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Nucleic Acids Research 2005 33(14):4433-4442; doi:10.1093/nar/gki757
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Published online 5 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region

Amy M. Hauth*, Uwe G. Maier1, B. Franz Lang and Gertraud Burger

Département de Biochimie, Robert Cedergren Research Center for Bioinformatics and Genomics, Canadian Institute for Advanced Research, Université de Montréal 2900 Boulevard Edouard-Montpetit, Montréal, Québec, Canada H3T 1J4 1Cell Biology, Philipps-University Marburg Karl-von-Frisch-Strasse, D35032 Marburg, Germany

*To whom correspondence should be addressed. Tel: +1 514 343 6111, ext. 2721; Fax: +1 514 343 2210; Email: amy.hauth{at}umontreal.ca

Received June 29, 2005. Revised July 21, 2005. Accepted July 21, 2005.

To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs ~40–700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, ~3 kb, inverted repeat and several potentially stable ~40–80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved.

DDBJ/EMBL/GenBank accession no. NC_002572


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