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MBE Advance Access originally published online on February 23, 2008
Molecular Biology and Evolution 2008 25(5):949-959; doi:10.1093/molbev/msn051
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Parallel Evolution of Truncated Transfer RNA Genes in Arachnid Mitochondrial Genomes

Susan E. Masta* and Jeffrey L. Boore{dagger},{ddagger},§

* Department of Biology, Portland State University
{dagger} Department of Evolutionary Genomics, Department of Energy Joint Genome Institute and University of California Lawrence Berkeley National Laboratory, Walnut Creek, CA
{ddagger} Department of Integrative Biology, University of California, Berkeley
§ Genome Project Solutions, Hercules, CA

E-mail: smasta{at}pdx.edu.

Accepted for publication February 5, 2008.

The cloverleaf secondary structure of transfer RNA (tRNA) is highly conserved across all forms of life. Here, we provide sequence data and inferred secondary structures for all tRNA genes from 8 new arachnid mitochondrial genomes, including representatives from 6 orders. These data show remarkable reductions in tRNA gene sequences, indicating that T-arms are missing from many of the 22 tRNAs in the genomes of 4 out of 7 orders of arachnids. Additionally, all opisthothele spiders possess some tRNA genes that lack sequences that could form well-paired aminoacyl acceptor stems. We trace the evolution of T-arm loss onto phylogenies of arachnids and show that a genome-wide propensity to lose sequences that encode canonical cloverleaf structures likely evolved multiple times within arachnids. Mapping of structural characters also shows that certain tRNA genes appear more evolutionarily prone to lose the sequence coding for the T-arm and that once a T-arm is lost, it is not regained. We use tRNA structural data to construct a phylogeny of arachnids and find high bootstrap support for a clade that is not supported in phylogenies that are based on more traditional morphological characters. Together, our data demonstrate variability in structural evolution among different tRNAs as well as evidence for parallel evolution of the loss of sequence coding for tRNA arms within an ancient and diverse group of animals.

Key Words: tRNA secondary structure • parallel evolution • mitochondrial genome • Arachnida • Chelicerata

Franz Lang, Associate Editor


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