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The Mitochondrial Genome of the Soybean Cyst Nematode, Heterodera Glycines

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The Mitochondrial Genome of the Soybean Cyst Nematode, Heterodera Glycines 565 The mitochondrial genome of the soybean cyst nematode, Heterodera glycines Tracey Gibson, Daniel Farrugia, Jeff Barrett, David J. Chitwood, Janet Rowe, Sergei Subbotin, and Mark Dowton Abstract: We sequenced the entire coding region of the mitochondrial genome of Heterodera glycines. The sequence ob- tained comprised 14.9 kb, with PCR evidence indicating that the entire genome comprised a single, circular molecule of ap- proximately 21–22 kb. The genome is the most T-rich nematode mitochondrial genome reported to date, with T representing over half of all nucleotides on the coding strand. The genome also contains the highest number of poly(T) tracts so far reported (to our knowledge), with 60 poly(T) tracts ≥ 12 Ts. All genes are transcribed from the same mitochon- drial strand. The organization of the mitochondrial genome of H. glycines shows a number of similarities compared with Ra- dopholus similis, but fewer similarities when compared with Meloidogyne javanica. Very few gene boundaries are shared with Globodera pallida or Globodera rostochiensis. Partial mitochondrial genome sequences were also obtained for Hetero- dera cardiolata (5.3 kb) and Punctodera chalcoensis (6.8 kb), and these had identical organizations compared with H. gly- cines. We found PCR evidence of a minicircular mitochondrial genome in P. chalcoensis, but at low levels and lacking a noncoding region. Such circularised genome fragments may be present at low levels in a range of nematodes, with multipar- tite mitochondrial genomes representing a shift to a condition in which these subgenomic circles predominate. Key words: mitochondrial, nematode, gene rearrangement, Punctodera, Punctoderinae, Heteroderidae, Heterodera cardio- lata. Résumé : Les auteurs ont séquencé complètement la région codante du génome mitochondrial de l’Heterodera glycines.La séquence obtenue mesure 14,9 kb et des évidences PCR indiquent que le génome entier serait composé d’une seule molé- cule circulaire d’environ 21–22 kb. Ce génome est le génome mitochondrial le plus riche en T jamais rapporté chez les né- matodes, les T constituant plus de la moitié de tous les nucléotides sur le brin codant. Le génome compte également le nombre le plus élevé de suites poly(T) vu à ce jour (au meilleur de leur connaissance), avec 60 suites comptant plus de 12 T. Tous les gènes sont transcrits à partir du même brin mitochondrial. L’organisation du génome mitochondrial chez l’H. glycines affiche de nombreuses similarités avec celui du Radopholus similis, mais moins de similitude lorsque comparé à ce- For personal use only. lui du Meloidogyne javanica. Très peu de frontières entre les gènes sont en commun avec le Globodera pallida ou le Globo- dera rostochiensis. Des séquences partielles du génome mitochondrial ont également été obtenues pour le Heterodera cardiolata (5,3 kb) et le Punctodera chalcoensis (6,8 kb), et ceux-ci présentaient une organisation identique à celle du H. glycines. Les auteurs ont trouvé des évidences PCR d’un génome mitochondrial circulaire miniature chez le P. chalcoensis, mais à de faibles niveaux et sans région non-codante. Des tels fragments de génome circularisés sont possiblement présents en faible nombre chez plusieurs nématodes, les génomes mitochondriaux multipartites constituant une transition vers une condition où ces cercles subgénomiques prédominent. Mots‐clés : mitochondrial, nématode, réarrangement de gènes, Punctodera, Punctoderinae, Heteroderidae, Heterodera car- diolata. [Traduit par la Rédaction] Genome Downloaded from www.nrcresearchpress.com by USDANALBF on 08/22/11 Introduction deridae. It is a major pest of soybean crops both in Asia and the USA (Subbotin et al. 2001a). A number of races (Riggs Heterodera glycines Ichinohe (the soybean cyst nematode) and Schmitt 1988) or types (Niblack et al. 2002) of H. gly- is a plant parasitic nematode belonging to the family Hetero- cines have been identified, primarily based on their ability to Received 10 February 2010. Accepted 3 February 2011. Published at www.nrcresearchpress.com/gen on 11 July 2011. Paper handled by Associate Editor Linda Bonen. T. Gibson, D. Farrugia, J. Barrett, and M. Dowton. Centre for Medical Bioscience, School of Biological Sciences, Wollongong University, Wollongong, NSW, 2522, Australia. D.J. Chitwood. Nematology Laboratory, United States Department of Agriculture, Agricultural Research Service, Bldg 011A, BARC-W, Beltsville, MD 20705, USA. J. Rowe. Nematode Interactions Unit, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, United Kingdom. S. Subbotin. Plant Pest Diagnostics Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832-1448, USA. Corresponding author: Mark Dowton (e-mail: [email protected]). Genome 54: 565–574 (2011) doi:10.1139/G11-024 Published by NRC Research Press 566 Genome, Vol. 54, 2011 infest a number of indicator soybean cultivars. Genetic ap- Amplification and sequencing