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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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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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Exon Recombination02:32

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
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Related Experiment Video

Updated: Dec 11, 2025

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
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Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

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Reconstructing protein-coding sequences from ancient DNA.

Michael Hofreiter1, Stefanie Hartmann1

  • 1Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.

Methods in Enzymology
|August 24, 2020
PubMed
Summary
This summary is machine-generated.

Researchers explore retrieving ancient DNA from fossils to study extinct species' proteins and their functions. Challenges include DNA degradation and assembly issues, with direct PCR as an alternative for shorter proteins.

Keywords:
Ancient DNAGenome assemblyMappingPaleogenomicsRe-sequencingReference sequenceSRAssemblerTargeted assembly

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Related Experiment Videos

Last Updated: Dec 11, 2025

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
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Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
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Area of Science:

  • Paleogenomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Understanding extinct species' functional biology is crucial for ecological and behavioral insights.
  • Paleogenomic data offers a potential source of genetic information from fossil specimens.

Purpose of the Study:

  • To discuss methods for retrieving DNA sequences from paleogenomic data for protein analysis.
  • To highlight challenges associated with ancient DNA and propose alternative approaches.

Main Methods:

  • Retrieving DNA sequences from fossil specimens.
  • Analyzing paleogenomic data for protein-coding regions.
  • Discussing ancient DNA degradation issues (e.g., miscoding lesions, short reads, incomplete assemblies).
  • Evaluating direct PCR amplification for ancient protein studies.

Main Results:

  • Paleogenomic data can yield DNA sequences for protein reconstruction.
  • Ancient DNA presents significant technical challenges impacting data quality and assembly.
  • Direct PCR amplification is a viable, though less common, method for specific protein targets.

Conclusions:

  • Reconstructing extinct proteins from paleogenomic data is feasible but challenging.
  • Overcoming ancient DNA degradation is key to advancing paleoproteomics.
  • Direct PCR offers a complementary strategy for studying ancient proteins.