The complete mitochondrial genome of Aphelenchoides besseyi (Nematoda: Aphelenchoididae), the first sequenced representative of the subfamily Aphelenchoidinae

in Nematology
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The complete mitochondrial genome (mitogenome) of Aphelenchoides besseyi is 16 216 bp in size and has the typical organisation of nematode mitogenomes of Chromadorea, including 12 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and the AT-rich non-coding region. The nucleotide composition of the mitogenome of A. besseyi is AT-biased (80.0%) and the AT skew is −0.289. The most common start codon for A. besseyi is ATT. The nad3 and nad4L genes have an incomplete stop codon consisting of just a T and the other PCGs stop with the full stop codons. All the tRNA genes display a non-typical cloverleaf structure of mitochondrial tRNA. The AT-rich non-coding region contains ten tandem repeat units with four different regions. Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes showed that three Tylenchomorpha species, including A. besseyi, Bursaphelenchus mucronatus and B. xylophilus from the superfamily Aphelenchoidea, are placed within a well-supported monophyletic clade, but far from the other six Tylenchomorpha species Meloidogyne chitwoodi, M. graminicola, M. incognita, Pratylenchus vulnus, Heterodera glycines and Radopholus similis of Tylenchoidea. This phylogeny suggests that Aphelenchoides has a close relative relationship with Bursaphelenchus and that the Tylenchomorpha is not monophyletic.

The complete mitochondrial genome of Aphelenchoides besseyi (Nematoda: Aphelenchoididae), the first sequenced representative of the subfamily Aphelenchoidinae

in Nematology

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References

AbascalF.ZardoyaR.PosadaD. (2005). ProtTest: selection of best-fit models of protein evolution. Bioinformatics 212104-2105.

BensonG. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27573-580.

BesnardG.HlingF.ChapuisÉ.ZedaneL.LhuillierÉ.MateilleT.BellafioreS. (2014). Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing. Comptes Rendus Biologies 337295-301.

BlaxterM.L.De LeyP.GareyJ.R.LiuL.X.ScheldemanP.VierstraeteA.VanfleterenJ.R.MackeyL.Y.DorrisM.FrisseL.M. (1998). A molecular evolutionary framework for the phylum Nematoda. Nature 39271-75.

BooreJ.L. (1999). Animal mitochondrial genomes. Nucleic Acids Research 271767-1780.

BooreJ.L. (2006). The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology & Evolution 21439-446.

CastresanaJ. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology Evolution 17540-552.

CuiR.Q.ZhuoK.WangH.H.LiaoJ.L. (2011). Aphelenchoides paradalianensis n. sp. (Nematoda: Aphelenchoididae) isolated at Guangzhou, China, in packaging wood from South Korea. Zootaxa 286457-64.

De LeyP.BlaxterM. (2002). Systematic position and phylogeny. In: LeeD.L. (Ed.). The biology of nematodes. London, UKTaylor and Francis pp.  1-30.

DecraemerW.HuntD.J. (2006). Structure and classification. In: PerryR.N.MoensM. (Eds). Plant nematology. Wallingford, UKCABI Publishing pp.  3-32.

DuretL.MouchiroudD. (1999). Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America 964482-4487.

GibsonT.FarrugiaD.BarrettJ.ChitwoodD.J.RoweJ.SubbotinS.DowtonM. (2011). The mitochondrial genome of the soybean cyst nematode, Heterodera glycines. Genome 54565-574.

GrossS.M.WilliamsonV.M. (2011). Tm1: a mutator/foldback transposable element family in root-knot nematodes. PLoS ONE 6e24534.

HeY.JonesJ.ArmstrongM.LambertiF.MoensM. (2005). The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes. Journal of Molecular Evolution 61819-833.

HoltermanM.van der WurffA.van den ElsenS.van MegenH.BongersT.HolovachovO.BakkerJ.HelderJ. (2006). Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades. Molecular Biology Evolution 231792-1800.

HuM.GasserR.B. (2006). Mitochondrial genomes of parasitic nematodes – progress and perspectives. Trends in Parasitology 2278-84.

