2017
Authors
Fonseca, NA; He, Y; Greger, L; Brazma, A; Zhang, Z; - PCAWG-3,;
Publication
Abstract
2015
Authors
Aguiar, B; Vieira, J; Cunha, AE; Fonseca, NA; Iezzoni, A; van Nocker, S; Vieira, CP;
Publication
PLOS ONE
Abstract
S-RNase-based gametophytic self-incompatibility (GSI) has evolved once before the split of the Asteridae and Rosidae. This conclusion is based on the phylogenetic history of the S-RNase that determines pistil specificity. In Rosaceae, molecular characterizations of Prunus species, and species from the tribe Pyreae (i.e., Malus, Pyrus, Sorbus) revealed different numbers of genes determining S-pollen specificity. In Prunus only one pistil and pollen gene determine GSI, while in Pyreae there is one pistil but multiple pollen genes, implying different specificity recognition mechanisms. It is thus conceivable that within Rosaceae the genes involved in GSI in the two lineages are not orthologous but possibly paralogous. To address this hypothesis we characterised the S-RNase lineage and S-pollen lineage genes present in the genomes of five Rosaceae species from three genera: M. x domestica (apple, self-incompatible (SI); tribe Pyreae), P. persica (peach, self-compatible (SC); Amygdaleae), P. mume (mei, SI; Amygdaleae), Fragaria vesca (strawberry, SC; Potentilleae), and F. nipponica (mori-ichigo, SI; Potentilleae). Phylogenetic analyses revealed that the Malus and Prunus S-RNase and S-pollen genes belong to distinct gene lineages, and that only Prunus S-RNase and SFB-lineage genes are present in Fragaria. Thus, S-RNase based GSI system of Malus evolved independently from the ancestral system of Rosaceae. Using expression patterns based on RNA-seq data, the ancestral S-RNase lineage gene is inferred to be expressed in pistils only, while the ancestral S-pollen lineage gene is inferred to be expressed in tissues other than pollen.
2022
Authors
Zhang, Y; Chen, F; Fonseca, NA; He, Y; Fujita, M; Nakagawa, H; Zhang, Z; Brazma, A; Amin, SB; Awadalla, P; Bailey, PJ; Brazma, A; Brooks, AN; Calabrese, C; Chateigner, A; Cortés-Ciriano, I; Craft, B; Craft, D; Creighton, CJ; Davidson, NR; Demircioglu, D; Erkek, S; Fonseca, NA; Frenkel-Morgenstern, M; Goldman, MJ; Greger, L; Göke, J; He, Y; Hoadley, KA; Hou, Y; Huska, MR; Kahles, A; Khurana, E; Kilpinen, H; Korbel, JO; Lamaze, FC; Lehmann, K; Li, C; Li, S; Li, X; Li, X; Liu, D; Liu, F; Liu, X; Marin, MG; Markowski, J; Meyerson, M; Nandi, T; Nielsen, MM; Ojesina, AI; Ouellette, BFF; Pan-Hammarström, Q; Park, PJ; Pedamallu, CS; Pedersen, JS; Perry, MD; Rätsch, G; Schwarz, RF; Shiraishi, Y; Siebert, R; Soulette, CM; Stark, SG; Stegle, O; Su, H; Tan, P; Teh, BT; Urban, L; Wang, J; Waszak, SM; Wu, K; Xiang, Q; Xiong, H; Yakneen, S; Yang, H; Ye, C; Yung, CK; Zhang, F; Zhang, J; Zhang, X; Zhang, Z; Zheng, L; Zhu, J; Zhu, S; Akdemir, KC; Alvarez, EG; Baez-Ortega, A; Beroukhim, R; Boutros, PC; Bowtell, DDL; Brors, B; Burns, KH; Campbell, PJ; Chan, K; Chen, K; Cortés-Ciriano, I; Dueso-Barroso, A; Dunford, AJ; Edwards, PA; Estivill, X; Etemadmoghadam, D; Feuerbach, L; Fink, JL; Frenkel-Morgenstern, M; Garsed, DW; Gerstein, M; Gordenin, DA; Haan, D; Haber, JE; Hess, JM; Hutter, B; Imielinski, M; Jones, DTW; Ju, YS; Kazanov, MD; Klimczak, LJ; Koh, Y; Korbel, JO; Kumar, K; Lee, EA; Lee, JJ; Li, Y; Lynch, AG; Macintyre, G; Markowetz, F; Martincorena, I; Martinez-Fundichely, A; Meyerson, M; Miyano, S; Nakagawa, H; Navarro, FCP; Ossowski, S; Park, PJ; Pearson, JV; Puiggròs, M; Rippe, K; Roberts, ND; Roberts, SA; Rodriguez-Martin, B; Schumacher, SE; Scully, R; Shackleton, M; Sidiropoulos, N; Sieverling, L; Stewart, C; Torrents, D; Tubio, JMC; Villasante, I; Waddell, N; Wala, JA; Weischenfeldt, J; Yang, L; Yao, X; Yoon, S; Zamora, J; Zhang, C; Creighton, CJ; Aaltonen, LA; Abascal, F; Abeshouse, A; Aburatani, H; Adams, DJ; Agrawal, N; Ahn, KS; Ahn, S; Aikata, H; Akbani, R; Akdemir, KC; Al-Ahmadie, H; 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Publication
Nature Communications
Abstract
In the published version of this paper, the members of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortiumwere listed in the Supplementary Information; however, these members shouldhave been included in themainpaper.The originalArticle has been corrected to include the members and affiliations of the PCAWG Consortium in the main paper; the corrections have been made to the HTML version of the Article but not the PDF version. In the PCAWG Transcriptome Working Group, the affiliation ‘BioForA, French National Institute for Agriculture, Food, and Environment (INRAE),ONF,Orléans, France’ for Aurélien Chateignerwas alsomissing. The original Article has been corrected. Additional corrections to affiliations have been made to the PDF and HTML versions of the original Article for consistency of information between the PCAWG list and the main paper. © The Author(s) 2022.
