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Related Experiment Video

Updated: Jul 9, 2025

The ITS2 Database
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GC heterogeneity reveals sequence-structures evolution of angiosperm ITS2.

Yubo Liu1,2, Nan Liang1,3, Qing Xian1

  • 1Marine College, Shandong University, Weihai, 264209, China.

BMC Plant Biology
|December 1, 2023
PubMed
Summary

GC variation in plant ITS2 DNA is driven by GC-biased gene conversion (gBGC) and selection for thermodynamic stability. These processes influence GC content in paired regions of the ITS2 secondary structure, impacting genome diversity.

Keywords:
GC-biased gene conversionITS2 contentSecondary structureThermodynamic stability

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Area of Science:

  • Molecular Evolution
  • Genomics
  • Phylogenetics

Background:

  • GC variation is key to genome and species diversity, but its drivers are not fully understood.
  • The ITS2 region in plants is a valuable marker for studying GC variation across angiosperms.

Purpose of the Study:

  • To investigate the mechanisms driving GC content variation in the ITS2 region of angiosperms.
  • To explore the roles of GC-biased gene conversion (gBGC) and secondary structure in shaping ITS2 GC content.

Main Methods:

  • Analyzed ITS2 sequence-structures from 8666 angiosperm species using 4SALE.
  • Partitioned secondary structures into paired and unpaired regions.
  • Calculated substitution rates and frequencies for GC base-pairs in paired regions using RNA-specific models in PHASE.

Main Results:

  • ITS2 GC content distribution is heterogeneous across angiosperm phylogeny.
  • Increased GC content correlates with ITS2 sequence homogenization, supporting gBGC.
  • Paired regions exhibit higher GC content than unpaired regions, suggesting selection for thermodynamic stability.
  • RNA substitution models indicate base-pair transformations favor GC elevation and fixation in paired regions, further supporting gBGC.

Conclusions:

  • The secondary structure of ITS2 is significant for GC content investigations.
  • Both gBGC and structure-based selection are crucial factors influencing angiosperm ITS2 GC content.