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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.<\/jats:p>","DOI":"10.3390\/pathogens11111273","type":"journal-article","created":{"date-parts":[[2022,11,1]],"date-time":"2022-11-01T06:01:28Z","timestamp":1667282488000},"page":"1273","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Identification of Novel Genes and Proteoforms in Angiostrongylus costaricensis through a Proteogenomic Approach"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9084-938X","authenticated-orcid":false,"given":"Esdras Matheus Gomes","family":"da Silva","sequence":"first","affiliation":[{"name":"Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil"},{"name":"Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9495-8399","authenticated-orcid":false,"given":"Karina Mastropasqua","family":"Rebello","sequence":"additional","affiliation":[{"name":"Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil"},{"name":"Laboratory of Integrated Studies in Protozoology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-360, RJ, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Young-Jun","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vitor","family":"Gregorio","sequence":"additional","affiliation":[{"name":"Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Corn\u00e9lio Proc\u00f3pio 86300-000, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8887-0582","authenticated-orcid":false,"given":"Alexandre Rossi","family":"Paschoal","sequence":"additional","affiliation":[{"name":"Bioinformatics and Pattern Recognition Group (Bioinfo-CP), Department of Computer Science (DACOM), Federal University of Technology-Parana (UTFPR), Corn\u00e9lio Proc\u00f3pio 86300-000, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9572-3436","authenticated-orcid":false,"given":"Makedonka","family":"Mitreva","sequence":"additional","affiliation":[{"name":"Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James H.","family":"McKerrow","sequence":"additional","affiliation":[{"name":"Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA 92093, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7863-9512","authenticated-orcid":false,"given":"Ana Gisele da Costa","family":"Neves-Ferreira","sequence":"additional","affiliation":[{"name":"Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, RJ, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5672-7848","authenticated-orcid":false,"given":"Fabio","family":"Passetti","sequence":"additional","affiliation":[{"name":"Instituto Carlos Chagas, Fiocruz, Curitiba 81350-010, PR, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,31]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1186\/s13059-019-1715-2","article-title":"Next-generation genome annotation: We still struggle to get it right","volume":"20","author":"Salzberg","year":"2019","journal-title":"Genome Biol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/gb-2006-7-s1-s10","article-title":"Automatic annotation of eukaryotic genes, pseudogenes and promoters","volume":"7","author":"Solovyev","year":"2006","journal-title":"Genome Biol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1006\/jmbi.1997.0951","article-title":"Prediction of complete gene structures in human genomic DNA","volume":"268","author":"Burge","year":"1997","journal-title":"J. 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