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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Related Experiment Video

Updated: Jun 23, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies.

Qussai Abbas1, Mathias Wilhelm2,3, Bernhard Kuster3,4

  • 1Chair of Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany.

BMC Genomics
|June 19, 2024
PubMed
Summary

Accurate plant genome annotation is crucial for crop improvement and food security. This study evaluates BRAKER2 and Helixer, finding genome complexity impacts their gene prediction accuracy for proteomics.

Keywords:
Bioinformatics algorithmsCrop genomicsGene predictionGenome annotationPeptide identificationPlant evolution

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Area of Science:

  • Plant genomics
  • Bioinformatics
  • Crop science

Background:

  • Plant genomics is vital for food security and sustainable agriculture.
  • Structural genome annotation faces challenges in crops due to size, polyploidy, and repetitive DNA.
  • Advancements in sequencing necessitate robust annotation tools.

Purpose of the Study:

  • To review the current state of crop genomics research.
  • To assess the accuracy of gene prediction tools (BRAKER2, Helixer) in crop genomes.
  • To evaluate the utility of predicted proteins for proteomics.

Main Methods:

  • Comparative analysis of BRAKER2 and Helixer performance on diverse crop genomes.
  • Investigation of factors influencing gene prediction accuracy (complexity, repeats, fragmentation).
  • Assessment of predicted protein sets for mass spectrometry-based proteomics.

Main Results:

  • BRAKER2 and Helixer show varying strengths and limitations in crop genome annotation.
  • Genome complexity, fragmentation, and repeat content significantly affect annotation accuracy.
  • Predicted proteins are suitable for proteomics, but annotation quality is critical.

Conclusions:

  • Refined structural genome annotation is essential for advancing plant genomics.
  • Understanding tool limitations is key for accurate crop genome analysis.
  • This work informs future improvements in gene prediction and proteomics applications.