Abstract
We sequenced a mitochondrial subgenome from the nematode Globodera rostochiensis, in two overlapping pieces. The subgenome was 9210 bp and contained four protein-coding genes (ND4, COIII, ND3, Cytb) and two tRNA genes (tRNA Thr, tRNA Gln). Genome organization was similar to that of Globodera pallida, which is multipartite. Together with the small number of genes on this subgenome, this suggests that the mitochondrial genome of G. rostochiensis is also multipartite. In the initial clones sequenced, COIII and ND3 were full-length, while ND4 and Cytb were interrupted by premature stop codons and contained point indels that disrupted the reading frame. However, sequencing of multiple clones, from DNA extracted both from multiple individuals and from single cysts, revealed a predominant source of variation—in the length of polythymidine tracts. Comparison of our genomic sequences with ESTs similarly revealed variation in the length of polythymidine tracts. We subsequently sequenced both genomic DNA and mRNA from populations of G. pallida. In each case, variation in the length of polythymidine tracts was observed. The levels of expression of mitochondrial genes in G. pallida were representative of the subgenomes present: little evidence of differential expression was observed. These observations are consistent with the operation of posttranscriptional editing in Globodera mitochondria, although this is difficult to show conclusively in the presence of intraindividual gene sequence variation. Further, alternative explanations cannot be discounted; these include the operation of slippage during translation or that genomic copies of most genes are pseudogenes with a small proportion of full-length sequences able to maintain mitochondrial function.
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References
Armstrong MR, Blok VC, Phillips MS (2000) A multipartite mitochondrial genome in the potato cyst nematode Globodera pallida. Genetics 154:181–192
Awata H, Noto T, Endoh H (2005) Differentiation of somatic mitochondria and the structural changes in mtDNA during development of the dicyemid Dicyema japonicum (Mesozoa). Mol Genet Genom 273:441–449
Beckenbach AT, Robson SKA, Crozier RH (2005) Single nucleotide +1 frameshifts in an apparently functional mitochondrial cytochrome b gene in ants of the genus Polyrhachis. J Mol Evol 60:141–152
Boore JL (1999) Animal mitochondrial genomes. Nucleic Acids Res 27:1767–1780
Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497–3500
Estevez AM, Simpson L (1999) Uridine insertion/deletion RNA editing in trypanosome mitochondria—a review. Gene 240:247–260
Gibson T, Blok VC, Dowton M (2007a) Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved amongst close nematode relatives. J Mol Evol 65:308–315
Gibson T, Blok VC, Phillips MS, Hong G, Kumarasinghe D, Riley IT, Dowton M (2007b) The mitochondrial subgenomes of the nematode Globodera pallida are mosaics: evidence of recombination in an animal mitochondrial genome. J Mol Evol 64:463–471
Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202
Horton TL, Landweber LF (2002) Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes. Curr Opin Microbiol 5:620–626
Kajander OA, Rovio AT, Majamaa K, Poulton J, Spelbrink JN, Holt IJ, Karhunen PJ, Jacobs HT (2000) Human mtDNA sublimons resemble rearranged mitochondrial genoms found in pathological states. Hum Mol Genet 9:2821–2835
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
Lunt DH, Hyman BC (1997) Animal mitochondrial DNA recombination. Nature 387:247
Mahendran R, Spottswood MR, Miller DL (1991) RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature 349:434–438
Mindell DP, Sorenson MD, Dimcheff DE (1998) An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles. Mol Biol Evol 15:1568–1571
Moritz C, Dowling TE, Brown WM (1987) Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annu Rev Ecol Syst 18:269–292
Mulholland V, Carde L, O’Donnell JJ, Fleming CC, Powers TO (1996) Use of the polymerase chain reaction to discriminate potato cyst nematode at the species level BCPC Symposium—Diagnostics in Crop Production 65:247–252
Orr AT, Rabets JC, Horton TL, Landweber LF (1997) RNA editing missing in mitochondria. RNA 3:335–336
Palmer JD, Shields CR (1984) Tripartite structure of the Brassica campestris mitochondrial genome. Nature 307:437–440
Rose TM, Henikoff JG, Henikoff S (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res 31:3763–3766
Subbotin SA, Vierstraete A, De Ley P, Rowe J, Waeyenberge L, Moens M, Vanfleteren JR (2001) Phylogenetic relationships within the cyst-forming nematodes (Nematoda, Heteroderidae) based on analysis of sequences from the ITS regions of ribosomal DNA. Mol. Phylogenet Evol 21:1–16
Suematsu T, Sato A, Sakurai M, Watanabe K, Ohtsuki T (2005) A unique tRNA recognition mechanism of Caenorhabditis elegans mitochondrial EF-Tu2. Nucleic Acids Res 33:4683–4691
Sunnucks P, Hales DF (1996) Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol Biol Evol 13:510–524
Vanfleteren JR, Vierstraete AR (1999) Insertional RNA editing in metazoan mitochondria: The cytochrome b gene in the nematode Teratocephalus lirellus. RNA 5:622–624
Watanabe KI, Bessho Y, Kawasaki M, Hori H (1999) Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema. J Mol Biol 286:645–650
Acknowledgments
The authors thank Vincent Dubois, who helped out with the sequencing of the G. pallida material. This work was funded by grants from the Australian Research Council, the Scottish Executive Environment and Rural Affairs Department, and EU AIR3 CT-92–0062.
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Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession no. EF193005.
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Riepsamen, A.H., Blok, V.C., Phillips, M. et al. Poly(T) Variation Within Mitochondrial Protein-Coding Genes in Globodera (Nematoda: Heteroderidae). J Mol Evol 66, 197–209 (2008). https://doi.org/10.1007/s00239-007-9064-2
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DOI: https://doi.org/10.1007/s00239-007-9064-2