9 Hu M, Chilton N B, Gasser R B. The mitochondrial genomics of parasitic nematodes of socio-economic importance: Recent progress, andimplications for population genetics and systematics. Adv Parasitol, 2003, 56: 133-212??
[5]
11 Okimoto R, Macfarlane J L, Wolstenholme D R. Evidence for the frequent use of TTG as the translation initiation codon of mitochondrialprotein genes in the nematodes, Ascaris suum and Caenorhabditis elegans. Nucleic Acids Res, 1990, 18: 6113-6118??
[6]
12 Okimoto R, Macfarlane J L, Clary D O, et al. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.Genetics, 1992, 130: 471-498
[7]
14 Keddie E M, Higazi T, Unnasch T R. The mitochondrial genome of Onchocerca volvulus: Sequence, structure and phylogenetic analysis.Mol Biochem Parasitol, 1998, 95: 111-127??
[8]
17 Nakao M, Yokoyama N, Sako Y, et al. The complete mitochondrial DNA sequence of the cestode Echinococcus multilocularis (Cyclophyllidea:Taeniidae). Mitochondrion, 2002, 1: 497-509??
[9]
21 Jex A R, Hu M, Littlewood D T, et al. Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome fromsingle Haemonchus contortus (Nematoda). BMC Genomics, 2008, 9: 11??
[10]
22 Jex A R, Hall R S, Gasser R B, et al. An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes.Nucleic Acids Res, 2010, 38: 522-533??
[11]
23 Hu M, Chilton N B, Gasser R B. Long PCR-based amplification of the entire mitochondrial genome from single parasitic nematodes. MolCell Probes, 2002, 16: 261-267??
[12]
24 Webb K M, Rosenthal B M. Next generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparisonof its divergence from the principal agent of human trichinellosis, Trichimella spiralis. Infect Genet Evol, 2011, 11: 116-123??
[13]
26 Laslett D, Canback B. ARWEN: A program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 2008,24: 172-175??
[14]
27 Mathews D H. Predicting a set of minimal free energy RNA secondary structures common to two sequences. Bioinformatics, 2005, 21:2246-2253??
[15]
28 Mathews D H, Disney M D, Childs J L, et al. Incorporating chemical modification constraints into a dynamic programming algorithm forprediction of RNA secondary structure. Proc Natl Acad Sci USA, 2004, 101: 7287-7292??
[16]
29 Wyman S K, Jansen R K, Boore J L. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 2004, 20: 3252-3255??
[17]
30 Lupi R, de Meo P D, Picardi E, et al. MitoZoa: A curated mitochondrial genome database of metazoans for comparative genomics studies.Mitochondrion, 2010, 10: 192-199??
[18]
34 He Y, Jones J, Armstrong M, et al. The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): Considerableeconomization in the length and structural features of encoded genes. J Mol Evol, 2005, 61: 819-833??
[19]
35 Jex A R, Waeschenbac A, Hu M, et al. The mitochondrial genomes of Ancylostoma caninum and Bunostomum phlebotomum—Twohookworms of animal health and zoonotic importance. BMC Genomics, 2009, 10: 79??
[20]
37 von Nickisch-Rosenegk M, Brown W M, Boore J L. Complete sequence of the mitochondrial genome of the tapeworm Hymenolepisdiminuta: Gene arrangements indicate that Platyhelminths are Eutrochozoans. Mol Biol Evol, 2001, 18: 721-730
[21]
39 Perkins E M, Donnellan S C, Bertozzi T, et al. Closing the mitochondrial circle on paraphyly of the Monogenea (Platyhelminthes) infersevolution in the diet of parasitic flatworms. Int J Parasitol, 2010, 40: 1237-1245??
[22]
41 Huyse T, Plaisance L, Webster B L, et al. The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogenof Atlantic salmon (Salmo salar). Parasitology, 2007, 134: 739-747??
[23]
42 Webster B L, Rudolfova J, Horak P, et al. The complete mitochondrial genome of the bird schistosome Trichobilharzia regenti (Platyhelminthes:Digenea), causative agent of cercarial dermatitis. J Parasitol, 2007, 93: 553-561??
