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2. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes

Author

Manni, Mosè, Berkeley, Matthew R, Seppey, Mathieu, Simao, Felipe A, and Zdobnov, Evgeny M

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Populations and Evolution
Abstract

Methods for evaluating the quality of genomic and metagenomic data are essential to aid genome assembly and to correctly interpret the results of subsequent analyses. BUSCO estimates the completeness and redundancy of processed genomic data based on universal single-copy orthologs. Here we present new functionalities and major improvements of the BUSCO software, as well as the renewal and expansion of the underlying datasets in sync with the OrthoDB v10 release. Among the major novelties, BUSCO now enables phylogenetic placement of the input sequence to automatically select the most appropriate dataset for the assessment, allowing the analysis of metagenome-assembled genomes of unknown origin. A newly-introduced genome workflow increases the efficiency and runtimes especially on large eukaryotic genomes. BUSCO is the only tool capable of assessing both eukaryotic and prokaryotic species, and can be applied to various data types, from genome assemblies and metagenomic bins, to transcriptomes and gene sets., Comment: for supplementary files, see https://gitlab.com/ezlab/busco_preprint_2021

Published
2021

3. COMPLICAÇÕES DA CIRROSE HEPÁTICA

Author

PEREIRA DA COSTA CRUZ, ISADORA, primary, DINIZ BARBIERI, JULIANA, additional, PRAUN SIMÃO, FELIPE, additional, HENRIQUE RIAL, GABRIEL, additional, CESTARI, LUCAS, additional, RITTER MALDANER, VITÓRIA, additional, ALTVATER SATURNINO, BRUNA, additional, MOREIRA MATEUS DA SILVA, BEATRIZ, additional, COLLET FURTADO, JULIA, additional, GOBBI DE FARIAS, LUCAS, additional, COELHO DE SOUZA, IZABELLE, additional, GUSTAVO ZANIS, JOSÉ, additional, and BEATRIZ DE JEZUS, ANNA, additional

Published
2023
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4. Correction to: Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Developmental Biology, Biological sciences
Abstract

An amendment to this paper has been published and can be accessed via the original article.

Published
2020

5. Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A, Ben-Mahmoud, Sulley, Christiaens, Olivier, Dermauw, Wannes, Ioannidis, Panagiotis, Jacobs, Chris GC, Vargas Jentzsch, Iris M, Oliver, Jonathan E, Poelchau, Monica F, Rajarapu, Swapna Priya, Schneweis, Derek J, Snoeck, Simon, Taning, Clauvis NT, Wei, Dong, Widana Gamage, Shirani MK, Hughes, Daniel ST, Murali, Shwetha C, Bailey, Samuel T, Bejerman, Nicolas E, Holmes, Christopher J, Jennings, Emily C, Rosendale, Andrew J, Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A, Cheng, Sammy, Childers, Christopher, Simão, Felipe A, Dietzgen, Ralf G, Chao, Hsu, Dinh, Huyen, Doddapaneni, Harsha Vardhan, Dugan, Shannon, Han, Yi, Lee, Sandra L, Muzny, Donna M, Qu, Jiaxin, Worley, Kim C, Benoit, Joshua B, Friedrich, Markus, Jones, Jeffery W, Panfilio, Kristen A, Park, Yoonseong, Robertson, Hugh M, Smagghe, Guy, Ullman, Diane E, van der Zee, Maurijn, Van Leeuwen, Thomas, Veenstra, Jan A, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Whitfield, Anna E, Zdobnov, Evgeny M, Gibbs, Richard A, and Richards, Stephen

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Animals, Crops, Agricultural, Feeding Behavior, Food Chain, Genome, Insect, Immunity, Innate, Life History Traits, Perception, Phylogeny, Reproduction, Thysanoptera, Transcriptome, Western flower thrips, Hemipteroid assemblage, Insect genomics, Tospovirus, Salivary glands, Chemosensory receptors, Opsins, Detoxification, Innate immunity, Developmental Biology, Biological sciences
Abstract

BackgroundThe western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set.ResultsWe report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta.ConclusionsAnalysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.

