Refinement of Leishmania donovani Genome Annotations in the Light of Ribosome-Protected mRNAs Fragments (Ribo-Seq Data)
Author:
Sánchez-Salvador Alejandro1ORCID, González-de la Fuente Sandra2ORCID, Aguado Begoña2ORCID, Yates Phillip A.3ORCID, Requena Jose M.14ORCID
Affiliation:
1. Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain 2. Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Genomic and NGS Facility (GENGS), 28049 Madrid, Spain 3. Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA 4. Centro de Investigación Biomédica en Red (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
Abstract
Advances in next-generation sequencing methodologies have facilitated the assembly of an ever-increasing number of genomes. Gene annotations are typically conducted via specialized software, but the most accurate results require additional manual curation that incorporates insights derived from functional and bioinformatic analyses (e.g., transcriptomics, proteomics, and phylogenetics). In this study, we improved the annotation of the Leishmania donovani (strain HU3) genome using publicly available data from the deep sequencing of ribosome-protected mRNA fragments (Ribo-Seq). As a result of this analysis, we uncovered 70 previously non-annotated protein-coding genes and improved the annotation of around 600 genes. Additionally, we present evidence for small upstream open reading frames (uORFs) in a significant number of transcripts, indicating their potential role in the translational regulation of gene expression. The bioinformatics pipelines developed for these analyses can be used to improve the genome annotations of other organisms for which Ribo-Seq data are available. The improvements provided by these studies will bring us closer to the ultimate goal of a complete and accurately annotated L. donovani genome and will enhance future transcriptomics, proteomics, and genetics studies.
Funder
Spanish Ministerio de Ciencia Instituto de Salud Carlos III Fundacion Ramon Areces National Institute of Allergy and Infectious Diseases
Subject
Genetics (clinical),Genetics
Reference32 articles.
1. Alvar, J., Velez, I.D., Bern, C., Herrero, M., Desjeux, P., Cano, J., Jannin, J., and den Boer, M. (2012). Leishmaniasis worldwide and global estimates of its incidence. PLoS ONE, 7. 2. Global leishmaniasis surveillance: 2019–2020, a baseline for the 2030 roadmap;Saurabh;Wkly. Epidemiol. Rec.,2021 3. McCall, L.I., Zhang, W.W., and Matlashewski, G. (2013). Determinants for the development of visceral leishmaniasis disease. PLoS Pathog., 9. 4. The Genome of the Kinetoplastid Parasite, Leishmania major;Ivens;Science,2005 5. Camacho, E., González-de la Fuente, S., Solana, J.C., Rastrojo, A., Carrasco-Ramiro, F., Requena, J.M., and Aguado, B. (2021). Gene annotation and transcriptome delineation on a de novo genome assembly for the reference Leishmania major Friedlin strain. Genes, 12.
|
|