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Open Access Short Report

A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis

Joachim EM Jacob1*, Bartel Vanholme2, Thomas Van Leeuwen3 and Godelieve Gheysen1

Author Affiliations

1 Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium

2 VIB (Flanders Institute for Biotechnology) Department of Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Gent, Belgium

3 Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000 Gent, Belgium

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BMC Research Notes 2009, 2:192  doi:10.1186/1756-0500-2-192

Published: 24 September 2009

Abstract

Background

Mitochondria (mt) contain their own autonomously replicating DNA, constituted as a small circular genome encoding essential subunits of the respiratory chain. Mt DNA is characterized by a genetic code which differs from the standard one. Interestingly, the mt genome of nematodes share some peculiar features, such as small transfer RNAs, truncated ribosomal RNAs and - in the class of Chromadorean nematodes - unidirectional transcription.

Findings

We present the complete mt genomic sequence (16,791 bp) of the plant-parasitic nematode Radopholus similis (class Chromadorea). Although it has a gene content similar to most other nematodes, many idiosyncrasies characterize the extremely AT-rich mt genome of R. similis (85.4% AT). The secondary structure of the large (16S) rRNA is further reduced, the gene order is unique, the large non-coding region contains two large repeats, and most interestingly, the UAA codon is reassigned from translation termination to tyrosine. In addition, 7 out of 12 protein-coding genes lack a canonical stop codon and analysis of transcriptional data showed the absence of polyadenylation. Northern blot analysis confirmed that only one strand is transcribed and processed. Furthermore, using nucleotide content bias methods, regions for the origin of replication are suggested.

Conclusion

The extraordinary mt genome of R. similis with its unique genetic code appears to contain exceptional features correlated to DNA decoding. Therefore the genome may provide an incentive to further elucidate these barely understood processes in nematodes. This comprehension may eventually lead to parasitic nematode-specific control targets as healthy mitochondria are imperative for organism survival. In addition, the presented genome is an interesting exceptional event in genetic code evolution.