| Author | Silva, Esdras Matheus Gomes da | |
| Author | Rebello, Karina Mastropasqua | |
| Author | Choi, Young-Jun | |
| Author | Gregorio, Vitor | |
| Author | Paschoal, Alexandre Rossi | |
| Author | Mitreva, Makedonka | |
| Author | McKerrow, James H. | |
| Author | Neves-Ferreira, Ana Gisele da Costa | |
| Author | Passetti, Fabio | |
| Access date | 2023-01-12T14:59:45Z | |
| Available date | 2023-01-12T14:59:45Z | |
| Document date | 2022 | |
| Citation | SILVA, Esdras Matheus Gomes da et al. Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach. Pathogens, v. 11, n. 1273, p. 1–16, 2022. | en_US |
| ISSN | 2076-0817 | en_US |
| URI | https://www.arca.fiocruz.br/handle/icict/56446 | |
| Language | por | en_US |
| Publisher | MDPI | en_US |
| Rights | open access | en_US |
| Subject in Portuguese | RNA-Seq | en_US |
| Subject in Portuguese | Nematodes | en_US |
| Subject in Portuguese | ncRNAs | en_US |
| Title | Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach | en_US |
| Type | Article | en_US |
| DOI | 10.3390/pathogens11111273 | |
| Abstract | RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis. We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Estudos Integrados em Protozoologia. Rio de Janeiro, RJ, Brasil. | en_US |
| Affilliation | Department of Medicine. Washington University School of Medicine. St. Louis, USA. | en_US |
| Affilliation | Universidade Tecnológica Federal do Paraná. Departamento de Ciência da Computação. Cornélio Procópio, PR, Brasil. | en_US |
| Affilliation | Universidade Tecnológica Federal do Paraná. Departamento de Ciência da Computação. Cornélio Procópio, PR, Brasil. | en_US |
| Affilliation | Department of Medicine. Washington University School of Medicine. St. Louis, USA. | en_US |
| Affilliation | Center for Discovery and Innovation in Parasitic Diseases. Skaggs School of Pharmacy and Pharmaceutical Sciences. University of California, San Diego, USA. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Toxinologia. Rio de Janeiro, RJ, Brasil. | en_US |
| Affilliation | Fundação Oswaldo Cruz. Instituto Carlos Chagas. Curitiba, PR, Brasil. | en_US |
| Subject | Mass Spectrometry | en_US |
| Subject | Nematoda | en_US |
| Subject | Molecular Sequence Annotation | en_US |
| Subject | RNA, Long Noncoding | en_US |
| Subject in Spanish | Espectrometría de Masas | en_US |
| Subject in Spanish | Nematodos | en_US |
| Subject in Spanish | Anotación de Secuencia Molecular | en_US |
| Subject in Spanish | ARN Largo no Codificante | en_US |
| Subject in French | Spectrométrie de masse | en_US |
| Subject in French | Nematoda | en_US |
| Subject in French | Annotation de séquence moléculaire | en_US |
| Subject in French | ARN long non codant | en_US |
| DeCS | Espectrometria de Massas | en_US |
| DeCS | Nematoides | en_US |
| DeCS | Anotação Gênica | en_US |
| DeCS | RNA Longo não Codificante | en_US |
| DeCS | Angiostrongylus | en_US |
