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MBE Advance Access published online on February 23, 2008
Molecular Biology and Evolution, 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 Article

Parallel Evolution of Truncated Transfer RNA Genes in Arachnid Mitochondrial Genomes

Susan E. Masta1,* and Jeffrey L. Boore2

1 Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207. Telephone: 503-725-8505, Fax: 503-725-3888, E-mail: smasta{at}pdx.edu
2 DOE Joint Genome Institute, Department of Evolutionary Genomics, 2800 Mitchell Drive, Walnut Creek, CA 94598, University of California Berkeley, Department of Integrative Biology, 3060 Valley Life Sciences Building, Berkeley, CA 94720, and Genome Project Solutions, 1024 Promenade Street, Hercules, CA 94547

* Corresponding author: Susan E. Masta

Received for publication January 2, 2008. 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 eight new arachnid mitochondrial genomes, including representatives from six 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 four out of seven 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


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