Published
2020

7. COVID-19 - O VÍRUS QUE MOVIMENTOU A CIÊNCIA - VOLUME 2

Author

Duarte, Fábio Biguelini, primary, Dutra, Angélica Paula Barbosa Silva, additional, Freitas, Guilherme Vasconcelos de, additional, Fukuoka, Vitória Morita, additional, Guimarães, Lizandra Ferrari, additional, Moeller, Amanda Gonçalves, additional, Oliveira, Fabiana de, additional, Paz, Adriana Aparecida, additional, Seroiska, Gabriel, additional, Silva, André Luiz da, additional, SARAIVA, GABRIEL BEZERRA DO NASCIMENTO, additional, PONTES, AMANDA DAIANA, additional, SALIN, ADRIANE BONOTTO, additional, FREIRE, ALINE ARAUJO MAIA MIOLA, additional, SOUZA, LUANA RODRIGUES MARQUES DE, additional, SOUZA, CAMILA DE OLIVEIRA, additional, OLIVEIRA, CLARA GOMES DE, additional, MORENO, DIEGO LEÃO ARAÚJO, additional, ALMEIDA, EMILE PEREIRA, additional, SANTOS, GUILHERME AUGUSTO DE ARAÚJO, additional, SOARES, RAFAELA DA SILVA, additional, SARTOR, LUIGI AURELIO, additional, Barcelos, João P P, additional, FERNANDES, JOÃO PAULO ARGENTON, additional, MAGALHÃES, JOÃO VICTOR STARLING, additional, BANDEIRA, LORENA DE SOUZA, additional, CUNHA, LUCAS LANNA, additional, TURCI, MARIA APARECIDA, additional, WINKLER, INGRED, additional, SILVA, THAÍS DA, additional, FREITAS, DANIELLE DA PAIXÃO, additional, SILVA, LAVÍNIA FERREIRA DA, additional, MOREIRA, ALINE MORAIS, additional, FARIA, CECÍLIA ALMEIDA E AMARAL, additional, MOREIRA, RAISSA DE SOUZA MERCEDO, additional, LEITE, THARICK ANTÔNIO XAVIER DE OLIVEIRA, additional, CRUZ, YOLANDA VALOIS CHAGAS, additional, Lima, Maria Adriely Cunha, additional, SANTOS, EVELEN ROUSE DE SOUZA, additional, CESTARI, YASMIM LAILA FRAGOSO, additional, SANTOS, ISABELA DE MOURA, additional, VIEIRA, THAÍS FRANCIELLE SANTANA, additional, SOUSA, LARYSSA FIALHO DE OLIVEIRA, additional, SOUZA, CAMILLA RADIMACK SANTOS DE, additional, NASCIMENTO, MONALYSA DA CRUZ, additional, REZENDE, MATEUS LENIER, additional, OLIVEIRA, HALLEY FERRARO, additional, RIBEIRO, DANIELLA DE LOURDES BAGGIO REHFELD, additional, FERREIRA, SOFIA GONÇALVES, additional, SADER, LUÍSA MACHADO CAMPOLINA, additional, RODRIGUES, EMANUELA CARVALHO, additional, PEREIRA, LUÍSA BAMBIRRA, additional, BOAVENTURA, JÚLIA VELOSO, additional, RODRIGUES, MARIANNE NETO, additional, SCHERRER, ISABELA RESENDE SILVA, additional, SILVEIRA, PRISCILA FARIAS DA, additional, SIMÃO, FELIPE PRAUN, additional, CAREGNATO, NATHALIA, additional, SOUZA, PHELIPE S, additional, Araujo, Maria Isadora Benedito de, additional, Mamede, Iascara Vitória de Oliveira, additional, Braga, Francisca Ivina Leite, additional, Nascimento, José Paulo Lima do, additional, Silva, Marcos Paulo Da, additional, Lourenço, Heitor Fernandes, additional, Ribeiro, Luana da Hora, additional, Duarte, Rany Magnaelle Rodrigues, additional, Araujo, Luciana Mara Peixoto, additional, Almeida, Bárbara M P De, additional, SANTOS, ELLEN ARAUJO, additional, Filippetti, Eloah P, additional, CARVALHO, GABRIELA BARTANHA, additional, OLIVEIRA, RAQUEL ZECHETTI DE, additional, CARDOSO, RENATA ARAUJO, additional, RATTI, ANA FLÁVIA SACURRATO, additional, BASTIANELLO, FERNANDA, additional, MENDES, MAYARA, additional, FERNANDES, ALEXANDRE PEREIRA, additional, BARSOTTI, NATHALIA SILVEIRA, additional, Santos, Larissa R, additional, Bastos, Ariane Lopes, additional, Filippetti, Eloah Pascuotte, additional, Batista, Lysa Laura Figueiredo, additional, Damaia, Pedro Batistel, additional, Almeida, Vitor Amaral de, additional, Araújo, Ana Carolina Vieira, additional, Dumas, Juliana Cedro de Souza, additional, COSTA, LOUISE VICTORIA VIEIRA TOSTA DA, additional, Silva, Ana Carina Faleta De Aquino, additional, MOREIRA, EMANUELLE ALVES, additional, SANTOS, FLÁVIO CAMPAGNOLI DOS, additional, Costa, João Paulo Dias, additional, SANTOS, RAFAELLY DOS, additional, SANTANA, STEFANNY RAFAELA DE, additional, SIQUEIRA, YGOR RIBEIRO, additional, CAVALCANTE, RAFAEL CIRO MARQUES, additional, MIRANDA, RENATA, additional, FERNANDES, ÍTALO RUFINO DE QUEIROZ, additional, OLIVEIRA, MARCOS DIVINO DE, additional, Oliveira, Maria Eduarda Ferreira de, additional, Sampaio, Matheus Vieira, additional, FONSECA, WEILER FERREIRA, additional, Sobrinho, Weberton Dorásio, additional, Silva, João Lucas Rocha, additional, Formiga, Rafaela Carneiro de Almeida, additional, Camurça, Alessandra Bezerra de Almeida, additional, Facundo, Andressa Lisboa de Carvalho, additional, Gadelha, Ana Beatriz Freire, additional, Basto, Giovana Lins, additional, Leite, Lara Horta de Araújo, additional, Pedrosa, Pedro Palitot Pereira, additional, Costa, Rayane