PXD034605

PXD034605 is an original dataset announced via ProteomeXchange.

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	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:36:43.182.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Esdras Matheus Gomes da Silva
SpeciesList	scientific name: Angiostrongylus costaricensis; NCBI TaxID: 334426;
ModificationList	carbamoylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

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.

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]

submitter keyword: RNA-Seq

mass spectrometry

nematode

genome annotation

ncRNAs

Ana Gisele da Costa Neves-Ferreira
contact affiliation	Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
contact email	anag@ioc.fiocruz.br
lab head
Esdras Matheus Gomes da Silva
contact affiliation	Fiocruz
contact email	matheusdras@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD034605

PRIDE project URI

• PRIDE
  1. PXD034605
     1. Label: PRIDE project
     2. Name: Identification of novel genes and proteoforms in Angiostrongylus costaricensis through a proteogenomic approach