2023
Authors
Guedes, JG; Ribeiro, R; Carqueijeiro, I; Guimaraes, AL; Bispo, C; Archer, J; Azevedo, H; Fonseca, NA; Sottomayor, M;
Publication
JOURNAL OF EXPERIMENTAL BOTANY
Abstract
Catharanthus roseus leaves produce a range of monoterpenoid indole alkaloids (MIAs) that include low levels of the anticancer drugs vinblastine and vincristine. The MIA pathway displays a complex architecture spanning different subcellular and cell type localizations, and is under complex regulation. As a result, the development of strategies to increase the levels of the anticancer MIAs has remained elusive. The pathway involves mesophyll specialized idioblasts where the late unsolved biosynthetic steps are thought to occur. Here, protoplasts of C. roseus leaf idioblasts were isolated by fluorescence-activated cell sorting, and their differential alkaloid and transcriptomic profiles were characterized. This involved the assembly of an improved C. roseus transcriptome from short- and long-read data, IDIO+. It was observed that C. roseus mesophyll idioblasts possess a distinctive transcriptomic profile associated with protection against biotic and abiotic stresses, and indicative that this cell type is a carbon sink, in contrast to surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the key to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs. Catharanthus mesophyll idioblasts are a hotspot of alkaloid accumulation. The idioblast transcriptome is associated with stress responses and provides a roadmap towards the increase of anticancer alkaloid levels.
2023
Authors
Pauperio, J; Gonzalez, LM; Martinez, J; Gonzalez, M; Martins, FM; Verissimo, J; Puppo, P; Pinto, J; Chaves, C; Pinho, CJ; Grosso-Silva, JM; Quaglietta, L; Silva, TL; Sousa, P; Alves, PC; Fonseca, N; Beja, P; Ferreira, S;
Publication
BIODIVERSITY DATA JOURNAL
Abstract
BackgroundThe Trichoptera are an important component of freshwater ecosystems. In the Iberian Peninsula, 380 taxa of caddisflies are known, with nearly 1/3 of the total species being endemic in the region. A reference collection of morphologically identified Trichoptera specimens, representing 142 Iberian taxa, was constructed. The InBIO Barcoding Initiative (IBI) Trichoptera 01 dataset contains records of 438 sequenced specimens. The species of this dataset correspond to about 37% of Iberian Trichoptera species diversity. Specimens were collected between 1975 and 2018 and are deposited in the IBI collection at the CIBIO (Research Center in Biodiversity and Genetic Resources, Portugal) or in the collection Marcos A. Gonzalez at the University of Santiago de Compostela (Spain).New informationTwenty-nine species, from nine different families, were new additions to the Barcode of Life Data System (BOLD). A success identification rate of over 80% was achieved when comparing morphological identifications and DNA barcodes for the species analysed. This encouraging step advances incorporation of informed Environmental DNA tools in biomonitoring schemes, given the shortcomings of morphological identifications of larvae and adult Caddisflies in such studies. DNA barcoding was not successful in identifying species in six Trichoptera genera: Hydropsyche (Hydropsychidae), Athripsodes (Leptoceridae), Wormaldia (Philopotamidae), Polycentropus (Polycentropodidae) Rhyacophila (Rhyacophilidae) and Sericostoma (Sericostomatidae). The high levels of intraspecific genetic variability found, combined with a lack of a barcode gap and a challenging morphological identification, rendered these species as needing additional studies to resolve their taxonomy.
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