Humphreys-PereiraD.A.EllingA.A. (2014). Mitochondrial genomes of Meloidogyne chitwoodi and M. incognita (Nematoda: Tylenchina): comparative analysis, gene order and phylogenetic relationships with other nematodes. Molecular and Biochemical Parasitology 19420-32.

HuntD.J. (1993). Aphelenchida Longidoridae and Trichodoridae: their systematics and bionomics. Wallingford, UKCABI Publishing.

HuntD.J. (2008). A checklist of the Aphelenchoidea (Nematoda: Tylenchina). Journal of Nematode Morphology and Systematics 10(2007) 99-135.

JacobJ.E.VanholmeB.Van LeeuwenT.GheysenG. (2009). A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Research Notes 2192.

KangS.SultanaT.EomK.S.ParkY.C.SoonthornpongN.NadlerS.A.ParkJ.K. (2009). The mitochondrial genome sequence of Enterobius vermicularis (Nematoda: Oxyurida) – an idiosyncratic gene order and phylogenetic information for chromadorean nematodes. Gene 42987-97.

KanzakiN. (2006). Description of Aphelenchoides xylocopae n. sp. (Nematoda: Aphelenchoididae), the first observed association between nematodes and carpenter bees. Nematology 8555-562.

KanzakiN.FutaiK. (2002). A PCR primer set for determination of phylogenetic relationships of Bursaphelenchus species within the xylophilus group. Nematology 435-41.

KatohK.StandleyD.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology Evolution 30772-780.

LiuG.H.ShaoR.LiJ.Y.ZhouD.H.LiH.ZhuX.Q. (2013). The complete mitochondrial genomes of three parasitic nematodes of birds: a unique gene order and insights into nematode phylogeny. BMC Genomics 14414.

LiuG.H.WangS.Y.HuangW.Y.ZhaoG.H.WeiS.J.SongH.Q.XuM.J.LinR.Q.ZhouD.H.ZhuX.Q. (2012). The complete mitochondrial genome of Galba pervia (Gastropoda: Mollusca), an intermediate host snail of Fasciola spp. PLoS ONE 7e42172.

LoweT.M.EddyS.R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25955-964.

OjalaD.MontoyaJ.AttardiG. (1981). tRNA punctuation model of RNA processing in human mitochondria. Nature 290470-474.

OkimotoR.MacfarlaneJ.L.WolstenholmeD.R. (1994). The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis. Journal of Molecular Evolution 39598-613.

PageR.D. (1996). TreeView: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences 12357-358.

ParkJ.K.SultanaT.LeeS.H.KangS.KimH.K.MinG.S.EomK.S.NadlerS.A. (2011). Monophyly of clade III nematodes is not supported by phylogenetic analysis of complete mitochondrial genome sequences. BMC Genomics 12392.

PernaN.T.KocherT.D. (1995). Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. Journal of Molecular Evolution 41353-358.

ProtJ. (1992). White tip. In: WebsterR.K.GunnelP.S. (Eds). Compendium of rice diseases. University of California, Davis, CA, USAAPS Press pp.  46-47.

ReiseR.W.HuettelR.N.SayreR.M. (1987). Carrot callus tissue for culture of endoparasitic nematodes. Journal of Nematology 19387-389.

RonquistF.TeslenkoM.Van Der MarkP.AyresD.L.DarlingA.HohnaS.LargetB.LiuL.SuchardM.A.HuelsenbeckJ.P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61539-542.

Rybarczyk-MydłowskaK.van MegenH.van den ElsenS.MooymanP.KarssenG.BakkerJ.HelderJ. (2013). Both SSU rDNA and RNA polymerase II data recognise that root-knot nematodes arose from migratory Pratylenchidae, but probably not from one of the economically high-impact lesion nematodes. Nematology 16125-136.

SharpP.M.MatassiG. (1994). Codon usage and genome evolution. Current Opinion in Genetics and Development 4851-860.

