Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution Rates and Elevated GC Content.
Abstract
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR)
region and two larger single copy (SC) regions. Patterns of molecular evolution in
the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution
in the IR compared to the SC region. In addition, the organization and structure of
plastomes is fluid, and rearrangements through time have repeatedly shuffled genes
into and out of the IR, providing recurrent natural experiments on how chloroplast
genome structure can impact rates and patterns of molecular evolution. Here we examine
four loci (psbA, ycf2, rps7, and rps12 exon 2-3) that were translocated from the SC
into the IR during fern evolution. We use a model-based method, within a phylogenetic
context, to test for substitution rate shifts. All four loci show a significant, 2-
to 3-fold deceleration in their substitution rate following translocation into the
IR, a phenomenon not observed in any other, nontranslocated plastid genes. Also, we
show that after translocation, the GC content of the third codon position and of the
noncoding regions is significantly increased, implying that gene conversion within
the IR is GC-biased. Taken together, our results suggest that the IR region not only
reduces substitution rates, but also impacts nucleotide composition. This finding
highlights a potential vulnerability of correlating substitution rate heterogeneity
with organismal life history traits without knowledge of the underlying genome structure.
Type
Journal articleSubject
PlastidsChloroplasts
Ferns
Codon
Evolution, Molecular
Phylogeny
Gene Conversion
Base Composition
Genome, Chloroplast
Inverted Repeat Sequences
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https://hdl.handle.net/10161/21733Published Version (Please cite this version)
10.1093/gbe/evw167Publication Info
Li, F; Kuo, L; Pryer, KM; & Rothfels, CJ (2016). Genes Translocated into the Plastid Inverted Repeat Show Decelerated Substitution
Rates and Elevated GC Content. Genome biology and evolution, 8(8). pp. 2452-2458. 10.1093/gbe/evw167. Retrieved from https://hdl.handle.net/10161/21733.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Kathleen M. Pryer
Professor of Biology

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