of mitochondrial fragments proaches for distinguishing H. glycines populations could We designed primers to anneal to conserved regions of provide a means of rapidly distinguishing these types. How- nematode mitochondrial genes and amplified a number of in- ever, such genetic markers have not yet been developed. The ternal gene fragments from each of the three nematodes mitochondrial genome of H. glycines may provide such ge- studied (primer sequences available upon request). We then netic markers. For example, intergenic regions in the mito- designed precisely matching primers, using the sequence chondrial genome of Apis mellifera have been used to data obtained, and amplified a number of multigenic frag- distinguish different populations (Cornuet et al. 1991). ments. All amplifications were performed as previously de- The mitochondrial genome of animals is normally a cir- scribed, using the Bio-X-Act long PCR system (Gibson et al. cular, double-stranded molecule containing 36–37 genes: 2007a). Owing to the presence of poly(T) variation in the 12–13 protein-coding genes, 2 rRNA genes, and 22 tRNA amplicons (Riepsamen et al. 2008), most multigenic frag- genes (Boore 1999). Mitochondrial genomes can provide ments were then cloned directly into the pGEM-T Easy vec- two types of characters for the resolution of phylogeny. The tor system (Promega, Madison, Wisconsin) and sequenced by first type is the more traditional set of aligned sequences primer walking. As this poly(T) variation has been found to that can be analyzed by parsimony or likelihood; mitochon- be primarily an artefact of amplification of templates with ex- drial genomes can provide datasets that are typically tensive poly(T) regions (Riepsamen et al. 2011), we se- 10 000–16 000 characters long. The second type of charac- quenced multiple clones to infer the biological length of ter is extracted from the organization of the mitochondrial these poly(T) regions. genome (Dowton et al. 2002). It has been argued that large-scale genome changes occur rarely and that reversions Step-out PCR amplification or secondary losses will be even rarer (Boore et al. 1998; An approximately 7-kb fragment of the H. glycines mito- Rokas and Holland 2000). As a result, mitochondrial gene chondrial genome was amplified and sequenced using long rearrangements have been used to infer phylogeny between PCR (described above). This fragment spanned the cox2–cob a number of animal groups (Boore et al. 1998; Boore and genes. Step-out PCR (Burger et al. 2007) was then used to Staton 2002; Dowton 1999; Dowton et al. 2002; Knudsen amplify the flanking regions of this fragment. In the first et al. 2006; Kurabayashi and Ueshima 2000; Smith et al. round of step-out PCR, genomic DNA was amplified using a 1993). The Heteroderidae represent a group in which mito- single outward-facing, species-specific primer. After an initial denaturation at 94 °C for 2 min, the cycling conditions for chondrial gene rearrangement characters may be informa- – tive. Extensive gene rearrangements have occurred during cycles 1 5 were as follows; 94 °C for 20 s, annealing (tem- the evolution of the Hoplolaimoidea (to which the Hetero- perature set at 5 °C below the melting temperature of the pri- deridae belong), as evident from the very different genome mer) for 20 s, and 68 °C for 8 min. The use of a high organizations of Meloidogyne javanica (from the Meloido- annealing temperature is designed to increase the concentra- tion of the desired template by linear (single stranded) ampli- gynidae) (Okimoto et al. 1991), Radopholus similis (Jacob For personal use only. fication. In cycle 6, the conditions remain the same, but the et al. 2009), Globodera pallida (Armstrong et al. 2000; annealing temperature is dropped to 30 °C (for 2 min) to fa- Gibson et al. 2007b), and Globodera rostochiensis (Gibson cilitate annealing of the species-specific primer to other re- a et al. 2007 ). gions of the desired template. Cycles 7–22 comprise a In this study, we report the complete coding sequence of touch-down PCR, in which the cycling conditions remain the the mitochondrial genome of H. glycines. Although a portion same, but the annealing temperature is increased to 65 °C of the noncoding region could not be sequenced, our data al- (for 20 s), dropping by 1 °C each cycle. The touch-down ap- low us to identify the relative position of each of the 36 mito- proach is designed to amplify only those double-stranded chondrial genes commonly found in nematodes and to molecules produced during cycle 6 (reducing the amount of compare the organization of the H. glycines mitochondrial nonspecific amplification). In cycles 23–40, the annealing genome with other nematodes. In addition, we sequence par- temperature is raised to that used during cycles 1–5. The ex- tial mitochondrial genomes of Heterodera cardiolata and tension time is increased by 30 s in each of cycles 23–40, to Genome Downloaded from www.nrcresearchpress.com by USDANALBF on 08/22/11 Punctodera chalcoensis, to obtain a more complete under- offset any reduction in enzyme activity that has occurred.
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