Mendonça da, additional, Camurça, Tainah Braga, additional, COSTA, YANNE GONÇALVES FERNANDES DA, additional, CAVALCANTI, MATHEUS DE ALMEIDA MURITIBA PORTELLA, additional, NOVAIS, THALLYS HENRIQUE DE OLIVEIRA, additional, NASCIMENTO, PEDRO HENRIQUE BRANDÃO DO, additional, MELO, IZABEL ROCHA DE, additional, MARQUES, THAÍS RAPOSO, additional, ALMEIDA, LETÍCIA MARIA PERRELLI RAMALHO DE, additional, SILVA, JÉSSICA BARBOSA MAIA DA, additional, BARBOSA, ARIANNA GONÇALVES, additional, SILVA, ALVARO BULHÕES DA, additional, Pereira, Lívia Leandro de Souza, additional, CAVALCANTI, BIANCA FRANCINE FERREIRA, additional, SILVA, GEOVANI ANDRIEL ALVES MARTINIANO DA, additional, STANFORD, GUSTAVO DE ALBUQUERQUE, additional, SANTANA, LETÍCIA KELLY MELO, additional, OLIVEIRA, MARIA EDUARDA TAVARES DE, additional, MARAFANTE, MARIA EDUARDA OSÓRIO, additional, Neves, Othilio Johanes Leite Ciraulo Ismael da Costa, additional, SILVA, MARIA FERNANDA LUZ, additional, AGUIAR, MILENA MARIA DA SILVA, additional, PENHA, WESLLEY JONATHAN LOPES DA, additional, BARROS, ANDRÉ LUIZ SOUZA, additional, ROCHA, GABRIELA ALMEIDA, additional, ROCHA, DANIELA ALMEIDA, additional, SANTOS, FILIPE VIANA, additional, FREITAS, GABRIEL BARBOSA DE, additional, COSTA, HENRIQUE REIS RABELO, additional, SILVA, LAIS GUSMÃO, additional, Hawerroth, Mayara Santana, additional, TOLENTINO, SOFIA LANNES, additional, MARTINS, THAYSA DRUMMOND, additional, RODRIGUES, VICTOR MUNIZ, additional, ASSIS, PEDRO IVO COSTA MORAIS DE, additional, ASSIS, VIVIAN COSTA MORAIS DE, additional, ROSA, LUIZA MARINHO MOTTA SANTA, additional, CISCOTTO, PAULA HENRIQUES CRUZ, additional, CRUZ, ANA BEATRIZ NOGUEIRA DA, additional, BRITO, GABRIELA SILVA DE, additional, ROSADO, LARA ANDRADE, additional, LOPES, LUIZA WANDERLEY PERSIANO, additional, CASSUNDÉ, MATHEUS ALHEIROS, additional, MENDONÇA, ARTHUR FARIA, additional, PERILLO, ANA LUISA PEREIRA, additional, SOUZA, ANA CAROLINE NOGUEIRA DE MOREIRA, additional, MATOS, ANDREA DE FARIA REZENDE, additional, JUBÉ, CAMILLA MACHADO FLEURY, additional, SILVA, DÉBORA CRISTINA RIBEIRO DA, additional, ROSA, HENRIQUE DANIN ARAÚJO, additional, OLIVEIRA, JESSYCA ZANELLA FERREIRA DE, additional, BORGES, JORDANA ARAÚJO, additional, ROSA, SUÉLIA DE SIQUEIRA RODRIGUES FLEURY, additional, BERNARDES, CELENE FERNANDES, additional, FAGIONATO, FELIPE WATANABE, additional, OLIVEIRA, VITOR SANCHES DE, additional, AMARAL, FELIPE AUGUSTO APARECIDO DO, additional, CARVALHO, ANA LUÍZA ZINATO DE, additional, ARAÚJO, BEATRIZ DE SÁ GUEDES, additional, Santos, Bárbara Aparecida Costa, additional, SANTOS, GENYSON CARVALHO, additional, Saldanha, Janaína Cláudia da Silva, additional, MELO, SILVIO JOSÉ, additional, SILVA, LARISSA NASCIMENTO PACHECO, additional, ROSÁRIO, JÚLIA FELIX ALMEIDA, additional, QUADROS, SOFIA FERREIRA PENA, additional, CARVALHO, LUANA IZABELA AZEVEDO DE, additional, BIASON, GIOVANNA GUIMARÃES, additional, EVANGELISTA, MARIA ESTHER LIMA RIOS, additional, ALVES, THAYNARA CASTELO DE LIMA, additional, FUJIMOTO, VICTÓRIA CRISTINA MENDONÇA, additional, SILVA, ANA CAROLINA MENDONÇA DA, additional, PALMA, MARIA EDUARDA ROCHA SOARES, additional, VIEIRA, VITOR MARTINS, additional, SILVA, THIAGO MAGELA GOMES DA, additional, REIS, LEVI EDUARDO SOARES, additional, BASTOS, MARIANA ARAÚJO PENA, additional, BASTOS, MARIANA RODRIGUES MARINHO DE, additional, Arão, Ana Elisa Choucair Hosken, additional, OLIVEIRA, AMANDA VASCONCELOS DE, additional, COSTA, BRUNA DIULY SANTOS, additional, COSTA, HELENA FONTENELLE DE CARVALHO, additional, SOUSA, KARLA SILVIA DE, additional, COSTA, JULIANA SILVEIRA MARTINS DA, additional, FRAZÃO, VICTOR CABREIRA, additional, ALVARENGA, ALICE MARTINS, additional, DIAS, FERNANDA DAS GRAÇAS, additional, BATISTA, TAINÁ RESENDE, additional, Braga, Regiane Helena Medeiros, additional, Saltara, Alessandra, additional, Medeiros, Daniela Virginia Rios Dias de, additional, Batista, Fernanda Rubia, additional, Paula, Fernanda Roberti Gil de, additional, Demoner, Frederico Octávio Perozini, additional, Correia, Rafaela Charles, additional, VILAÇA, JHEMILY LOPES LIMA, additional, SILVA, GABRIEL SOUZA SANTOS DA, additional, SOBRINHO, WEBERTON DORÁSIO, additional, SILVA, JOÃO LUCAS ROCHA, additional, SANTOS, VINICIUS DE OLIVEIRA, additional, FERREIRA, VITÓRIA DE ARAÚJO, additional, PACHECO, LETÍCIA MESQUITA, additional, SANTOS, JOÃO VITOR MORAIS, additional, DANTAS, VERIDIANA CÉLIA BEZERRA, additional, CEMBRANEL, VINICIUS MORAIS, additional, COSTA, TIAGO ALMEIDA, additional, SOBRAL, LARISSA