFRH/BD/146660/2019, respectively)

Identification of Eschweilenol C in derivative of Terminalia fagifolia Mart. and green synthesis of bioactive and biocompatible silver nanoparticles

A green synthetic route was developed to prepare silver nanoparticles (AgNPs) in aqueous solution for biological applications. Eschweilenol C, a compound derivative ellagic acid was identified as the main constituent of the aqueous fraction of the ethanolic extract of Terminalia fagifolia Mart. by NMR analysis. In the green synthesis, the ethanolic extract of T. fagifolia and its aqueous fraction were used to promote silver reduction and nanoparticle stabilization. The synthesized AgNPs presented a spherical or polygonal morphology shape by TEM analysis and AgNPs showed high levels of antioxidant and considerable antibacterial and antifungal activities. Synthesized nanoparticles presented significant antioxidant activity by sequestration of DPPH and ABTS radicals, in addition to iron reduction (FRAP assay) and measurement of antioxidant capacity in ORAC units, in addition, AgNP synthesized with the aqueous fraction also demonstrated antioxidant potential in microglial cells. Gram-positive and Gram-negative bacteria were susceptible to growth inhibition by the nanoparticles, among which the AgNPs formed by the ethanolic extract was the most effective. The data obtained by AFM images suggested that AgNPs could lead to the lysis of bacteria and subsequent death. The antifungal assays showed high efficiency against yeasts and dermatophytes. This work represents the first description of antifungal activity by AgNPs against Fonsecaea pedrosoi, the etiologic agent of chromoblastomycosis. In relation to biocompatibility, the AgNPs induced lower haemolysis than AgNO3.We thank Herbert Kogler and Reinhard Wimmer for the identification of Eschweilenol C. The NMR laboratory at Aalborg University is supported by the Obel Family, SparNord and Carlsberg foundations.The authors are grateful to Carla Eiras (LIMAV/CT/UFPI) and to FCT and EU for financial support through project UID/QUI/50006/2013– POCI-01-0145-FEDER-007265 from COMPETE and projectNORTE-01-0145-FEDER-000011 from COMPETE. Thanks to Andreia Pinto for help with the TEM measurements at Instituto de Medicina Molecular (IMM). This work was supported by the Histology and Comparative Pathology Laboratory of the IMMinfo:eu-repo/semantics/publishedVersio

SARS-CoV-2 introductions and early dynamics of the epidemic in Portugal

Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARSCoV-2 introductions and early dissemination in Portugal. Results We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.We gratefully acknowledge to Sara Hill and Nuno Faria (University of Oxford) and Joshua Quick and Nick Loman (University of Birmingham) for kindly providing us with the initial sets of Artic Network primers for NGS; Rafael Mamede (MRamirez team, IMM, Lisbon) for developing and sharing a bioinformatics script for sequence curation (https://github.com/rfm-targa/BioinfUtils); Philippe Lemey (KU Leuven) for providing guidance on the implementation of the phylodynamic models; Joshua L. Cherry (National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health) for providing guidance with the subsampling strategies; and all authors, originating and submitting laboratories who have contributed genome data on GISAID (https://www.gisaid.org/) on which part of this research is based. The opinions expressed in this article are those of the authors and do not reflect the view of the National Institutes of Health, the Department of Health and Human Services, or the United States government. This study is co-funded by Fundação para a Ciência e Tecnologia and Agência de Investigação Clínica e Inovação Biomédica (234_596874175) on behalf of the Research 4 COVID-19 call. Some infrastructural resources used in this study come from the GenomePT project (POCI-01-0145-FEDER-022184), supported by COMPETE 2020 - Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT).info:eu-repo/semantics/publishedVersio

Mapping and assessment of forest ecosystems and their services - Applications and guidance for decision making in the framework of MAES

The aim of this report is to illustrate by means of a series of case studies the implementation of mapping and assessment of forest ecosystem services in different contexts and geographical levels. Methodological aspects, data issues, approaches, limitations, gaps and further steps for improvement are analysed for providing good practices and decision making guidance. The EU initiative on Mapping and Assessment of the state of Ecosystems and their Services (MAES), with the support of all Member States, contributes to improve the knowledge on ecosystem services. MAES is one of the building-block initiatives supporting the EU Biodiversity Strategy to 2020.JRC.H.3-Forest Resources and Climat

MAMMALS IN PORTUGAL : A data set of terrestrial, volant, and marine mammal occurrences in P ortugal

Mammals are threatened worldwide, with 26% of all species being includedin the IUCN threatened categories. This overall pattern is primarily associatedwith habitat loss or degradation, and human persecution for terrestrial mam-mals, and pollution, open net fishing, climate change, and prey depletion formarine mammals. Mammals play a key role in maintaining ecosystems func-tionality and resilience, and therefore information on their distribution is cru-cial to delineate and support conservation actions. MAMMALS INPORTUGAL is a publicly available data set compiling unpublishedgeoreferenced occurrence records of 92 terrestrial, volant, and marine mam-mals in mainland Portugal and archipelagos of the Azores and Madeira thatincludes 105,026 data entries between 1873 and 2021 (72% of the data occur-ring in 2000 and 2021). The methods used to collect the data were: live obser-vations/captures (43%), sign surveys (35%), camera trapping (16%),bioacoustics surveys (4%) and radiotracking, and inquiries that represent lessthan 1% of the records. The data set includes 13 types of records: (1) burrowsjsoil moundsjtunnel, (2) capture, (3) colony, (4) dead animaljhairjskullsjjaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8),observation in shelters, (9) photo trappingjvideo, (10) predators dietjpelletsjpine cones/nuts, (11) scatjtrackjditch, (12) telemetry and (13) vocalizationjecholocation. The spatial uncertainty of most records ranges between 0 and100 m (76%). Rodentia (n=31,573) has the highest number of records followedby Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496),Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data setincludes records of species classified by the IUCN as threatened(e.g.,Oryctolagus cuniculus[n=12,159],Monachus monachus[n=1,512],andLynx pardinus[n=197]). We believe that this data set may stimulate thepublication of other European countries data sets that would certainly contrib-ute to ecology and conservation-related research, and therefore assisting onthe development of more accurate and tailored conservation managementstrategies for each species. There are no copyright restrictions; please cite thisdata paper when the data are used in publications.info:eu-repo/semantics/publishedVersio