[24]
43 Huyse T, Buchmann K, Littlewood D T. The mitochondrial genome of Gyrodactylus derjavinoides (Platyhelminthes: Monogenea)—Amitogenomic approach for Gyrodactylus species and strain identification. Gene, 2008, 417: 27-34??
[25]
45 Yatawara L, Wickramasinghe S, Rajapakse R P, et al. The complete mitochondrial genome of Setaria digitata (Nematoda: Filarioidea):Mitochondrial gene content, arrangement and composition compared with other nematodes. Mol Biochem Parasitol, 2010, 173: 32-38??
[26]
46 Van der Veer M, de Vries E. A single nucleotide polymorphism map of the mitochondrial genome of the parasitic nematode Cooperiaoncophora. Parasitology, 2004, 128: 421-431??
[27]
47 Jia W Z, Yan H B, Guo A J, et al. Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: Additional molecularmarkers for a tapeworm genus of human and animal health significance. BMC Genomics, 2010, 11: 447??
[28]
48 Nakao M, Sako Y, Ito A. The mitochondrial genome of the tapeworm Taenia solium: A finding of the abbreviated stop codon U. J Parasitol,2003, 89: 633-635??
[29]
51 Jeon H K, Lee K H, Kim K H, et al. Complete sequence and structure of the mitochondrial genome of the human tapeworm, Taenia asiatica(Platyhelminthes; Cestoda). Parasitology, 2005, 130: 717-726??
[30]
52 Jeon H K, Eom K S. Taenia asiatica and Taenia saginata: Genetic divergence estimated from their mitochondrial genomes. Exp Parasitol,2006, 113: 58-61??
[31]
53 Bowles J, McManus D P. Genetic characterization of the Asian Taenia, a newly described taeniid cestodes of human. Am J Trop Med Hyg,1994, 50: 33-44
[32]
55 Bowles J, Blair D, McManus D P. A molecular phylogeny of the genus Echinococcus. Parasitology, 1995, 110: 317-328??
[33]
56 Bowles J, McManus D P. NADH dehydrogenase 1 gene sequences compared for species and strains of the genus Echinococcus. Int J Parasitol,1993, 23: 969-972??
[34]
57 Lavikainen A, Lehtinen M J, Meri T, et al. Molecular genetic characterization of the Fennoscandian cervid strain, a new genotypic group(G10) of Echinococcus granulosus. Parasitology, 2003, 127: 207-215
[35]
58 Le T H, Pearson M S, Blair D, et al. Complete mitochondrial genomes confirm the distinctiveness of the horse-dog and sheep-dog strainsof Echinococcus granulosus. Parasitology, 2003, 124: 97-112
[36]
59 Thompson R C A, McManus D P. Towards a taxonomic revision of the genus Echinococcus. Trends Parasitol, 2002, 18: 452-457??
[37]
60 Thompson R C A. The taxonomy, phylogeny and transmission of Echinococcus. Exp Parasitol, 2008, 119: 439-446??
[38]
61 Romig T. Epidemiology of echinococcosis. Langenbeck’s Arch Surg, 2003, 388: 209-217??
[39]
62 Scott J C, Stafaniak J, Pawlowski Z S, et al. Molecular genetic analysis of human cystic hydatid cases from Poland: Identification of a newgenotypic group (G9) of Echinococcus granulosus. Parasitology, 1997, 114: 37-43??
[40]
63 Moks E, Jōgisalu I, Valdmann H, et al. First report of Echinococcus granulosus G8 in Eurasia and a reappraisal of the phylogenetic relationshipsof ‘genotypes’ G5-G10. Parasitology, 2008, 135: 647-654
[41]
64 Nakao M, McManus D P, Schantz P M, et al. A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrialgenomes. Parasitology, 2007, 134: 713-722??
[42]
65 Hüttner M, Nakao M, Wassermann T, et al. Genetic characterization and phylogenetic position of Echinococcus felidis (Cestoda: Taeniidae)from the African lion. Int J Parasitol, 2008, 38: 861-868??
