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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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.
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout.

Hooman K Moghadam1, Moira M Ferguson, Roy G Danzmann

  • 1Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada. hkhalegh@uoguelph.ca

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Summary

Conserved noncoding elements (CNE) help identify ancient gene duplications in salmonid fish. These CNE act as anchor markers for comparative genomics, revealing paralogous affinities and evolutionary history.

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Area of Science:

  • Comparative genomics
  • Evolutionary biology
  • Genetics

Background:

  • Salmonid fishes are believed to have an autopolyploid origin (4R).
  • Paralogy relationships from earlier polyploidization events (2R/3R) remain largely unknown due to unbalanced pseudogenization.
  • Inter-specific conserved noncoding elements (CNE) may identify ancient duplicated regions if linked to conserved syntenic genes.

Purpose of the Study:

  • Investigate chromosomal positions of CNE in rainbow trout.
  • Utilize a comparative genomic framework to identify ancient paralogous affinities.
  • Test the hypothesis that CNE associated with conserved genes can reveal duplicated genomic segments.

Main Methods:

  • Genome-wide analysis to select adjacent CNE pairs in zebrafish.
  • Obtained intervening sequences from rainbow trout.
  • Localized CNE fragments to rainbow trout chromosomes and compared synteny with model vertebrates.

Main Results:

  • Identified 56 distinct CNE fragments localized to 67 chromosomal regions in rainbow trout.
  • Duplicated CNE supported previously suggested homeologies.
  • Proposed 40 new potential paralogous affinities, some showing signatures of 1R, 2R, or 3R duplications.
  • CNE markers aided in identifying homologous segments in Atlantic salmon and Arctic charr.

Conclusions:

  • CNE are more effective than coding sequences for revealing ancient paralogous affinities in vertebrate genomes.
  • CNE serve as valuable 'anchor' markers in comparative genomics.
  • Facilitates investigation of distally located candidate genes on homologous genomic segments across species.