2021
Autores
Garg, M; Couturier, DL; Nsengimana, J; Fonseca, NA; Wongchenko, M; Yan, YB; Lauss, M; Jonsson, GB; Newton Bishop, J; Parkinson, C; Middleton, MR; Bishop, DT; McDonald, S; Stefanos, N; Tadross, J; Vergara, IA; Lo, S; Newell, F; Wilmott, JS; Thompson, JF; Long, GV; Scolyer, RA; Corrie, P; Adams, DJ; Brazma, A; Rabbie, R;
Publicação
NATURE COMMUNICATIONS
Abstract
Adjuvant systemic therapies are now routinely used following resection of stage III melanoma, however accurate prognostic information is needed to better stratify patients. We use differential expression analyses of primary tumours from 204 RNA-sequenced melanomas within a large adjuvant trial, identifying a 121 metastasis-associated gene signature. This signature strongly associated with progression-free (HR=1.63, p=5.24 x 10(-5)) and overall survival (HR=1.61, p=1.67 x 10(-4)), was validated in 175 regional lymph nodes metastasis as well as two externally ascertained datasets. The machine learning classification models trained using the signature genes performed significantly better in predicting metastases than models trained with clinical covariates (p(AUROC) = 7.03 x 10(-4)), or published prognostic signatures (p(AUROC) < 0.05). The signature score negatively correlated with measures of immune cell infiltration (
2021
Autores
Fernandes, C; Martins, L; Teixeira, M; Blom, J; Pothier, JE; Fonseca, NA; Tavares, F;
Publicação
MICROORGANISMS
Abstract
The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424(T), and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.
2021
Autores
Teixeira, M; Fernandes, C; Chaves, C; Pinto, J; Tavares, F; Fonseca, NA;
Publicação
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
Abstract
We report the genome sequence of Xanthomonas arboricola pv. juglandis strain CPBF 427, which was isolated from early-season buds of a diseased walnut tree, suggesting overwinter potential. This study provides a consistent genomic reference for this pathovar and may contribute to addressing the overwinter survival of these walnut pathogens.
2021
Autores
Martins, FM; Fonseca, NA; Egeter, B; Pinto, J; Assunção, T; Chaves, C; Sousa, P; Jesus, J; Beja, P;
Publicação
ARPHA Conference Abstracts
Abstract
2021
Autores
Oliveira, D; Chaves, C; Pinto, J; Pauperio, J; Fonseca, N; Beja, P; Ferreira, S;
Publicação
ZOOKEYS
Abstract
The orders Neuroptera and Raphidioptera include the species of insects known as lacewings and snake flies, respectively. In Portugal, these groups account for over 100 species, some of which are very difficult to identify by morphological analysis. This work is the first to sample and DNA sequence lacewings and snakeflies of Portugal. A reference collection was built with captured specimens that were identified morphologically. DNA barcode sequences of 658 bp were obtained from 243 specimens of 54 species. The results showed that most species can be successfully identified through DNA barcoding, with the exception of seven species of Chrysopidae (Neuroptera). Additionally, the first published distribution data are presented for Portugal for the neuropterans Gymnocnemia variegata (Schneider, 1845) and Myrmecaelurus (Myrmecaelurus) trigrammus (Pallas, 1771).
2021
Autores
Andrade, P; Cataldo, D; Fontaine, R; Rodrigues, TM; Queiros, J; Neves, V; Fonseca, A; Carneiro, M; Goncalves, D;
Publicação
ZOOLOGICA SCRIPTA
Abstract
The study of phenotypic evolution in island birds following colonization is a classic topic in island biogeography. However, few studies explicitly test for the role of selection in shaping trait evolution in these taxa. Here, we studied the Azores woodpigeon (Columba palumbus azorica) to investigate differences between island and mainland populations, between females and males, and interactions between geographical origin and sex, by using spectrophotometry to quantify plumage colour and linear measurements to examine external and skeletal morphology. We further tested if selection explains the observed patterns by comparing phenotypic differentiation to genome-wide neutral differentiation. Our findings are consistent with several predictions of morphological evolution in island birds, namely differences in bill, flight and leg morphology and coloration differences between island and mainland birds. Interestingly, some plumage and morphological traits that differ between females and males respond differently according to geographical origin. Sexual dimorphism in colour saturation is more pronounced in the mainland, but this is driven by selection on female plumage coloration. Differences in flight morphology between females and males are also more pronounced in the mainland, possibly to accommodate contrasting pressures between migration and flight displays. Overall, our results suggest that phenotypic differentiation between mainland and island populations leading to divergent sexual dimorphism patterns can arise from selection acting on both females and males on traits that are likely under the influence of natural and sexual selection.
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