DANTAS, additional, FARIA, MARIANA SOARES, additional, ARAÚJO, JULIANY LINS, additional, MENEZES, VICTORIA CAROLINA LUNA, additional, SOUZA, HAYANNA CÂNDIDA CARVALHO DE, additional, AZEVEDO, MARIA REGINA DOMINGUES DE, additional, CARVALHO, NAYARA ALMEIDA, additional, TEIXEIRA, BEATRIZ NASSER, additional, ARANTES, OTÁVIO AUGUSTO LANDIM, additional, SALES, PRISCILA MAGALHÃES ESTEVES DE, additional, BORGES, RAQUEL CAMARGOS, additional, QUISTE, SARAH SOUZA, additional, OLIVEIRA, THAYENE BARBOSA DE, additional, Costa, Ana Luísa Mendes Pinheiro, additional, COSTA, ANA LUÍSA MENDES PINHEIRO, additional, RODRIGUES, MARCELA DE CASTRO BASTOS, additional, Ribeiro, Luana, additional, PEREIRA, LÍVIA VILAÇA COTA, additional, Fernandes, Thalita Baptisteli, additional, Costa, Liliana Larissa Bandeira, additional, MENDES, JOÃO FERREIRA, additional, SANTOS, MAÍSA SARGES, additional, SILVEIRA, SANDRA MARIA DO CARMO, additional, MARTINS, BEATRIZ FREITAS DE ALBUQUERQUE, additional, PAIXA, LARISSA GABRIELLE SIQUEIRA, additional, OLIVEIRA, JÉSSICA DANIELE SILVA DE, additional, VENTURA, MARIA EDUARDA MALCHER, additional, PINTO, AYLA VITÓRIA CARRÉRA DA SILVA, additional, LOBO, MIKÉY MONTEIRO, additional, ALMEIDA, JULIANA VIEIRA QUEIROZ, additional, ALMADA, BRUNO HENRIQUE GONÇALVES, additional, TORQUETTE, SARAH LOUREDO, additional, BLASSIOLI, VITOR COURI, additional, DIAS, YVES HENRIQUE FARIA, additional, ALMEIDA, FERNANDA VIEIRA QUEIROZ, additional, RODRIGUES, ELDA CRISTINA DE SOUZA RIBEIRO, additional, CASTILHO, CÉSAR TEIXEIRA, additional, Sander, Renata Cury, additional, OLIVEIRA, ANA CORINA BANDEIRA ALMEIDA RODRIGUES DE, additional, SILVA, DIOVANNA LIMA, additional, PINHEIRO, LUZIA FRANCINY DE SOUZA, additional, BITTENCOURT, MARIANA LOUZADA, additional, TANAJURA, NADYNNE PORTO MAGALHÃES, additional, AGUIAR, NATÁLIA MENDES, additional, CORRÊA, SHESLLEN MIKAELLY CRUZ, additional, MARQUES, VALERIA GOMES, additional, ARAGÃO, VITOR SANTOS, additional, SOUZA, JOANA TRENGROUSE LAIGNIER DE, additional, ZAMBOM, DANIELLE DE AQUINO, additional, SANTOS, GRACIELLE DE JESUS, additional, DÓREA, GABRIEL SILVA, additional, TELES, DANILO OLIVEIRA, additional, LACERDA, ROBERTO DOS SANTOS, additional, Souza, Letícia Karen Rodrigues de, additional, Miranda, Ana Maria Ramos, additional, Maia, Jade Menezes, additional, Desteffani, Karine Gomes Bandeira, additional, Nascimento, Andressa Schmidt do, additional, Rizziolli, Daniele Sutherland Wallauer, additional, Diniz, Lilian Coelho Heringer, additional, Lima, Cristiane dos Santos, additional, Silva, Mara Iza Alves, additional, Fecury, Priscylla Celeste Milhomem Silva, additional, SANTOS, CAROLINA TEODORO DOS, additional, NASCIMENTO, NATÁLIA SILVA, additional, BUENO, MARCELA ELISA, additional, ARAÚJO, GABRIELY TRINDADE, additional, Ferreira, Luis Marcos, additional, Sousa, Christianna Eller Silva, additional, GOMES, BRUNA LUÍSA PALHARES, additional, AMARAL, DEIVID RIBEIRO DO, additional, NASCIMENTO, DEBORAH RIBEIRO, additional, MONTEIRO, FERNANDA MENESES, additional, NASCIMENTO, IGOR RIBEIRO, additional, Souza, Thaynara N, additional, FARIAS, JOÃO VICTOR TRINDADE, additional, BARBOSA, CARLA DÉA TRINDADE, additional, Bogea, Eduarda G, additional, NASCIMENTO, RENAN MONTEIRO DO, additional, SANTOS, GIOVANA BORGES, additional, GAMA, SÁVIO FRANÇA, additional, LISBOA, THIAGO RODRIGUES, additional, SERAFIM, ISAK BATISTA MEDEIROS, additional, RAMOS, AYLA CAMPANHA, additional, RONER, MÁRCIA NUNES BANDEIRA, additional, VASCONCELLOS, ANNA FERNANDA, additional, CHARNEAU, SÉBASTIEN, additional, Silva, Maria Marta Lino de Oliveira, additional, castro, Joane Ramos Viana de, additional, Fanaia, Raphaela Tingo Narita, additional, FUJIMOTO, Camila Kazue, additional, Lopes, Franciane Silva, additional, Rêgo, Alexsandra Maria Calheiros de Almeida, additional, Silva, Graciete Mirian Pereira, additional, Takaki, Eduardo Costa, additional, Silveira, Fernanda Maria Magalhães, additional, VASCONCELOS, RAQUEL LEITE, additional, LINHARES, LIDUINA JOYCE PRADO, additional, DUARTE, ALESSANDRA CARVALHO NÓBREGA, additional, MEDEIROS, TELMA ALVES, additional, SILVA, RITA WIGNA DE SOUZA, additional, OLIVEIRA, KARINE DA SILVA, additional, VASCONCELOS, FRANCISCO HERLON PONTE DE, additional, BATISTA, CARULINA CARDOSO, additional, MARRONE, VITTORIA GIULIA DA SILVA, additional, NOIA, CHARMYLLY BISPO, additional, OLIVEIRA, ANNA VITORIA GONÇALVES SOARES DE, additional, NOGUEIRA, MARIA ISABEL TELES, additional, ARAÚJO, IOHANNA MELO DE, additional, and FREITAS, ELUANY NOGUEIRA DE, additional

Published
2021
Full Text
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8. Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

Author

Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Medical Microbiology, Infectious Diseases, Rare Diseases, Vector-Borne Diseases, Biotechnology, Malaria, Infection, Good Health and Well Being, Animals, Anopheles, Base Sequence, Chromosomes, Insect, Drosophila, Evolution, Molecular, Genome, Insect, Humans, Insect Vectors, Molecular Sequence Data, Phylogeny, Sequence Alignment, General Science & Technology
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

9. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

Author

Neafsey, Daniel E, Waterhouse, Robert M, Abai, Mohammad R, Aganezov, Sergey S, Alekseyev, Max A, Allen, James E, Amon, James, Arcà, Bruno, Arensburger, Peter, Artemov, Gleb, Assour, Lauren A, Basseri, Hamidreza, Berlin, Aaron, Birren, Bruce W, Blandin, Stephanie A, Brockman, Andrew I, Burkot, Thomas R, Burt, Austin, Chan, Clara S, Chauve, Cedric, Chiu, Joanna C, Christensen, Mikkel, Costantini, Carlo, Davidson, Victoria LM, Deligianni, Elena, Dottorini, Tania, Dritsou, Vicky, Gabriel, Stacey B, Guelbeogo, Wamdaogo M, Hall, Andrew B, Han, Mira V, Hlaing, Thaung, Hughes, Daniel ST, Jenkins, Adam M, Jiang, Xiaofang, Jungreis, Irwin, Kakani, Evdoxia G, Kamali, Maryam, Kemppainen, Petri, Kennedy, Ryan C, Kirmitzoglou, Ioannis K, Koekemoer, Lizette L, Laban, Njoroge, Langridge, Nicholas, Lawniczak, Mara KN, Lirakis, Manolis, Lobo, Neil F, Lowy, Ernesto, MacCallum, Robert M, Mao, Chunhong, Maslen, Gareth, Mbogo, Charles, McCarthy, Jenny, Michel, Kristin, Mitchell, Sara N, Moore, Wendy, Murphy, Katherine A, Naumenko, Anastasia N, Nolan, Tony, Novoa, Eva M, O'Loughlin, Samantha, Oringanje, Chioma, Oshaghi, Mohammad A, Pakpour, Nazzy, Papathanos, Philippos A, Peery, Ashley N, Povelones, Michael, Prakash, Anil, Price, David P, Rajaraman, Ashok, Reimer, Lisa J, Rinker, David C, Rokas, Antonis, Russell, Tanya L, Sagnon, N'Fale, Sharakhova, Maria V, Shea, Terrance, Simão, Felipe A, Simard, Frederic, Slotman, Michel A, Somboon, Pradya, Stegniy, Vladimir, Struchiner, Claudio J, Thomas, Gregg WC, Tojo, Marta, Topalis, Pantelis, Tubio, José MC, Unger, Maria F, Vontas, John, Walton, Catherine, Wilding, Craig S, Willis, Judith H, Wu, Yi-Chieh, Yan, Guiyun, Zdobnov, Evgeny M, Zhou, Xiaofan, Catteruccia, Flaminia, Christophides, George K, Collins, Frank H, and Cornman, Robert S

Subjects
Animals, Humans, Anopheles, Drosophila, Malaria, Sequence Alignment, Insect Vectors, Evolution, Molecular, Phylogeny, Base Sequence, Molecular Sequence Data, Genome, Insect, Chromosomes, Insect, Evolution, Molecular, Genome, Insect, Chromosomes, General Science & Technology
Abstract

Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution. Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila. Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts.

Published
2015

10. Genetic determinants of antimicrobial resistance in polymyxin B resistant Pseudomonas aeruginosaisolated from airways of patients with cystic fibrosis

Author

Simão, Felipe A., Almeida, Mila M., Rosa, Heloísa S., Marques, Elizabeth A., and Leão, Robson S.

Abstract

Pseudomonas aeruginosais the main pathogen associated with pulmonary exacerbation in patients with cystic fibrosis (CF). CF is a multisystemic genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, which mainly affects pulmonary function. P. aeruginosaisolated from individuals with CF in Brazil is not commonly associated with multidrug resistance (MDR), especially when compared to global occurrence, where the presence of epidemic clones, capable of expressing resistance to several drugs, is often reported. Due to the recent observations of MDR isolates of P. aeruginosain our centers, combined with these characteristics, whole-genome sequencing was employed for analyses related to antimicrobial resistance, plasmid identification, search for phages, and characterization of CF clones. All isolates in this study were polymyxin B resistant, exhibiting diverse mutations and reduced susceptibility to carbapenems. Alterations in mexZcan result in the overexpression of the MexXY efflux pump. Mutations in oprD, pmrB, parS, gyrAand parCmay confer reduced susceptibility to antimicrobials by affecting permeability, as observed in phenotypic tests. The phage findings led to the assumption of horizontal genetic transfer, implicating dissemination between P. aeruginosaisolates. New sequence types were described, and none of the isolates showed an association with epidemic CF clones. Analysis of the genetic context of P. aeruginosaresistance to polymyxin B allowed us to understand the different mechanisms of resistance to antimicrobials, in addition to subsidizing the understanding of possible relationships with epidemic strains that circulate among individuals with CF observed in other countries.

Published
2024
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18. Pré-vestibulares populares e a democratização do acesso ao ensino superior

Author

SIMÃO, Felipe Pinto, SILVA NETO, Nathanael da Cruz e, and TORRES, Julio Cesar

Subjects
Enseñanza superior, Educação. Cursinhos populares. Ensino Superior, Educacíon. Cursos populares
Abstract

En Brasil, aunque la Constitución federal garantiza el derecho a la educación pública y gratuita para todos, lo que se observa en la práctica es que ciertos niveles educativos, especialmente la educación superior, siguen limitados a la clase dominante, que utiliza estos espacios para perpetuar la división social del trabajo. Este artículo analiza el papel de los cursos de ingreso preuniversitarios populares en la democratización del acceso a la educación superior. Se supone que estos proyectos contribuyen a una lucha más amplia para superar la sociedad de clases en sí, ya que actúan socializando el conocimiento y permitiendo su apropiación por parte de la sociedad. Submetido em: 20/01/2020Aceito em: 01/06/2020 No Brasil, embora a Constituição Federal garanta o direito à educação pública e gratuita a todos, o que se observa, na prática, é que determinados níveis educacionais – em especial o Ensino Superior – continuam limitados à classe dominante, que utiliza desses espaços para perpetuar a divisão social do trabalho. Neste artigo, discute-se o papel dos cursinhos pré-vestibulares populares na democratização do acesso ao ensino superior. Parte-se do pressuposto que tais projetos contribuem para uma luta mais ampla pela superação da própria sociedade de classes à medida que atuam socializando os saberes e viabilizando sua apropriação pela sociedade. Submetido em: 20/01/2020Aceito em: 01/06/2020

Published
2020

19. Popular courses pre-entry examination being in public universities in the state of São Paulo

Author

Simão, Felipe Pinto [UNESP], Universidade Estadual Paulista (Unesp), and Torres, Julio Cesar [UNESP]

Subjects
Pre entrance exam, University extension, Educação, Cursinhos populares, Pré-vestibular, Higher education, Popular coursesworks, Extensão universitária, Ensino superior, Education
Abstract

