PXD034605 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach |
Description | Data from multiple high throughput technologies such as RNA sequencing (RNA-Seq) and protein mass spectrometry (MS/MS) are often used to assist in predicting eukaryote genome features such as genes, splice variants, and single nucleotide variants (SNVs). The genomes of parasitic nematodes causing neglected tropical diseases are often poorly annotated. Angiostrongylus costaricensis, a nematode that causes an intestinal inflammatory disease known as abdominal angiostrongyliasis (AA), is one example. Currently, no drugs or treatments are available for AA, a public health problem in Latin America, especially in Costa Rica and Brazil. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version 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 supplemented the reference annotation with a) novel coding and non-coding genes; b) pieces of evidence of alternative splicing generating new proteoforms; c) a list of SNVs specific to the Brazilian strain (Crissiumal). 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 parasitic nematode. We hope this supplemented genome annotation can assist the future development of drugs to treat AA caused by either Brazil strain (Crissiumal) or Costa Rica strain. |
HostingRepository | PRIDE |
AnnounceDate | 2023-03-11 |
AnnouncementXML | Submission_2023-03-10_20:09:37.367.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Esdras MatheusGomes da Silva |
SpeciesList | scientific name: Angiostrongylus costaricensis; NCBI TaxID: 334426; |
ModificationList | carbamoylated residue; deamidated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-06-16 03:52:37 | ID requested | |
⏵ 1 | 2023-03-10 20:09:38 | announced | |
2 | 2023-11-14 08:36:44 | announced | 2023-11-14: Updated project metadata. |
Publication List
da Silva EMG, Rebello KM, Choi YJ, Gregorio V, Paschoal AR, Mitreva M, McKerrow JH, Neves-Ferreira AGDC, Passetti F, through a Proteogenomic Approach. Pathogens, 11(11):(2022) [pubmed] |
Keyword List
submitter keyword: RNA-Seq |
mass spectrometry |
nematode |
genome annotation |
ncRNAs |
Contact List
Ana Gisele da CostaNeves-Ferreira |
contact affiliation | Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil |
contact email | anag@ioc.fiocruz.br |
lab head | |
Esdras MatheusGomes da Silva |
contact affiliation | Fiocruz |
contact email | matheusdras@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD034605
- Label: PRIDE project
- Name: Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach