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Processing the Loblolly Pine PtGen2 cDNA Microarray
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Development of a Target Enrichment Probe Set for Conifer (REMcon).

Raees Khan1,2,3,4, Ed Biffin2, Kor-Jent van Dijk1

  • 1School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, SA 5005, Australia.

Biology
|June 27, 2024
PubMed
Summary
This summary is machine-generated.

A new probe set, REMcon, enables large-scale nuclear data generation for conifer phylogenetics. This tool efficiently captures target loci, providing robust data for evolutionary studies of conifers.

Keywords:
conifersgymnospermsphylogenomicsprobe designtarget capture sequencing

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Area of Science:

  • Botany
  • Evolutionary Biology
  • Genomics

Background:

  • Conifers are vital seed plants for understanding land plant evolution.
  • Molecular phylogenetics using nuclear genes is crucial but data-limited in conifers.
  • Target enrichment sequencing is a key phylogenomic tool, but a conifer-specific probe set was lacking.

Purpose of the Study:

  • To develop and evaluate REMcon, a target sequence capture probe set for conifer phylogenetics.
  • To assess the efficiency of REMcon in generating comparable nuclear DNA sequence data across diverse conifer lineages.
  • To facilitate family- and species-level phylogenetic studies within conifers.

Main Methods:

  • Designed REMcon, a probe set targeting approximately 100 single-copy nuclear loci.
  • Tested REMcon on 69 species, representing 44 conifer genera across six families and four other gymnosperm taxa.
  • Performed phylogenetic analysis on the generated DNA sequence data.

Main Results:

  • High recovery of target loci, averaging 94% across samples with substantial read coverage.
  • Generated a well-supported phylogenetic tree consistent with existing conifer relationships.
  • Demonstrated REMcon's efficiency in producing comparable nuclear data for conifer lineages.

Conclusions:

  • REMcon is an effective tool for generating large-scale nuclear data in conifers.
  • The probe set supports robust phylogenetic analyses at family and species levels.
  • REMcon will advance evolutionary and systematic studies of the entire conifer clade.