SultanaT.KimJ.LeeS.H.HanH.KimS.MinG.S.NadlerS.A.ParkJ.K. (2013a). Comparative analysis of complete mitochondrial genome sequences confirms independent origins of plant-parasitic nematodes. BMC Evolutionary Biology 1312.

SultanaT.HanH.ParkJ.K. (2013b). Comparison of complete mitochondrial genomes of pine wilt nematode Bursaphelenchus xylophilus and Bursaphelenchus mucronatus (Nematoda: Aphelenchoidea) and development of a molecular tool for species identification. Gene 52039-46.

SunL.ZhuoK.LinB.R.WangH.H.LiaoJ.L. (2014). The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications. PLoS ONE 9e98558.

TsayT.ChengY.TengY.LeeM.WuW.LinY. (1998). Bionomics and control of rice white tip disease nematode, Aphelenchoides besseyi. Plant Protection Bulletin 40277-286.

van MegenH.van den ElsenS.HoltermanM.KarssenG.MooymanP.BongersT.HolovachovO.BakkerJ.HelderJ. (2009). A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences. Nematology 11927-950.

von Nickisch-RosenegkM.BrownW.M.BooreJ.L. (2001). Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans. Molecular Biology Evolution 18721-730.

WolstenholmeD.R. (1992). Animal mitochondrial DNA: structure and evolution. International Review of Cytology 141173-216.

XiaX. (2013). DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Molecular Biology Evolution 301720-1728.

ZhangD.X.SzymuraJ.M.HewittG.M. (1995). Evolution and structural conservation of the control region of insect mitochondrial DNA. Journal of Molecular Evolution 40382-391.

ZhaoZ.Q.YeW.M.Giblin-DavisR.A.LiD.M.ThomasW.K.DaviesK.A.RileyI.T. (2008). Morphological and molecular analysis of six aphelenchoidoids from Australian conifers and their relationship to Bursaphelenchus (Fuchs, 1937). Nematology 10663-678.

ZhuoK.CuiR.Q.YeW.M.LuoM.WangH.H.HuX.N.LiaoJ.L. (2010). Morphological and molecular characterization of Aphelenchoides fujianensis n. sp. (Nematoda: Aphelenchoididae) from Pinus massoniana in China. Zootaxa 250939-52.

Figures

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    Circular map of the mitochondrial genome of Aphelenchoides besseyi. Gene scaling is only approximate. All genes are encoded by the same DNA strand, and the arrow indicates the direction of transcription. The tRNA genes are labelled according to the IUPAC-IUB; One-letter symbol L1/L2 and S1/S2 indicate tRNA genes for tRNALeu(CUN)/tRNALeu(UUR) and tRNASer(AGN)/tRNASer(UCN), respectively. ‘NCR’ refers to the non-coding region.

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    Compositional patterns of the mitochondrial genomes of Aphelenchoides besseyi and nine other plant-parasitic nematodes. AT skew, GC skew and AT content are computed for each single gene and for many genomic regions following the legend below the chart. The asterisk indicates that no non-coding region (NCR) data is available for Heterodera glycines. This figure is published in colour in the online edition of this journal, which can be accessed via http://booksandjournals.brillonline.com/content/journals/15685411.

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    Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Aphelenchoides besseyi. Numbers on the y-axis refer to the total number of codons (A) and the RSCU value (B). Codon families are provided on the x-axis. The codon CGC at the top of the column indicates that it is not present in the mitochondrial genome. This figure is published in colour in the online edition of this journal, which can be accessed via http://booksandjournals.brillonline.com/content/journals/15685411.

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    Predicted secondary structures of 22 tRNAs of Aphelenchoides besseyi.

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    Features of tandem repeat units present in the non-coding region of Aphelenchoides besseyi mitogenome. The ‘n’ indicates the number ranging from 7 to 46 in the AT block.

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    Phylogenetic tree from Bayesian analysis of amino acid sequences for 12 protein-coding genes for 42 nematode mitochondrial genomes. Two arthropod species (Lithobius forficatus and Limulus polyphemus) were used as outgroups. Numbers along the branches indicate Bayesian posterior probability (BPP) values. Classification according to De Ley & Blaxter (2002).

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