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Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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Functional genomic tools for emerging model species.

Erik Gudmunds1, Christopher W Wheat2, Abderrahman Khila3

  • 1Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.

Trends in Ecology & Evolution
|August 1, 2022
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Summary
This summary is machine-generated.

Functional validation in ecology and evolution is crucial. We advocate for gene editing via homology-directed repair (HDR) to overcome limitations of current RNA interference (RNAi) and CRISPR-Cas methods for genotype-phenotype studies.

Keywords:
CRISPR-CasRNAiemerging model organismsfunctional genomicsfunctional validationgene mapping

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Area of Science:

  • Ecology
  • Evolutionary Biology
  • Genetics

Background:

  • Connecting genotype to phenotype is a key goal in ecology and evolution.
  • Functional validation of genetic loci is often lacking in current studies.
  • RNA interference (RNAi) and CRISPR-Cas genome editing have advanced functional validation but present challenges.

Purpose of the Study:

  • To highlight the limitations of current functional validation tools in ecology and evolution.
  • To propose homology-directed repair (HDR) gene editing as a superior method for functional validation.
  • To encourage the adoption of HDR for ecologically relevant genotype-phenotype research.

Main Methods:

  • Review of current functional validation techniques in ecological and evolutionary studies.
  • Analysis of challenges associated with RNA interference (RNAi) and CRISPR-Cas in emerging model organisms.
  • Discussion of the advantages of homology-directed repair (HDR) for allelic replacement.

Main Results:

  • Current methods like RNAi and CRISPR-Cas face limitations in spatial control, efficiency, and throughput for emerging models.
  • Existing functional studies often fail to reflect ecologically relevant genetic variation.
  • Homology-directed repair (HDR) offers precise allelic replacement, enhancing functional validation capabilities.

Conclusions:

  • Homology-directed repair (HDR) gene editing is essential for advancing genotype-phenotype research in ecology and evolution.
  • Increased use of HDR will enable more robust functional validation and deeper insights into evolutionary processes.
  • Addressing the limitations of current tools through HDR adoption is critical for the field.