Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In ...this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree. Each of the resulting data-specific substitution models was used to calculate the maximum likelihood score of the simulation tree and simulated data that was used to calculate the model, and compared with the maximum likelihood scores of the known simulation model and simulation tree on the same simulated data. Additionally, the commonly-used empirical models, cpREV and WAG, were assessed similarly. Data-specific models performed better than the empirical models, which under-fitted the simulated alignments, had the highest difference to the simulation model maximum-likelihood score, clustered further from the simulation model in principal component analysis ordination, and inferred less accurate trees. Data-specific models and the simulation model shared statistically indistinguishable maximum-likelihood scores, indicating that the five methods were reasonably accurate at estimating substitution models by this measure. Nevertheless, tree statistics showed differences between optimal maximum likelihood trees. Unlike other model estimating methods, trees inferred using data-specific models generated with IQ-TREE and P4 (maximum likelihood) were not significantly different from the trees derived from the simulation model in each analysis, indicating that these two methods alone were the most accurate at estimating data-specific models. To show the benefits of using data-specific protein models several published data sets were reanalysed using IQ-TREE-estimated models. These newly estimated models were a better fit to the data than the empirical models that were used by the original authors, often inferred longer trees, and resulted in different tree topologies in more than half of the re-analysed data sets. The results of this study show that software availability and high computation burden are not limitations to generating better-fitting data-specific amino-acid substitution models for phylogenetic analyses.
The domesticated grapevine spread along the Mediterranean basin from the primary Near East domestication area, where the greatest genetic diversity is found in its ancestor, the wild vine ...populations. Portuguese wild populations are on the southwestern fringe of the distribution of the
L. ssp
in Europe. During the last Glacial Period they became isolated from the previous continuum that had been the territory of wild vine populations. Archaeological remains of domesticated
grapevines in Portugal date back from 795 Before Common Era (BCE) in the lower Tagus river basin. In this work, 258 Portuguese
varieties and
plants were characterized using 261 single nucleotide polymorphism (SNP) markers. The study of the genetic diversity of this local germplasm, its population structure and kinship, all framed in their historical and geographical backgrounds, revealed a complex network of first-degree relationships, where only Iberian varieties are involved. Some Iberian genotypes, like Alfrocheiro (Bruñal, in Spain), Sarigo (Cayetana Blanca), Mourisco Branco (Hebén), Amaral (Caiño Bravo), and Marufo (Moravia Dulce) are ancestors of a considerable fraction of all the autochthonous analyzed varieties. A part of the diversity developed was mostly local in some cases as shown by the closeness of several varieties (Vinhos Verdes) to the wild cluster in different analyses. Besides, several evidences of introgression of domesticated germplasm into wild vines was found, substantiating the high risk of genetic contamination of the
subspecies. All these findings together to the known matching between the wild maternal lineage of the Iberian Peninsula and an important number of Portuguese grapevine varieties (chlorotype A), point out that some of these varieties derive, directly or indirectly, from originally local wild populations, supporting the possible occurrence of secondary events of local domestication, or, at least, of an introgression process of wild into cultivated grapevines.
Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear ...and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.
•Label-free DNA-based biosensor applied to authenticity.•Varietal identification in different matrices (leaf, must and wine samples)•PCR-free detection.
The diversity found among the Vitis vinifera ...L. species allows the production of wines with very different characteristics. The development of platforms suitable for food composition analysis is currently an emerging area. Among these, DNA biosensors have been developed for a wide variety of applications, ranging from food safety to authenticity. The main aim of this work was to study the detection capacity of the DNA-based optical biosensor using different V. vinifera matrices (leaf, must and wine). Genomic DNA was extracted from leaf, must and wine of three V. vinifera varieties and was tested on the long-period grating (LPG) DNA-based biosensor developed within our group. The biosensor was able to distinguish the varieties even using DNA extracted from complex matrices, revealing its potential to be applied in wine authenticity.
•Combinations of Touriga Nacional scions with rootstock 110R were examined.•Gallic acid, sinapic acid and catechin are potential markers of the graft success.•Lower levels of these compounds at graft ...union seem crucial to a successful graft.
