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MBE Advance Access published online on March 7, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn058
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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

Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis

Koushirou Suga1,2, David B. Mark Welch3,§, Yukari Tanaka1,5, Yoshitaka Sakakura4 and Atsushi Hagiwara5

Graduate School of Science and Technology, Nagasaki University, Nagasaki, Japan and The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, MA, USA
1 Nagasaki Industrial Promotion Foundation, Omura 856-0026, Japan
2 Institute for East China Sea Research, Nagasaki University, Nagasaki 852-8521, Japan
3 Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biology Laboratory, Woods Hole, MA 02543, United States
4 Faculty of Fisheries, Nagasaki University, Nagasaki 852-8521, Japan
5 Graduate School of Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan

§ Corresponding author: email: dmarkwelch{at}mbl.edu. voice: (508) 289-7377. fax : (508) 457-4727.

Received for publication November 26, 2007. Revision received February 5, 2008. Accepted for publication February 27, 2008.

The monogonont rotifer Brachionus plicatilis is an emerging model system for a diverse array of questions in limnological ecosystem dynamics, the evolution of sexual recombination, cryptic speciation, and the phylogeny of basal metazoans. We sequenced the complete mitochondrial genome of B. plicatilis sensu strictu NH1L and found that it is composed of two circular chromosomes, designated mtDNA-I (11,153 bp) and mtDNA-II (12,672 bp). Hybridization to DNA isolated from mitochondria demonstrated that mtDNA-I is present at 4 times the copy number of mtDNA-II. The only nucleotide similarity between the two chromosomes is a 4.9 kbp region of 99.5% identity including a tRNA gene and an extensive non-coding region which contains putative D-loop and control sequence. The mtDNA-I chromosome encodes 4 proteins (ATP6, COB, NAD1 and 2), 13 transfer RNAs, and the large and small subunit ribosomal RNAs; mtDNA-II encodes 8 proteins (COX1–3, NAD3–6 and 4L) and 9 transfer RNAs. Gene order is not conserved between B. plicatilis and its closest relative with a sequenced mitochondrial genome, the acanthocephalan Leptorhynchoides thecatus, or other sequenced mitochondrial genomes. PCR assays and Southern hybridization to DNA from 18 strains of Brachionus suggest that the two-chromosome structure has been stable for millions of years. The novel organization of the B. plicatilis mitochondrial genome into two nearly equal chromosomes of 4-fold different copy number may provide insight into the evolution of metazoan mitochondria and the phylogenetics of rotifers and other basal animal phyla.

Key Words: aneuploidly • mitochondrial genome structure • metazoan evolution • Gnathifera • Rotifera • Brachionus plicatilis


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