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What is a Species?01:17

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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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Speciation describes the formation of one or more new species from one or sometimes multiple original species. The resulting species are discrete from the parent species, and barriers to reproduction will typically exist. There are two primary mechanisms, speciation with and without geographic isolation—allopatric and sympatric speciation, respectively.
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Measures of species biodiversity, such as richness (i.e., the number of species present) and evenness (i.e., their relative abundance), describe an ecological community’s structure. Many factors affect community structure, including abiotic factors (e.g., sunlight and nutrients), disturbances (e.g., fire or flood), species interactions (e.g., predation or competition), and chance events (e.g., foreign species invasion). Certain species—such as keystone species—also play a...
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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Updated: Jan 21, 2026

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
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Developing Well-Annotated Species-Specific Protein Databases Using Comparative Proteogenomics.

Emmalyn J Dupree1, Bernard S Crimmins2,3, Thomas M Holsen2

  • 1Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA.

Advances in Experimental Medicine and Biology
|July 27, 2019
PubMed
Summary
This summary is machine-generated.

Proteomics and proteogenomics advance protein identification. Proteogenomics integrates genomics and transcriptomics to improve proteome database annotation, crucial for mass spectrometry-based studies.

Keywords:
Evolutionary proteomicsFishLake troutProtein databaseProteogenomics

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Area of Science:

  • Proteomics and Proteogenomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Proteomics studies require well-annotated protein databases, which are often lacking for non-model organisms.
  • Current methods like six-frame translation have limitations in maximizing protein identification.

Purpose of the Study:

  • To review current proteomic and proteogenomic methods.
  • To demonstrate a comparative proteomics approach for enhancing proteome annotation.

Main Methods:

  • Review of existing proteomic and proteogenomic techniques.
  • Application of comparative proteomics on lake trout liver samples.

Main Results:

  • Proteogenomics offers a unified approach to peptide identification and database enhancement.
  • Comparative proteomics can identify novel proteins and improve annotation accuracy.

Conclusions:

  • Proteogenomics is essential for building comprehensive proteome databases.
  • Integrating multiple 'omics' data improves the depth and accuracy of proteomic analysis.