The lack of graft success is a problem that causes economic loss to nursery growers and wine growers, especially because it is often expressed when the vineyard is already established. Grafting is a complex phenomenon, involving anatomical, physiological, biochemical and molecular interactions between the scion and the rootstock. For this reason, the lack of graft success is a complex problem to study. However, it is believed that through a joint analysis of the different mechanisms of graft success, one can advance more quickly in the knowledge of this phenomenon. Despite the scarce information available on the role of phenolic compounds in Vitis grafts, an analytical method was developed and validated for phenolic compounds quantification in vine graft tissues reviling some chemical markers for the cv. ‘Syrah’ with 110R and SO4 rootstocks. This work aims to determine, among phenolic acids and two flavanols, the chemical markers of graft compatibility between scions from two clones of cv. ‘Touriga Nacional’ (TN 21 and TN 112) and the rootstock 110R. For this purpose, extracts of grafting tissues were prepared at three different locations (above, below and at the grafting union), and were analyzed in three different stages of the grafting cycle. From all sections analyzed, the graft union tissue is the one to discriminate better the two combinations. Gallic acid, catechin and sinapic acid were found in higher amount at graft union in the less compatible combination later in graft development. Furthermore, the chlorogenic acid had a higher content in the more compatible combination at the early stage when compared to the less compatible graft.
A riqueza do património genético vitícola existente em Portugal leva a considerá-lo como um dos países da Europa com maior densidade de castas autóctones, embora cerca de 85 % dessas castas só ocupem ...aproximadamente 10 % da área total de vinha. Apesar da preservação destas castas muito pouco cultivadas, que se designa de castas minoritárias, estar praticamente garantida em coleções ampelográficas, torna-se necessário a sua valorização e difusão pelo sector vitivinícola. Este trabalho constitui uma primeira abordagem para a caracterização físico-química e sensorial de vinhos produzidos, em duas vindimas, a partir de quatro castas brancas e de quatro castas tintas. No caso dos vinhos das castas tintas, a caracterização físico-química incluiu também o estudo do perfil de antocianinas, bem como a determinação dos teores de antocianas totais e de polifenóis totais. Os resultados obtidos mostraram uma diferenciação dos vinhos das duas vindimas, verificando-se também, ao nível organolético, apreciações globais superiores para os vinhos brancos das castas ‘Galego Dourado’ e ‘Códega do Larinho’ e para os vinhos tintos das castas ‘Malvasia Preta’ e ‘Cornifesto’. Verificou-se, ainda, que os vinhos que apresentaram teores mais elevados de antocianas foram os das castas ‘Cornifesto’ e ‘Malvasia Preta’, sendo os vinhos das castas ‘Tinta Negra’ e ‘Malvasia Preta’ os que evidenciaram ser mais ricos em polifenóis totais. Um resultado importante de notar é que os teores de polifenóis totais dos vinhos da mesma casta mostraram ser idênticos ou muito similares, nas duas vindimas. Contudo, considera-se que sejam necessários mais estudos para uma caracterização mais robusta dos vinhos destas castas.
The richness of the viticultural genetic heritage in Portugal leads to consider it as one of the European countries with the highest density of native varieties, although about 85 % of these varieties only occupy approximately 10 % of the total vineyard area. Despite the preservation of these very little cultivated varieties, which are called minority varieties, being practically guaranteed in ampelographic collections, their valorization and dissemination by the wine sector is necessary. This work was focused on preliminary studies of the physicochemical, anthocyanic, and sensory characterisation of wines produced in two harvests, from four white and four red grapevine varieties. For the wines of the red grapevine varieties, the physicochemical characterisation also included the study of the anthocyanins profile, as well as the determination of total anthocyanins and total polyphenols contents. The results obtained showed differentiation of wines from the two vintages. In addition, higher sensory global scores for the white wines from ‘Galego Dourado’ and ‘Códega do Larinho’ varieties and for the red wines from ‘Malvasia Preta’ and ‘Cornifesto’ varieties were observed. It was also found that the wines from ‘Cornifesto’ and ‘Malvasia Preta’ varieties presented the highest levels of anthocyanins, and the wines from ‘Tinta Negra’ and ‘Malvasia Preta’ varieties were richer in total polyphenols. It should be highlighted that the total polyphenols content of the wines from the same variety were identical or very similar in the two harvests. However, further studies are needed for a more robust characterisation of the wines from these grapevine varieties.
This work focused on the characterization of the volatile compounds and sensory profile of white wines produced from three minority grapevine varieties of Portugal namely ‘Malvasia’ (Colares), ...‘Verdelho’ and ‘Galego Dourado’. The characterization took place using sensory and gas chromatography analysis. Furthermore, the data obtained were analysed through the use of multivariate analysis, which made it possible to evaluate the similarities and dissimilarities between the varieties. The results obtained show a differentiation of the wines produced from each grapevine variety but above all a differentiation of the two vintages was verified. The results obtained, both from a sensory and a chemical point of view, show an interesting oenological potential of these varieties, but still require further studies, in order to evaluate the influence of climatic effects on the profile of volatile compounds and also on the sensory profile.
Este trabalho centrou-se na caracterização sensorial e da composição volátil de vinhos brancos produzidos a partir de três castas minoritárias, designadamente ‘Malvasia’ (Colares), ‘Verdelho’ e ‘Galego Dourado’. A caracterização ocorreu por meio de análise sensorial e por cromatografia gás líquido de alta resolução, e os resultados obtidos foram analisados através de análise multivariada, que permitiu avaliar as semelhanças e as diferenças entre as castas. Os resultados obtidos mostram uma diferenciação dos vinhos produzidos a partir de cada casta, mas acima de tudo uma diferenciação das duas colheitas. Os resultados obtidos, tanto do ponto de vista sensorial como na composição química, mostram um potencial enológico interessante destas castas, embora sejam necessários mais estudos para avaliar a influência dos efeitos climáticos no perfil de compostos voláteis e também no perfil sensorial.
This work describes the first molecular characterization of grapevine virus B (GVB) in Portuguese grapevine cultivars. During a routine screening of 44 accessions in the National Collection of ...Grapevine Varieties (CAN PRT051), 17 were found infected with GVB in DAS-ELISA assays with commercial antibodies. However, only six of the corresponding isolates were successfully amplified using primer pairs described in the literature. The sequence variants (ORF4-3’UTR, 1147 nt) retrieved from these isolates segregated into two phylogenetic groups, which included sequences from complete genomes available in GenBank. The highly discrepant results obtained using serological and RT-PCR-based diagnostic tools led to the design of a primer pair for detection of GVB, which allowed the amplification of a 606-bp GVB-specific fragment from all DAS-ELISA-positive isolates and also revealed the existence of false negatives in the serological testing.
Since the last decade of the last century, it is known that many old grapevine varieties are descendants of other varieties through natural crossing. Portugal has an important program for the ...conservation of representative samples of intra-varietal variability of all autochthonous varieties, managed by the Portuguese Association for Grapevine Diversity (PORVID), which makes looking for genotypes with dubious identification an important activity from a perspective of its valorisation. This communication presents the results of the molecular analysis of 5,000 samples (accessions) from the PORVID’s collection, using nine microsatellite
loci
currently recommended by the International Organization of Vine and Wine (OIV) for genetic grapevine identification. The results obtained confirmed the molecular identity of 4,220 samples corresponding to 214 varieties present in the official list of Portuguese varieties. In 780 samples, 95 profiles with a plural number of accessions revealed not to be listed in the Vitis International Variety Catalogue (VIVC) database, corresponding to possible varieties either descendent from natural crossing from at least one known parental variety, or from undetermined origin. Furthermore, the need for a comprehensive strategy aimed at uncovering other hidden varieties is discussed to prevent their imminent loss, deepen understanding of their origin, and add economic value and sustainability to the vine and wine sector.
The wine sector is a billion euro business and therefore subjected to multiple attempts of fraudulent practices. This requires the development of rapid and reliable methods to detect such situations. ...Several methodologies have been developed based on the chemical profiles of the wines, but they are limited due to the environmental conditions that cannot be controlled. The use of DNA-based detection systems are an emergent research field that have been extended to a wide variety of food prod- ucts and are still the most reliable methods for varietal identification. However these methods are not suitable for geographical determination. Soil related fingerprints have a primary role considering that there is a relationship between the elemental compo- sition of wine and the composition of the provenance soil. WineBioCode is a project aiming to define the best strategy for wine authenticity based on a multidisciplinary approach. Two DNA-based strategies have been developed based on Real-time PCR and a label free optical biosensor platform. Both platforms enabled successful identification of specific DNA-targets when applied to Vitis vinifera L., and can be applied throughout the grape-wine chain. The methods are complementary and can be used in dif- ferent situations, according to the requirements. The geographical evaluation has been assessed by the strontium 87Sr/86Sr isotope ratio determination involving soil evaluation in the vineyards followed by its assay in the wine samples. The results are being integrated in order to establish the best procedure to be undertaken for wine fingerprinting, including varietal composition and geographical origin, therefore fulfilling the requirements of the geographical denominations in wine certification.
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