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Publicações

Publicações por Nuno Fonseca

2022

Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison

Autores
Egeter, B; Verissimo, J; Lopes Lima, M; Chaves, C; Pinto, J; Riccardi, N; Beja, P; Fonseca, NA;

Publicação
MOLECULAR ECOLOGY RESOURCES

Abstract
Traditional detection of aquatic invasive species via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation responses. Environmental DNA (eDNA) detection approaches of multiple species using Illumina-based sequencing technology have been used to overcome these hindrances, but sample processing is often lengthy. More recently, portable nanopore sequencing technology has become available, which has the potential to make molecular detection of invasive species more widely accessible and substantially decrease sample turnaround times. However, nanopore-sequenced reads have a much higher error rate than those produced by Illumina platforms, which has so far hindered the adoption of this technology. We provide a detailed laboratory protocol and bioinformatic tools (msi package) to increase the reliability of nanopore sequencing to detect invasive species, and we test its application using invasive bivalves while comparing it with Illumina-based sequencing. We sampled water from sites with pre-existing bivalve occurrence and abundance data, and contrasting bivalve communities, in Italy and Portugal. Samples were extracted, amplified, and sequenced by the two platforms. The mean agreement between sequencing methods was 69% and the difference between methods was nonsignificant. The lack of detections of some species at some sites could be explained by their known low abundances. This is the first reported use of MinION to detect aquatic invasive species from eDNA samples.

2024

MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification

Autores
Cabezas, MP; Fonseca, NA; Muñoz-Mérida, A;

Publicação
ENVIRONMENTAL MICROBIOME

Abstract
MotivationAccurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy or a high percentage of sequences with missing taxonomic information. This may lead to erroneous identifications and, thus, to inaccurate conclusions regarding the ecological role and importance of those microorganisms in the ecosystem.ResultsThe current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequences from RefSeq Targeted loci with 32 086 sequences. MIMt aims to be updated twice a year to include all newly sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and taxonomic assignments accuracy. Our results showed that MIMt contains less redundancy, and despite being 20 to 500 times smaller than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.

2022

Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations (Nature Communications, (2020), 11, 1, (736), 10.1038/s41467-019-13885-w)

