Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies.

Autor: Abbas Q; Chair of Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany., Wilhelm M; Computational Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.; Munich Data Science Institute, Technical University of Munich, Garching, Germany., Kuster B; Munich Data Science Institute, Technical University of Munich, Garching, Germany.; Chair of Proteomics and Bioanalytics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany., Poppenberger B; Biotechnology of Horticultural Crops, TUM School of Life Sciences, Technical University of Munich, Freising, Germany., Frishman D; Chair of Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany. dimitri.frischmann@tum.de.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2024 Jun 19; Vol. 25 (1), pp. 619. Date of Electronic Publication: 2024 Jun 19.
DOI: 10.1186/s12864-024-10521-w
Abstrakt: Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation.
(© 2024. The Author(s).)
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje