IMPROVED GENOME ANNOTATION OF ANGIOSTRONGYLUS COSTARICENSIS NEMATODE BASED ON PROTEOGENOMICS DATA ANALYSIS

Esdras Matheus Gomes da Silva; Karina Mastropasqua Rebello; Makedonka Mitreva; James McKerrow; Ana Gisele da Costa Neves-Ferreira; Fabio Passetti

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Paper Title

IMPROVED GENOME ANNOTATION OF ANGIOSTRONGYLUS COSTARICENSIS NEMATODE BASED ON PROTEOGENOMICS DATA ANALYSIS

Authors

Esdras Matheus Gomes da Silva
Karina Mastropasqua Rebello
Makedonka Mitreva
James McKerrow
Ana Gisele da Costa Neves-Ferreira
Fabio Passetti

Modality

Xpress presentation

Subject area

Omics

Publishing Date

26/04/2022

Country of Publishing

Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeetingxp2021/421939-improved-genome-annotation-of-angiostrongylus-costaricensis-nematode-based-on-proteogenomics-data-analysis

ISBN

978-65-5941-645-5

Keywords

RNA-Seq, mass spectrometry, nematode

Summary

RNA sequencing (RNA-Seq) and mass spectrometry-based proteomics data are often integrated in proteogenomic studies to assist the prediction of eukaryote genome features, such as genes, splicing forms, single nucleotide variants (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 nematode that causes an intestinal inflammatory illness known as abdominal angiostrongyliasis (AA). This disease is a public health problem in Latin America, especially in Costa Rica and Brazil, and no drugs or treatments are available. The current draft version of the A. costaricensis genome (WBPS15) is specific to the Costa Rican strain and is not supported by transcript or protein pieces of evidence. This study employed computational tools to integrate RNA-Seq and MS/MS data to improve A. costaricensis genome annotation. As a result, 2,359 novel genes and 11,818 novel transcripts, including splicing variants, are provided in this new genome annotation. A list of 544 nonsense SNVs, 62,758 conservative missense SNVs, and 68,133 non-conservative missense SNVs specific to the Brazilian strain (Crissiumal) were identified based on the corresponding RNA-Seq data. All protein-coding transcripts with complete ORFs were computationally translated to build a customized protein sequence database used to investigate the proteome of A. costaricensis. This database also contained protein sequences with computationally translated missense SNVs. These missense SNVs were confirmed at the protein level by identifying 11,273 peptides containing SAAVs in the MS data. The abundances of 1,242 transcripts and their corresponding proteins were estimated, and the transcript/protein pairs were clustered. Interestingly, this analysis revealed two main groups of mRNAs and proteins with equivalent abundance and two other groups with inversely proportional mRNA/protein abundance levels. These observations should be further explored and may contribute to a better understanding of the biology of A. costaricensis. Our integrated computational analysis of transcriptomic and proteomic data allowed the proposal of an optimized gene annotation for the A. costaricensis genome, encompassing specific characteristics of the Brazilian strain.

Title of the Event: X-Meeting XPerience 2021
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

SILVA, Esdras Matheus Gomes da et al.. IMPROVED GENOME ANNOTATION OF ANGIOSTRONGYLUS COSTARICENSIS NEMATODE BASED ON PROTEOGENOMICS DATA ANALYSIS.. In: X-Meeting presentations. Anais...São Paulo(SP) AB3C, 2021. Available in: https//www.even3.com.br/anais/xmeetingxp2021/421939-IMPROVED-GENOME-ANNOTATION-OF-ANGIOSTRONGYLUS-COSTARICENSIS-NEMATODE-BASED-ON-PROTEOGENOMICS-DATA-ANALYSIS. Access in: 08/05/2025