Autores
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; Al-Sedairy, ST; Al-Shahrour, F; Alawi, M; Albert, M; Aldape, K; Alexandrov, LB; Ally, A; Alsop, K; Alvarez, EG; Amary, F; Amin, SB; Aminou, B; Ammerpohl, O; Anderson, MJ; Ang, Y; Antonello, D; Anur, P; Aparicio, S; Appelbaum, EL; Arai, Y; Aretz, A; Arihiro, K; Ariizumi, S; Armenia, J; Arnould, L; Asa, S; Assenov, Y; Atwal, G; Aukema, S; Auman, JT; Aure, MRR; Awadalla, P; Aymerich, M; Bader, GD; Baez-Ortega, A; Bailey, MH; Bailey, PJ; Balasundaram, M; Balu, S; Bandopadhayay, P; Banks, RE; Barbi, S; Barbour, AP; Barenboim, J; Barnholtz-Sloan, J; Barr, H; Barrera, E; Bartlett, J; Bartolome, J; Bassi, C; Bathe, OF; Baumhoer, D; Bavi, P; Baylin, SB; Bazant, W; Beardsmore, D; Beck, TA; Behjati, S; Behren, A; Niu, B; Bell, C; Beltran, S; Benz, C; Berchuck, A; Bergmann, AK; Bergstrom, EN; Berman, BP; Berney, DM; Bernhart, SH; Beroukhim, R; Berrios, M; Bersani, S; Bertl, J; Betancourt, M; Bhandari, V; Bhosle, SG; Biankin, AV; Bieg, M; Bigner, D; Binder, H; Birney, E; Birrer, M; Biswas, NK; Bjerkehagen, B; Bodenheimer, T; Boice, L; Bonizzato, G; De Bono, JS; Boot, A; Bootwalla, MS; Borg, A; Borkhardt, A; Boroevich, KA; Borozan, I; Borst, C; Bosenberg, M; Bosio, M; Boultwood, J; Bourque, G; Boutros, PC; Bova, GS; Bowen, DT; Bowlby, R; Bowtell, DDL; Boyault, S; Boyce, R; Boyd, J; Brazma, A; Brennan, P; Brewer, DS; Brinkman, AB; Bristow, RG; Broaddus, RR; Brock, JE; Brock, M; Broeks, A; Brooks, AN; Brooks, D; Brors, B; Brunak, S; Bruxner, TJC; Bruzos, AL; Buchanan, A; Buchhalter, I; Buchholz, C; Bullman, S; Burke, H; Burkhardt, B; Burns, KH; Busanovich, J; Bustamante, CD; Butler, AP; Butte, AJ; Byrne, NJ; Børresen-Dale, A; Caesar-Johnson, SJ; Cafferkey, A; Cahill, D; Calabrese, C; Caldas, C; Calvo, F; Camacho, N; Campbell, PJ; Campo, E; Cantù, C; Cao, S; Carey, TE; Carlevaro-Fita, J; Carlsen, R; Cataldo, I; Cazzola, M; Cebon, J; Cerfolio, R; Chadwick, DE; Chakravarty, D; Chalmers, D; Chan, CWY; Chan, K; Chan-Seng-Yue, M; Chandan, VS; Chang, DK; Chanock, SJ; Chantrill, LA; Chateigner, A; Chatterjee, N; Chayama, K; Chen, H; Chen, J; Chen, K; Chen, Y; Chen, Z; Cherniack, AD; Chien, J; Chiew, Y; Chin, S; Cho, J; Cho, S; Choi, JK; Choi, W; Chomienne, C; Chong, Z; Choo, SP; Chou, A; Christ, AN; Christie, EL; Chuah, E; Cibulskis, C; Cibulskis, K; Cingarlini, S; Clapham, P; Claviez, A; Cleary, S; Cloonan, N; Cmero, M; Collins, CC; Connor, AA; Cooke, SL; Cooper, CS; Cope, L; Corbo, V; Cordes, MG; Cordner, SM; Cortés-Ciriano, I; Covington, K; Cowin, PA; Craft, B; Craft, D; Creighton, CJ; Cun, Y; Curley, E; Cutcutache, I; Czajka, K; Czerniak, B; Dagg, RA; Danilova, L; Davi, MV; Davidson, NR; Davies, H; Davis, IJ; Davis-Dusenbery, BN; Dawson, KJ; De La Vega, FM; De Paoli-Iseppi, R; Defreitas, T; Tos, APD; Delaneau, O; Demchok, JA; Demeulemeester, J; Demidov, GM; Demircioglu, D; Dennis, NM; Denroche, RE; Dentro, SC; Desai, N; Deshpande, V; Deshwar, AG; Desmedt, C; Deu-Pons, J; Dhalla, N; Dhani, NC; Dhingra, P; Dhir, R; DiBiase, A; Diamanti, K; Ding, L; Ding, S; Dinh, HQ; Dirix, L; Doddapaneni, H; Donmez, N; Dow, MT; Drapkin, R; Drechsel, O; Drews, RM; Serge, S; Dudderidge, T; Dueso-Barroso, A; Dunford, AJ; Dunn, M; Dursi, LJ; Duthie, FR; Dutton-Regester, K; Eagles, J; Easton, DF; Edmonds, S; Edwards, PA; Edwards, SE; Eeles, RA; Ehinger, A; Eils, J; Eils, R; El-Naggar, A; Eldridge, M; Ellrott, K; Erkek, S; Escaramis, G; Espiritu, SMG; Estivill, X; Etemadmoghadam, D; Eyfjord, JE; Faltas, BM; Fan, D; Fan, Y; Faquin, WC; Farcas, C; Fassan, M; Fatima, A; Favero, F; Fayzullaev, N; Felau, I; Fereday, S; Ferguson, ML; Ferretti, V; Feuerbach, L; Field, MA; Fink, JL; Finocchiaro, G; Fisher, C; Fittall, MW; Fitzgerald, A; Fitzgerald, RC; Flanagan, AM; Fleshner, NE; Flicek, P; Foekens, JA; Fong, KM; Fonseca, NA; Foster, CS; Fox, NS; Fraser, M; Frazer, S; Frenkel-Morgenstern, M; Friedman, W; Frigola, J; Fronick, CC; Fujimoto, A; Fujita, M; Fukayama, M; Fulton, LA; Fulton, RS; Furuta, M; Futreal, PA; Füllgrabe, A; Gabriel, SB; Gallinger, S; Gambacorti-Passerini, C; Gao, J; Gao, S; Garraway, L; Garred, Ø; Garrison, E; Garsed, DW; Gehlenborg, N; Gelpi, JLL; George, J; Gerhard, DS; Gerhauser, C; Gershenwald, JE; Gerstein, M; Gerstung, M; Getz, G; Ghori, M; Ghossein, R; Giama, NH; Gibbs, RA; Gibson, B; Gill, AJ; Gill, P; Giri, DD; Glodzik, D; Gnanapragasam, VJ; Goebler, ME; Goldman, MJ; Gomez, C; Gonzalez, S; Gonzalez-Perez, A; Gordenin, DA; Gossage, J; Gotoh, K; Govindan, R; Grabau, D; Graham, JS; Grant, RC; Green, AR; Green, E; Greger, L; Grehan, N; Grimaldi, S; Grimmond, SM; Grossman, RL; Grundhoff, A; Gundem, G; Guo, Q; Gupta, M; Gupta, S; Gut, IG; Gut, M; Göke, J; Ha, G; Haake, A; Haan, D; Haas, S; Haase, K; Haber, JE; Habermann, N; Hach, F; Haider, S; Hama, N; Hamdy, FC; Hamilton, A; Hamilton, MP; Han, L; Hanna, GB; Hansmann, M; Haradhvala, NJ; Harismendy, O; Harliwong, I; Harmanci, AO; Harrington, E; Hasegawa, T; Haussler, D; Hawkins, S; Hayami, S; Hayashi, S; Hayes, DN; Hayes, SJ; Hayward, NK; Hazell, S; He, Y; Heath, AP; Heath, SC; Hedley, D; Hegde, AM; Heiman, DI; Heinold, MC; Heins, Z; Heisler, LE; Hellstrom-Lindberg, E; Helmy, M; Heo, SG; Hepperla, AJ; Heredia-Genestar, JM; Herrmann, C; Hersey, P; Hess, JM; Hilmarsdottir, H; Hinton, J; Hirano, S; Hiraoka, N; Hoadley, KA; Hobolth, A; Hodzic, E; Hoell, JI; Hoffmann, S; Hofmann, O; Holbrook, A; Holik, AZ; Hollingsworth, MA; Holmes, O; Holt, RA; Hong, C; Hong, EP; Hong, JH; Hooijer, GK; Hornshøj, H; Hosoda, F; Hou, Y; Hovestadt, V; Howat, W; Hoyle, AP; Hruban, RH; Hu, J; Hu, T; Hua, X; Huang, K; Huang, M; Huang, MN; Huang, V; Huang, Y; Huber, W; Hudson, TJ; Hummel, M; Hung, JA; Huntsman, D; Hupp, TR; Huse, J; Huska, MR; Hutter, B; Hutter, CM; Hübschmann, D; Iacobuzio-Donahue, CA; Imbusch, CD; Imielinski, M; Imoto, S; Isaacs, WB; Isaev, K; Ishikawa, S; Iskar, M; Islam, SMA; Ittmann, M; Ivkovic, S; Izarzugaza, JMG; Jacquemier, J; Jakrot, V; Jamieson, NB; Jang, GH; Jang, SJ; Jayaseelan, JC; Jayasinghe, R; Jefferys, SR; Jegalian, K; Jennings, JL; Jeon, S; Jerman, L; Ji, Y; Jiao, W; Johansson, PA; Johns, AL; Johns, J; Johnson, R; Johnson, TA; Jolly, C; Joly, Y; Jonasson, JG; Jones, CD; Jones, DR; Jones, DTW; Jones, N; Jones, SJM; Jonkers, J; Ju, YS; Juhl, H; Jung, J; Juul, M; Juul, RI; Juul, S; Jäger, N; Kabbe, R; Kahles, A; Kahraman, A; Kaiser, VB; Kakavand, H; Kalimuthu, S; von