[43]
66 Blouin M S, Yowell C A, Courthey C H, et al. Haemonchus placei and Haemonchus contortus are distinct species based on mtDNA evidence.Int J Parasitol, 1997, 27: 1383-1387??
[44]
67 Park J K, Kim K H, Kang S, et al. A common origin of complex life cycles in parasitic flatworms: Evidence from the complete mitochondrialgenome of Microcotyle sebastis (Monogenea: Platyhelminthes). BMC Evol Biol, 2007, 7: 11??
[45]
71 Nakao M, Li T Y, Han X M, et al. Genetic polymorphisms of Echinococcus tapeworms in China as determined by mitochondrial and nuclearDNA sequences. Int J Parasitol, 2010, 40: 379-385??
[46]
72 Eckert J, Gemmell M A, Meslin F X, et al. WHO/OIE Manual on Echinococcosis in Humans and Animals: A Public Health Problem ofGlobal Concern M. Paris: World Organisation for Animal Health (Office International des Epizooties) and World Organisation for AnimalHealth, 2001
[47]
79 Anantaphruti M T, Yamasaki H, Nakao M, et al. Sympatric occurrence of Taenia solium, T. saginata, and T. asiatica, Thailand. EmergInfect Dis, 2007, 13: 1413-1416
[48]
80 Murell K D. Epidemiology of taeniosis and cysticercosis. In: Murell K D, ed. WHO/FAO/OIE Guidelines for the Surveillance, Preventionand Control of Taeniosis/Cysticercosis. Paris: World Organisation for Animal Health, 2005. 27-44
[49]
81 Mayta H, Gilman R H, Prendergast E, et al. Nested PCR for the specific diagnosis of Taenia solium taeniasis. J Clin Microbiol, 2008, 46:286-289??
[50]
82 Yamasaki H, Allan J C, Sato M O, et al. DNA differential diagnosis of taeniasis and cysticercosis by multiplex PCR. J Clin Microbiol,2004, 42: 548-553??
[51]
83 Yamasaki H, Nakao M, Sako Y, et al. Mitochondrial DNA diagnosis for taeniasis and cysticercosis. Parasitol Int, 2006, 55: S81-S85??
[52]
85 Yamasaki H, Nakao M, Sako Y, et al. DNA differential diagnosis of human taeniid cestodes by base excision sequence scanning thymine-base reader analysis with mitochondrial genes. J Clin Microbiol, 2002, 40: 3818-3821??
[53]
86 Nkouawa A, Sako Y, Nakao M, et al. Loop-mediated isothermal amplification method for differentiation and rapid detection of Taeniaspecies. J Clin Microbiol, 2009, 47: 168-174??
[54]
1 Keiser J, Utzinger J. Food-borne trematodiases. Clin Microbiol Rev, 2009, 22: 466-483??
[55]
2 Pawlowski Z S. Cestodiases: Taeniasis, cysticercosis, diphyllobothriasis, hymenolepiasis, and others. In: Warren K S, Mahmoud A A F,eds. Tropical and Geographical Medicine. 2nd ed. New York: McGraw-Hill Information Services, 1990
[56]
3 Chai J Y, Murrell K D, Lymbery A J. Fish-borne parasitic zoonoses: Status and issues. Int J Parasitol, 2005, 35: 1233-1254??
[57]
4 Koenning S R, Overstreet C, Noling J W, et al. Survey of crop losses in response to phytoparastic nematodes in the United States for 1994.J Nematol, 1999, 31: 587-618
[58]
5 Olson P D, Tkach V V. Advances and trends in the molecular systematic of the parasitic platyhelminthes. Adv Parasitol, 2005, 60:165-243??
[59]
10 Gasser R B, Newton S E. Genomic and genetic research on bursate nematodes: Significance, implications and prospects. Int J Parasitol,2000, 30: 509-534??
[60]
13 Littlewood D T, Gasser R B. Toward next-generation sequencing of mitochondrial genomes—Focus on parasitic worms of animals andbiotechnological implications. Biotechnol Adv, 2010, 18: 151-159
[61]
15 Burger G, Lavrov D V, Forget L, et al. Sequencing complete mitochondrial and plastid genomes. Nat Protoc, 2007, 2: 603-614??