Submitted by Felipe Pinto Simão (fp.simao@unesp.br) on 2020-09-15T22:25:48Z No. of bitstreams: 1 Dissertaçao Felipe P Simao.pdf: 947288 bytes, checksum: 85aa143faf3c2a301509b73704d2cd4e (MD5) Approved for entry into archive by Satie Tagara (satie@marilia.unesp.br) on 2020-09-15T23:47:12Z (GMT) No. of bitstreams: 1 simao_fp_me_mar.pdf: 947288 bytes, checksum: 85aa143faf3c2a301509b73704d2cd4e (MD5) Made available in DSpace on 2020-09-15T23:47:12Z (GMT). No. of bitstreams: 1 simao_fp_me_mar.pdf: 947288 bytes, checksum: 85aa143faf3c2a301509b73704d2cd4e (MD5) Previous issue date: 2020-03-05 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Esta pesquisa – de natureza bibliográfica e documental - teve como objetivo analisar o funcionamento e as atividades desenvolvidas pelos cursinhos pré-vestibulares populares presentes em universidades públicas no estado de São Paulo, buscando informações referentes ao número de vagas disponibilizadas, ao número de professores (discentes) e docentes participantes, ao número de bolsas de estudos e o número de egressos aprovados nos vestibulares das universidades públicas e particulares, além de identificar as parcerias realizadas entre os cursinhos e diferentes entidades públicas e/ou privadas. Desse modo, buscamos compreender qual o caráter social das universidades analisadas a partir de uma vertente que busca a inserção de uma população que historicamente foi marginalizada destes espaços. Conforme produção acadêmica sobre o tema, os cursinhos pré-vestibulares populares são iniciativas sem fins lucrativos, que contam com a participação de instituições religiosas, associações comunitárias, universidades, estudantes egressos desses mesmos cursos, professores, entre outros atores sociais. A proposta comum a todos os cursinhos populares é a democratização do acesso ao ensino superior para uma população que historicamente vinha sofrendo um processo de exclusão do ensino superior público, principalmente negros, pessoas de baixa renda e egressos de escolas públicas. O estado da arte de teses e dissertações que versam sobre cursinhos pré-vestibulares populares no estado de São Paulo, apresentado no primeiro capítulo desta dissertação, também nos permitiu criar três grandes eixos temáticos, definidos a partir das tendências de temas abordados dentro das pesquisas: 1) cursinhos populares e os movimentos sociais; 2) práticas pedagógicas e formação de professores; e 3) trajetória e identidade dos alunos de cursinhos populares. Por se tratarem de ações que são desenvolvidas em parceria com as universidades, também utilizamos como referencial teórico autores que discutem sobre extensão universitária, o que nos permitiu, em nosso ver, referenciar a extensão universitária enquanto ação política e social das universidades. Para tanto, nossas análises partem do referencial teórico em Paulo Freire e Boaventura de Sousa Santos. No que tange a atuação dos cursinhos, o levantamento resultou na identificação de 62 núcleos de pré-vestibulares populares, sendo que destes, 53 (85%) encontram-se associados a universidades estaduais. Juntos, os cursinhos disponibilizaram em 2019 ao menos 9762 vagas. Embora tenham os mesmos objetivos, os cursinhos diferem-se, entre outros fatores, por estarem ou não institucionalizados por meio de Pró-reitorias de extensão universitária. Todavia, é possível afirmar que as atividades desenvolvidas por estes cursinhos - independentemente de estarem ou não institucionalizados -, resultam em uma interação transformadora entre as universidades e os demais setores da sociedade que lutam pelo acesso ao ensino superior de milhares de estudantes egressos da rede pública de ensino e de camadas socioeconomicamente desfavorecidas. Posto isto, esperamos que a pesquisa contribua cientificamente com este movimento dos pré-vestibulares populares, sobretudo em relação ao papel social das universidades por meio de suas associações com estes cursinhos no estado de São Paulo. This research - of a bibliographic and documentary nature - had as objective to analyze the operation and the activities developed by popular courses pre-entry examination being in public universities in the state of São Paulo, searching for information regarding the number of places available, the number of teachers ( students) and participating teachers, to the number of scholarships and the number of graduates approved in public and private university entrance exams, as well as to identify the partnerships between the schools and different public and / or private entities. In this way, we seek to understand the social character of the universities analyzed from a perspective that seeks the insertion of a population that historically has been marginalized from these spaces. According to academic production on the subject, popular courses pre-entry examination are non-profit initiatives, with the participation of religious institutions, community associations, universities, students graduating from these courses, teachers, among other social actors. The common proposal for all popular courses is the democratization of access to higher education for a population that has historically been undergoing a process of exclusion from public higher education, mainly blacks, low-income people and public school graduates. The state of the art of theses and dissertations on popular pre-entry examination courses in the state of São Paulo, presented in the first chapter of this dissertation, also allowed us to create three main thematic axes, defined based on the trends of topics covered in the research: 1) popular coursework and social movements; 2) pedagogical practices and teacher training; and 3) trajectory and identity of students from popular schools. Because they are actions that are developed in partnership with the universities, we also use as theoretical reference authors that discuss about university extension, which allowed us, in our view, to refer to university extension as a political and social action of universities. For that, our analyzes depart from the theoretical reference in Paulo Freire and Boaventura de Sousa Santos. Regarding the activities of the courses, the survey resulted in the identification of 62 nuclei of pre-university entrance exams, of which 53 (85%) are associated with state universities. Together, the courses made available in 2019 at least 9762places. Although they have the same objectives, the courses differ, among other factors, because they are institutionalized or not through Pro-rectorships of university extension. However, it is possible to affirm that the activities carried out by these schools, regardless of whether they are institutionalized or not, result in a transformative interaction between the universities and other sectors of society that struggle for access to higher education for thousands of students who leave public schools socioeconomically disadvantaged sectors. Having said this, we hope that the research contributes scientifically to this movement of the popular pre-entry examination, especially in relation to the social role of universities through their associations with these coursesworks in the state of São Paulo. CAPES: 88882.180656/2018-01

Published
2020

20. Additional file 4 of Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Abstract

Additional file 4. Chemosensory receptor sequences.

Published
2020
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21. Additional file 7 of Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Abstract

Additional file 7. Complete ATP-binding cassette transporter (ABC) and carboxylesterase sequences.

Published
2020
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22. Additional file 1 of Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Abstract

Additional file 1. Supplementary notes, figures and small tables.

Published
2020
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23. Additional file 6 of Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Subjects
enzymes and coenzymes (carbohydrates), organic chemicals, heterocyclic compounds, respiratory system, urologic and male genital diseases
Abstract

Additional file 6. Complete and partial cytochrome p450 (CYP) sequences.

