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Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes.

Mao-Lun Weng1, Tracey A Ruhlman2, Robert K Jansen2,3

  • 1Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57006, USA.

The New Phytologist
|December 20, 2016
PubMed
Summary
This summary is machine-generated.

Large-scale changes in the inverted repeat (IR) regions of plastid genomes significantly impact nucleotide substitution rates. Plastome evolution in Pelargonium reveals complex interactions between locus, lineage, and IR effects on sequence variation.

Keywords:
Pelargoniumgenome rearrangementinverted repeats (IR)nucleotide substitution rateplastid genome

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Area of Science:

  • * Evolutionary Biology
  • * Genomics
  • * Molecular Biology

Background:

  • * Nucleotide substitution rates in plastid genomes (plastomes) are generally lower in inverted repeat (IR) regions compared to single-copy (SC) regions.
  • * Previous studies focused on minor IR boundary changes, leaving the impact of large-scale IR expansion/contraction on substitution rates unclear.

Purpose of the Study:

  • * To investigate the influence of IR expansion and contraction on plastid nucleotide substitution rates in closely related species.
  • * To analyze sequence evolution across diverse plastome organizations within the Pelargonium genus.

Main Methods:

  • * Comparative analysis of plastomes from 22 Pelargonium species, including eight newly sequenced genomes.
  • * Application of both pairwise and model-based comparative approaches to assess sequence evolution.
  • * Identification and classification of different plastome organizations based on IR boundary variations and inversions.

Main Results:

  • * Ten distinct types of plastome organization were identified in Pelargonium, characterized by varying inversions and IR boundary alterations.
  • * Simple inclusion within the IR region was insufficient to explain observed variations in nucleotide substitution rates.
  • * Rate heterogeneity in Pelargonium plastomes resulted from a combination of locus-specific, lineage-specific, and IR-dependent factors.

Conclusions:

  • * The evolutionary consequences of IR repeat retention in plastomes are more complex than previously understood.
  • * Plastome sequence evolution is shaped by intricate interactions between genomic region, evolutionary lineage, and IR dynamics.