Kalle, C; Kang, KJ; Karaszi, K; Karlan, B; Karlic, R; Karsch, D; Kasaian, K; Kassahn, KS; Katai, H; Kato, M; Katoh, H; Kawakami, Y; Kay, JD; Kazakoff, SH; Kazanov, MD; Keays, M; Kebebew, E; Kefford, RF; Kellis, M; Kench, JG; Kennedy, CJ; Kerssemakers, JNA; Khoo, D; Khoo, V; Khuntikeo, N; Khurana, E; Kilpinen, H; Kim, HK; Kim, H; Kim, H; Kim, H; Kim, J; Kim, J; Kim, JK; Kim, Y; King, TA; Klapper, W; Kleinheinz, K; Klimczak, LJ; Knappskog, S; Kneba, M; Knoppers, BM; Koh, Y; Jan Komorowski; Komura, D; Komura, M; Kong, G; Kool, M; Korbel, JO; Korchina, V; Korshunov, A; Koscher, M; Koster, R; Kote-Jarai, Z; Koures, A; Kovacevic, M; Kremeyer, B; Kretzmer, H; Kreuz, M; Krishnamurthy, S; Kube, D; Kumar, K; Kumar, P; Kumar, S; Kumar, Y; Kundra, R; Kübler, K; Küppers, R; Lagergren, J; Lai, PH; Laird, PW; Lakhani, SR; Lalansingh, CM; Lalonde, E; Lamaze, FC; Lambert, A; Lander, E; Landgraf, P; Landoni, L; Langerød, A; Lanzós, A; Larsimont, D; Larsson, E; Lathrop, M; Lau, LMS; Lawerenz, C; Lawlor, RT; Lawrence, MS; Lazar, AJ; Lazic, AM; Le, X; Lee, D; Lee, D; Lee, EA; Lee, HJ; Lee, JJ; Lee, J; Lee, J; Lee, MTM; Lee-Six, H; Lehmann, K; Lehrach, H; Lenze, D; Leonard, CR; Leongamornlert, DA; Leshchiner, I; Letourneau, L; Letunic, I; Levine, DA; Lewis, L; Ley, T; Li, C; Li, CH; Li, HI; Li, J; Li, L; Li, S; Li, S; Li, X; Li, X; Li, X; Li, Y; Liang, H; Liang, S; Lichter, P; Lin, P; Lin, Z; Linehan, WM; Lingjærde, OC; Liu, D; Liu, EM; Liu, FF; Liu, F; Liu, J; Liu, X; Livingstone, J; Livitz, D; Livni, N; Lochovsky, L; Loeffler, M; Long, GV; Lopez-Guillermo, A; Lou, S; Louis, DN; Lovat, LB; Lu, Y; Lu, Y; Lu, Y; Luchini, C; Lungu, I; Luo, X; Luxton, HJ; Lynch, AG; Lype, L; López, C; López-Otín, C; Ma, EZ; Ma, Y; MacGrogan, G; MacRae, S; Macintyre, G; Madsen, T; Maejima, K; Mafficini, A; Maglinte, DT; Maitra, A; Majumder, PP; Malcovati, L; Malikic, S; Malleo, G; Mann, GJ; Mantovani-Löffler, L; Marchal, K; Marchegiani, G; Mardis, ER; Margolin, AA; Marin, MG; Markowetz, F; Markowski, J; Marks, J; Marques-Bonet, T; Marra, MA; Marsden, L; Martens, JWM; Martin, S; Martin-Subero, JI; Martincorena, I; Martinez-Fundichely, A; Maruvka, YE; Mashl, RJ; Massie, CE; Matthew, TJ; Matthews, L; Mayer, E; Mayes, S; Mayo, M; Mbabaali, F; McCune, K; McDermott, U; McGillivray, PD; McLellan, MD; McPherson, JD; McPherson, JR; McPherson, TA; Meier, SR; Meng, A; Meng, S; Menzies, A; Merrett, ND; Merson, S; Meyerson, M; Meyerson, W; Mieczkowski, PA; Mihaiescu, GL; Mijalkovic, S; Mikkelsen, T; Milella, M; Mileshkin, L; Miller, CA; Miller, DK; Miller, JK; Mills, GB; Milovanovic, A; Minner, S; Miotto, M; Arnau, GM; Mirabello, L; Mitchell, C; Mitchell, TJ; Miyano, S; Miyoshi, N; Mizuno, S; Molnár-Gábor, F; Moore, MJ; Moore, RA; Morganella, S; Morris, QD; Morrison, C; Mose, LE; Moser, CD; Muiños, F; Mularoni, L; Mungall, AJ; Mungall, K; Musgrove, EA; Mustonen, V; Mutch, D; Muyas, F; Muzny, DM; Muñoz, A; Myers, J; Myklebost, O; Möller, P; Nagae, G; Nagrial, AM; Nahal-Bose, HK; Nakagama, H; Nakagawa, H; Nakamura, H; Nakamura, T; Nakano, K; Nandi, T; Nangalia, J; Nastic, M; Navarro, A; Navarro, FCP; Neal, DE; Nettekoven, G; Newell, F; Newhouse, SJ; Newton, Y; Ng, AWT; Ng, A; Nicholson, J; Nicol, D; Nie, Y; Nielsen, GP; Nielsen, MM; Nik-Zainal, S; Noble, MS; Nones, K; Northcott, PA; Notta, F; O’Connor, BD; O’Donnell, P; O’Donovan, M; O’Meara, S; O’Neill, BP; O’Neill, JR; Ocana, D; Ochoa, A; Oesper, L; Ogden, C; Ohdan, H; Ohi, K; Ohno-Machado, L; Oien, KA; Ojesina, AI; Ojima, H; Okusaka, T; Omberg, L; Ong, CK; Ossowski, S; Ott, G; Ouellette, BFF; P’ng, C; Paczkowska, M; Paiella, S; Pairojkul, C; Pajic, M; Pan-Hammarström, Q; Papaemmanuil, E; Papatheodorou, I; Paramasivam, N; Park, JW; Park, J; Park, K; Park, K; Park, PJ; Parker, JS; Parsons, SL; 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Robertson, AJ; Rodriguez, JB; Rodriguez-Martin, B; Rodríguez-González, FG; Roehrl, MHA; Rohde, M; Rokutan, H; Romieu, G; Rooman, I; Roques, T; Rosebrock, D; Rosenberg, M; Rosenstiel, PC; Rosenwald, A; Rowe, EW; Royo, R; Rozen, SG; Rubanova, Y; Rubin, MA; Rubio-Perez, C; Rudneva, VA; Rusev, BC; Ruzzenente, A; Rätsch, G; Sabarinathan, R; Sabelnykova, VY; Sadeghi, S; Sahinalp, SC; Saini, N; Saito-Adachi, M; Saksena, G; Salcedo, A; Salgado, R; Salichos, L; Sallari, R; Saller, C; Salvia, R; Sam, M; Samra, JS; Sanchez-Vega, F; Sander, C; Sanders, G; Sarin, R; Sarrafi, I; Sasaki-Oku, A; Sauer, T; Sauter, G; Saw, RPM; Scardoni, M; Scarlett, CJ; Scarpa, A; Scelo, G; Schadendorf, D; Schein, JE; Schilhabel, MB; Schlesner, M; Schlomm, T; Schmidt, HK; Schramm, S; Schreiber, S; Schultz, N; Schumacher, SE; Schwarz, RF; Scolyer, RA; Scott, D; Scully, R; Seethala, R; Segre, AV; Selander, I; Semple, CA; Senbabaoglu, Y; Sengupta, S; Sereni, E; Serra, S; Sgroi, DC; Shackleton, M; Shah, NC; Shahabi, S; Shang, CA; 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Publicação
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.

2024

The leaf idioblastome of the medicinal plant Catharanthus roseus is associated with stress resistance and alkaloid metabolism

Autores
Guedes, JG; Ribeiro, R; Carqueijeiro, I; Guimaraes, AL; Bispo, C; Archer, J; Azevedo, H; Fonseca, NA; Sottomayor, M;

Publicação
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

The InBIO barcoding initiative database: DNA barcodes of Iberian Trichoptera, documenting biodiversity for freshwater biomonitoring in a Mediterranean hotspot

Autores
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;

Publicação
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.

2023

Idioblasts accumulating anticancer alkaloids in Catharanthus roseus leaves are a unique cell type

Autores
Guedes, JG; Ribeiro, R; Carqueijeiro, I; Guimaraes, AL; Bispo, C; Archer, J; Azevedo, H; Fonseca, NA; Sottomayor, M;

Publicação

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 specialised 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 characterised. 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 with surrounding mesophyll cells. Moreover, it is shown that idioblasts are a hotspot of alkaloid accumulation, suggesting that their transcriptome may hold the keys to the in-depth understanding of the MIA pathway and the success of strategies leading to higher levels of the anticancer drugs.

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