Published
2020
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24. Additional file 5 of Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, Baumann, Aaron A., Sulley Ben-Mahmoud, Christiaens, Olivier, Wannes Dermauw, Ioannidis, Panagiotis, Jacobs, Chris G. C., Jentzsch, Iris M. Vargas, Oliver, Jonathan E., Poelchau, Monica F., Rajarapu, Swapna Priya, Schneweis, Derek J., Snoeck, Simon, Clauvis N. T. Taning, Wei, Dong, Shirani M. K. Widana Gamage, Hughes, Daniel S. T., Shwetha C. Murali, Bailey, Samuel T., Bejerman, Nicolas E., Holmes, Christopher J., Jennings, Emily C., Rosendale, Andrew J., Rosselot, Andrew, Hervey, Kaylee, Schneweis, Brandi A., Cheng, Sammy, Childers, Christopher, Simão, Felipe A., Dietzgen, Ralf G., Hsu Chao, Dinh, Huyen, Harsha Vardhan Doddapaneni, Dugan, Shannon, Han, Yi, Lee, Sandra L., Muzny, Donna M., Jiaxin Qu, Worley, Kim C., Benoit, Joshua B., Friedrich, Markus, Jones, Jeffery W., Panfilio, Kristen A., Yoonseong Park, Robertson, Hugh M., Smagghe, Guy, Ullman, Diane E., Maurijn Van Der Zee, Leeuwen, Thomas Van, Veenstra, Jan A., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Whitfield, Anna E., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Abstract

Additional file 5. Neuropeptide and protein hormone peptide sequences with highlighted features.

Published
2020
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25. Genome-enabled insights into the biology of thrips as crop pests

Author

Rotenberg, Dorith, primary, Baumann, Aaron A., additional, Ben-Mahmoud, Sulley, additional, Christiaens, Olivier, additional, Dermauw, Wannes, additional, Ioannidis, Panagiotis, additional, Jacobs, Chris G.C., additional, Vargas Jentzsch, Iris M., additional, Oliver, Jonathan E., additional, Poelchau, Monica F., additional, Rajarapu, Swapna Priya, additional, Schneweis, Derek J., additional, Snoeck, Simon, additional, Taning, Clauvis N.T., additional, Wei, Dong, additional, Widana-Gamage, Shirani M. K., additional, Hughes, Daniel S.T., additional, Murali, Shwetha C., additional, Bailey, Sam, additional, Bejerman, Nicolas E., additional, Holmes, Christopher J, additional, Jennings, Emily C., additional, Rosendale, Andrew J., additional, Rosselot, Andrew, additional, Hervey, Kaylee, additional, Schneweis, Brandi A., additional, Cheng, Sammy, additional, Childers, Christopher, additional, Simão, Felipe A., additional, Dietzgen, Ralf G., additional, Chao, Hsu, additional, Dinh, Huyen, additional, Doddapaneni, HarshaVardhan, additional, Dugan, Shannon, additional, Han, Yi, additional, Lee, Sandra L., additional, Muzny, Donna M., additional, Qu, Jiaxin, additional, Worley, Kim C., additional, Benoit, Joshua B., additional, Friedrich, Markus, additional, Jones, Jeffery W., additional, Panfilio, Kristen A., additional, Park, Yoonseong, additional, Robertson, Hugh M., additional, Smagghe, Guy, additional, Ullman, Diane E., additional, van der Zee, Maurijn, additional, Van Leeuwen, Thomas, additional, Veenstra, Jan A., additional, Waterhouse, Robert M., additional, Weirauch, Matthew T., additional, Werren, John H., additional, Whitfield, Anna E., additional, Zdobnov, Evgeny M., additional, Gibbs, Richard A., additional, and Richards, Stephen, additional

Published
2020
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26. La nueva/vieja Discusión sobre el 'Escola sem Partido'

Author

Senna, Luiz Felipe Garcia de and Simão, Felipe Pinto

Subjects
Escola sem Partido, Educação, Educación, Science Teaching, Enseñanza de las ciencias, Education, Ensino de Ciências
Abstract

This text presents reflections about the “Escola sem Partido (ESP)” movement, which had its genesis in 2014. Like other conservative movements that have taken place in North America, the “ESP” states to fight against “the political and ideological indoctrination of students by teachers”, and the “usurpation of parental rights in the moral and religious education of their children.” Behind the naive assertion of a neutral school defense there are banners that are poorly understood, but very well-articulated with religious conservatives, market, and elitist sectors that see public education as threatening to their privileges. Este texto presenta reflexiones sobre el movimiento “Escola sem Partido (ESP)”, que tuvo su origen en 2014. Al igual que otros movimientos conservadores que han tenido lugar en América del Norte, el “ESP” declara luchar contra “el adoctrinamiento político e ideológico de estudiantes por parte de los maestros”, y la “usurpación de los derechos de los padres en la educación moral y religiosa de sus hijos”. Detrás de la simple afirmación de una defensa escolar neutral, hay banderas poco claras, pero que están muy bien articuladas con sectores conservadores religiosos, mercadológicos y elitistas, que ven la educación pública como una amenaza para sus privilegios. Este texto apresenta reflexões acerca do movimento Escola sem Partido (ESP), que teve sua gênese em 2014. Assim como outros movimentos conservadores que têm ocorrido na América do Norte, o ESP afirma lutar contra: “a doutrinação política e ideológica dos alunos por parte de professores” e a “usurpação dos direitos dos pais na educação moral e religiosa de seus filhos”. Por trás da ingênua afirmação de defesa de uma escola neutral, encontram-se bandeiras pouco esclarecidas, mas muito bem articuladas com setores conservadores religiosos, mercadológicos e elitistas, que veem na educação pública ameaças aos seus privilégios.

Published
2019

27. Using BUSCO to Assess Insect Genomic Resources

Author

Waterhouse, Robert M., Seppey, Mathieu, Simão, Felipe A., Zdobnov, Evgeny M., Waterhouse, Robert M., Seppey, Mathieu, Simão, Felipe A., and Zdobnov, Evgeny M.

Abstract

The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships amongst different species or orders and to build ‘omics’ resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.

Published
2019

31. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Author

Simão, Felipe A., Waterhouse, Robert M., Ioannidis, Panagiotis, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Simão, Felipe A., Waterhouse, Robert M., Ioannidis, Panagiotis, Kriventseva, Evgenia V., and Zdobnov, Evgeny M.

