Molecular Biology and Evolution, Vol 16, 441-452, Copyright © 1999 by Society for Molecular Biology and Evolution
J Laroche and J Bousquet
The plant mitochondrial rps3 intron was analyzed for substitution and indel
rate variation among 15 monocot and dicot angiosperms from 10 genera,
including perennial and annual taxa. Overall, the intron sequence was very
conserved among angiosperms. Based on length polymorphism, 10 different
alleles were identified among the 10 genera. These allelic differences were
mainly attributable to large indels. An insertion of 133 nucleotides,
observed in the Alnus intron was partially or completely absent in the
other lineages of the family Betulaceae. This insertion was located within
domain IV of the secondary-structure model of this group IIA intron. A
mobile element of 47 nucleotides that showed homology to sequences located
in rice rps3 intron and in intergenic plant mitochondrial genomes was found
within this insertion. Both substitution and indel rates were low among the
Betulaceae sequences, but substitution rates were increasingly larger than
indel rates in comparisons involving more distantly related taxa. From a
secondary-structure model, regions involved in helical structures were
shown to be well preserved from indels as compared to substitutions, but
compensatory changes were not observed among the angiosperm sequences
analyzed. Using approximate divergence times based on the fossil record,
substitution and indel rate heterogeneity was observed between different
pairs of annual and perennial taxa. In particular, the annual petunia and
primrose evolved more than 15 and 10 times faster, for substitution and
indel rates respectively, than the perennial birch and alder. This is the
first demonstration of an evolutionary rate difference between perennial
and annual forms in noncoding DNA, lending support to neutral causes such
as the generation time, population size, and speciation rate effects to
explain such rate heterogeneity. Surprisingly, the sequence from the rps3
intron had a high identity with the sequence of intron 1 from the
angiosperm mitochondrial nad5 gene, suggesting a common origin of these two
group IIA introns.
ORIGINAL ARTICLE
Evolution of the mitochondrial rps3 intron in perennial and annual angiosperms and homology to nad5 intron 1
Centre de Recherche en Biologie Forestiere, Universite Laval, Quebec, Canada.
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