206 Review TRENDS in Parasitology Vol.18 No.5 May 2002 Mitochondrial genomes of parasitic flatworms Thanh H Le, David Blair and Donald P McManus Complete or near-complete mitochondrial genomes are now available for 11 species or strains of parasitic flatworms belonging to the Trematoda and the Cestoda The organization of these genomes is not strikingly different from those of other eumetazoans, although one gene (atp8) commonly found in other phyla is absent from flatworms The gene order in most flatworms has similarities to those seen in higher protostomes such as annelids However, the gene order has been drastically altered in Schistosoma mansoni, which obscures this possible relationship Among the sequenced taxa, base composition varies considerably, creating potential difficulties for phylogeny reconstruction Long non-coding regions are present in all taxa, but these vary in length from only a few hundred to ~10 000 nucleotides Among Schistosoma spp., the long non-coding regions are rich in repeats and length variation among individuals is known Data from mitochondrial genomes are valuable for studies on species identification, phylogenies and biogeography Thanh H Le Donald P McManus* Molecular Parasitology Laboratory, Australian Centre for International and Tropical Health and Nutrition, The Queensland Institute of Medical Research and The University of Queensland, Brisbane, Queensland 4029, Australia *e-mail: donm@qimr.edu.au David Blair School of Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia Mitochondria are involved in respiratory metabolism in most eukaryotes (Box 1) Mitochondrial (mt) genomes are small, generally circular and haploid, with characteristics that indicate a prokaryotic origin [1] and an abundance of genetic novelties [2,3] In animals, mt genomes (~13 000–16 000 nt) contain genes encoding 12 or 13 proteins which are vital components of the respiratory-chain enzyme complexes, two ribosomal RNAs (rRNA) and 22 transfer RNAs (tRNA) (Box 1) Intergenic sequences are usually very short However, there is also at least one long non-coding region (LNR), often variable in length [2,4,5], with an initiation site for replication in some species which could be associated with stable secondary structures Mt genomes are inherited maternally in almost all metazoans This is presumably the case for parasitic flatworms, although there are suggestions of occasional paternal inheritance in Schistosoma mansoni [6] Flatworm mt genomes Over 130 complete or partially sequenced metazoan mt genomes are available for study [3,5] Until recently, no complete mt genomes were available for any flatworm species Echinococcus multilocularis was the first to be sequenced (M Nakao et al., unpublished; GenBank no AB018440) Available complete or near-complete mt genomes from flatworms are listed in Table (Box 2) [7–11] Flatworm mt genomes are similar to those of other eumetazoans in length, gene composition, and in their tRNA and rRNA structure (Box 1) As is also the case in nematodes and a few other metazoans, atp8 is missing It is noteworthy that the mt genome of http://parasites.trends.com Taenia crassiceps (13 503 nt) is the smallest of all metazoan mtDNA examined to date Gene order In animals, mt gene order generally remains stable over a long time Differences between members of the same family are rare, although marked differences can occur at higher taxonomic levels, in particular, classes or phyla [2,3,5] A substantial difference in gene order was found [7] between S mansoni (and probably other African Schistosoma spp.) and all other trematodes and cestodes (Box 3) The magnitude of the differences in mt gene order between the African and Asian schistosomes is unprecedented among metazoans belonging to the same genus This illustrates the potential pitfalls of using mt gene order for phylogenetic inference without including a diverse sampling of species within each major taxon The considerable difference in gene order is also reflected in the marked difference in sequence between S mansoni and S japonicum [9] Genetic code Mt codon assignments for flatworms have been proposed in several studies [12–15], including some on non-parasitic turbellarians [16] It is now well established that mitochondria of parasitic flatworms and all rhabditophoran platyhelminths use AAA to specify Asn (Lys in the universal code), AGA and AGG to specify Ser (Arg in the universal code), and TGA to specify Trp (‘stop’ in the universal code) Furthermore, TAG and TAA act as stop codons (there is some evidence that abbreviated stop codons, T or TA, exist in a few cases [10]) (Fig 1) This code is the same as that seen in the Echinodermata, apparently as a result of convergent evolution [16] Although ATG is the usual start codon, GTG is sometimes used and perhaps other codons rarely [9–11] Nucleotide composition and codon usage Invertebrate mt genomes tend to be AT-rich [4], a feature also noted in protein-coding genes of several parasitic flatworms However, nucleotide composition is not uniform among the species (Fig 1) Values for >70% AT are seen in T crassiceps and in all Schistosoma spp except for S mansoni (68.7%), whereas Fasciola hepatica is 63.5% AT and Paragonimus westermani is only 51.5% AT Cytosine is poorly represented in most species with the exception of P westermani (Fig 1) In addition to the 1471-4922/02/$ – see front matter © 2002 Elsevier Science Ltd All rights reserved PII: S1471-4922(02)02252-3 Review TRENDS in Parasitology Vol.18 No.5 May 2002 207 Box Mitochondrial genomes: structure and terminology S d5 LNR 800 16 L 00 136 cob d4 00 na 00 0 11200 200 48 00 1040 4000 rrnS 60 Q F M 56 V 00 00 640 7200 800 88 rr n L d1 A D na T cox1 nad3 K IP N W S1 Fig I bias in base composition, there is also an asymmetry (skew) in the number of complementary bases on a given strand [3] Thus, the concatenated proteincoding genes of S mansoni have 45.7% T, but only 23.1% A, on the sense strand A similar situation occurs in other species The considerable differences among species in base composition in protein-coding genes might be reflected to differences in the protein sequences However, the redundancy in the genetic code provides a means by which a mt genome could theoretically compensate for base-composition bias Increased use of unusually abundant bases in the (largely redundant) third codon position means that base composition bias will be less marked in the first and second codon positions Hence, atp6 3200 cox2 C nad 12 00 24 R L2 S2 L1 Y cox3 nad E nad6 Reference a Le, T.H et al (2001) Complete DNA sequence and gene organization of the mitochondrial genome of the liver fluke, Fasciola hepatica L (Platyhelminthes; Trematoda) Parasitology 123, 609–621 H G NR na The liver fluke Fasciola hepatica has a mitochondrial (mt) genome typical of those of most animals [a] The circular genome consists of 14 462 nt (Fig I) The 12 protein-coding genes fall into the following categories: nicotinamide dehydrogenase complex (nad1–nad6 and nad4L subunits); cytochrome c oxidase complex (cox1–cox3 subunits); cytochrome b (cob) and adenosine triphosphatase subunit (atp6) Two genes encoding ribosomal RNA subunits are present: the large subunit (rrnL or 16S) and small subunit (rrnS or 12S), which are separated by trnC, encoding the transfer RNA (tRNA) for cysteine As in other mt genomes, there are 22 tRNA genes, denoted in the figure by the one-letter code for the amino acid they specify Leu and Ser are each specified by two different tRNAs, reflecting the number and base composition of the relevant codons As in other flatworms, all genes are transcribed in the same direction (indicated by arrows in Fig I) Genes lack introns and are usually adjacent to one another or separated by only a few nucleotides However, some genes overlap, most notably nad4 and nad4L (40 nt in F hepatica) Another example of possible overlap is shown in Fig in the main text In F hepatica, the largest non-coding region is divided by trnG into two parts, the short non-coding region (SNR, 187 nt) and the long non-coding region (LNR, 817 nt), the LNR containing eight identical tandem repeats of 85 nt and one additional imperfect copy of the repeat TRENDS in Parasitology protein sequences could differ less than might be expected from raw base-composition data Figure shows that unusually common bases (relative to other parasitic flatworms) are over-represented at third codon positions (e.g C constitutes