Abstract

Motivation: Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. Results: We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. Availability and implementation: Software implemented in Python and datasets available for download from http://busco.ezlab.org. Contact: evgeny.zdobnov@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online

Published
2017

32. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

Author

Kriventseva, Evgenia V., Tegenfeldt, Fredrik, Petty, Tom J., Waterhouse, Robert M., Simão, Felipe A., Pozdnyakov, Igor A., Ioannidis, Panagiotis, Zdobnov, Evgeny M., Kriventseva, Evgenia V., Tegenfeldt, Fredrik, Petty, Tom J., Waterhouse, Robert M., Simão, Felipe A., Pozdnyakov, Igor A., Ioannidis, Panagiotis, and Zdobnov, Evgeny M.

Abstract

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software)

Published
2017

38. Genome Sequencing of the Phytoseiid Predatory MiteMetaseiulus occidentalisReveals Completely AtomizedHoxGenes and Superdynamic Intron Evolution

Author

Hoy, Marjorie A., primary, Waterhouse, Robert M., additional, Wu, Ke, additional, Estep, Alden S., additional, Ioannidis, Panagiotis, additional, Palmer, William J., additional, Pomerantz, Aaron F., additional, Simão, Felipe A., additional, Thomas, Jainy, additional, Jiggins, Francis M., additional, Murphy, Terence D., additional, Pritham, Ellen J., additional, Robertson, Hugh M., additional, Zdobnov, Evgeny M., additional, Gibbs, Richard A., additional, and Richards, Stephen, additional

Published
2016
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39. BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics.

Author

Waterhouse, Robert M, Seppey, Mathieu, Simão, Felipe A, Manni, Mosè, Ioannidis, Panagiotis, Klioutchnikov, Guennadi, Kriventseva, Evgenia V, and Zdobnov, Evgeny M

Abstract

Genomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness of genomic data sets in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). The latest software release implements a complete refactoring of the code tomake itmore flexible and extendable to facilitate high-throughput assessments. The original six lineage assessment data sets have been updated with improved species sampling, 34 new subsets have been built for vertebrates, arthropods, fungi and prokaryotes that greatly enhance resolution and data sets are now also available for nematodes, protists, and plants. Here, we present BUSCO v3 with example analyses that highlight the wideranging utility of BUSCO assessments, which extend beyond quality control of genomics data sets to applications in comparative genomics analyses, gene predictor training, metagenomics and phylogenomics. [ABSTRACT FROM AUTHOR]

Published
2018
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42. Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution.

Author

Hoy, Marjorie A., Waterhouse, Robert M., Ke Wu, Estep, Alden S., Ioannidis, Panagiotis, Palmer, William J., Pomerantz, Aaron F., Simão, Felipe A., Thomas, Jainy, Jiggins, Francis M., Murphy, Terence D., Pritham, Ellen J., Robertson, Hugh M., Zdobnov, Evgeny M., Gibbs, Richard A., and Richards, Stephen

Subjects
PHYTOSEIIDAE, PARASITIFORMES, GENOMES, PHYSIOLOGICAL control systems, TRANSPOSONS
Abstract

Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr of evolution and radically different lifestyles. We present a 152-Mb draft assembly of the M. occidentalis genome: Larger than that of its favored prey, Tetranychus urticae, but considerably smaller than those ofmany other chelicerates, enabling an extremely contiguous and complete assembly to be built-the best arachnid to date. Aided by transcriptome data, genome annotation cataloged 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. Comparisonswith other arthropods revealed a particularly dynamic and turbulent genomic evolutionary history. Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis.Uniquely among examined arthropods, this predatorymite's Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNAprocessingDicer-2 gene. Examining gene families linked to characteristic biological traits of this tiny predator provides initial insights into processes of sex determination,development,immunedefense,andhowitdetects,disables, anddigests its prey.As thefirst referencegenome for the Phytoseiidae, and for any species with the rare sex determination system of parahaploidy, the genome of the western orchard predatorymite improves genomic sampling of chelicerates and provides invaluable newresources for functional genomic analyses of this family of agriculturally important mites. [ABSTRACT FROM AUTHOR]

Published
2016
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43. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

Author

Kriventseva, Evgenia V., Tegenfeldt, Fredrik, Petty, Tom J., Waterhouse, Robert M., Simão, Felipe A., Pozdnyakov, Igor A., Ioannidis, Panagiotis, Zdobnov, Evgeny M., Kriventseva, Evgenia V., Tegenfeldt, Fredrik, Petty, Tom J., Waterhouse, Robert M., Simão, Felipe A., Pozdnyakov, Igor A., Ioannidis, Panagiotis, and Zdobnov, Evgeny M.

Abstract

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software)

44. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Author

Simão, Felipe A., Waterhouse, Robert M., Ioannidis, Panagiotis, Kriventseva, Evgenia V., Zdobnov, Evgeny M., Simão, Felipe A., Waterhouse, Robert M., Ioannidis, Panagiotis, Kriventseva, Evgenia V., and Zdobnov, Evgeny M.

Abstract

Motivation: Genomics has revolutionized biological research, but quality assessment of the resulting assembled sequences is complicated and remains mostly limited to technical measures like N50. Results: We propose a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. We implemented the assessment procedure in open-source software, with sets of Benchmarking Universal Single-Copy Orthologs, named BUSCO. Availability and implementation: Software implemented in Python and datasets available for download from http://busco.ezlab.org. Contact: evgeny.zdobnov@unige.ch Supplementary information: Supplementary data are available at Bioinformatics online

45. Using BUSCO to Assess Insect Genomic Resources.

Author

Waterhouse RM, Seppey M, Simão FA, and Zdobnov EM

Subjects
Animals, Benchmarking, Gene Dosage, High-Throughput Nucleotide Sequencing methods, Computational Biology methods, Genome, Insect, Insecta genetics, Molecular Sequence Annotation methods, Sequence Analysis, DNA methods, Software, Transcriptome
Abstract

The increasing affordability of sequencing technologies offers many new and exciting opportunities to address a diverse array of biological questions. This is evidenced in entomological research by numerous genomics and transcriptomics studies that attempt to decipher the often complex relationships among different species or orders and to build "omics" resources to drive advancement of the molecular understanding of insect biology. Being able to gauge the quality of the sequencing data is of critical importance to understanding the potential limitations on the types of questions that these data can be reliably used to address. This chapter details the use of the Benchmarking Universal Single-Copy Orthologue (BUSCO) assessment tool to estimate the completeness of transcriptomes, genome assemblies, and annotated gene sets in terms of their expected gene content.

Published
2019
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