[62]
16 Hu M, Chilton N B, Gasser R B. The mitochondrial genomes of the human hookworms, Ancylostoma duodenale and Necator americanus(Nematoda: Secernentea). Int J Parasitol, 2002, 32: 145-158??
[63]
18 Le T H, Blair D, Agatsuma T, et al. Phylogenies inferred from mitochondrial gene orders—A cautionary tale from the parasitic flatworms.Mol Biol Evol, 2000, 17: 1123-1125
[64]
19 Tang S, Hyman B C. Rolling circle amplification of complete nematode mitochondrial genomes. J Nematol, 2005, 37: 236-241
[65]
20 Hu M, Jex A R, Campbell B E, et al. Long PCR amplification of the entire mitochondrial genome from individual helminths for directsequencing. Nat Protoc, 2007, 2: 2339-2344??
[66]
25 Lowe T M, Eddy S R. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res,1997, 25: 955-964??
[67]
31 Littlewood D T, Lockyer A E, Webster B L, et al. The complete mitochondrial genomes of Schistosoma haematobium and Schistosomaspindale and the evolutionary history of mitochondrial genome changes among parasitic flatworms. Mol Phylogenet Evol, 2006, 39:452-467??
[68]
32 Steinauer M L, Nickol B B, Broughton R, et al. First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoidesthecatus) and its phylogenetic position within Metazoa. J Mol Evol, 2005, 60: 706-715??
[69]
33 Lavrov D V, Brown W M. Trichinella spiralis mtDNA: A nematode mitochondrial genome that encodes a putative ATP8 and normallystructured tRNAS and has a gene arrangement relatable to those of coelomate metazoans. Genetics, 2001, 157: 621-637
[70]
36 Powers T O, Harris T S, Hyman B C. Mitochondrial DNA sequence divergence among Meloidogyne incognita, Romanomermis culicivorax,Ascaris suum, and Caenorhabditis elegans. J Nematol, 1993, 25: 564-572
[71]
38 Shekhovtsov S V, Katokhin A V, Kolchanov N A, et al. The complete mitochondrial genomes of the liver flukes Opisthorchis felineus andClonorchis sinensis (Trematoda). Parasitol Int, 2010, 59: 100-103??
[72]
40 Plaisance L, Huyse T, Littlewood D T, et al. The complete mitochondrial DNA sequence of the monogenean Gyrodactylus thymalli(Platyhelminthes: Monogenea), a parasite of grayling (Thymallus thymallus). Mol Biochem Parasitol, 2007, 154: 190-194??
[73]
44 Le T H, Humair P F, Blair D, et al. Mitochondrial gene content, arrangement and composition compared in African and Asian schistosomes.Mol Biochem Parasitol, 2001, 117: 61-71??
[74]
49 Wolstenholme D R, Okimoto R, Macfarlane J L. Nucleotide correlations that suggest tertiary interactions in the TV-replacementloop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum. Nucleic Acids Res, 1994, 22:4300-4306??
[75]
50 Jeon H K, Kim K H, Eom K S. Complete sequence of the mitochondrial genome of Taenia saginata: Comparison with T. solium and T.asiatica. Parasitol Int, 2007, 56: 243-246??
[76]
54 Bowles J, Blair D, McManus D P. Genetic variants within the genus Echinococcus identified by mitochondrial DNA sequencing. MolBiochem Parasitol, 1992, 54: 165-173??
[77]
68 Justin J L. Non-monophyly of the monogeneans? Int J Parasitol, 1998, 28: 1653-1657
[78]
69 Nakao M, Xiao N, Okamoto M, et al. Geographic pattern of genetic variation in the fox tapeworm Echinococcus multilocularis. ParasitolInt, 2009, 58: 384-389
[79]
70 Xiao N, Qiu J M, Nakao M, et al. Echinococcus shiquicus n. sp., a taeniid cestode from Tibetan fox and plateau pika in China. Int J Parasitol,2005, 35: 693-701??
[80]
73 Hancock K, Broughel D E, Moura I N, et al. Sequence variation in the cytochrome oxidase I, internal transcribed spacer 1, and Ts14 diagnosticantigen sequences of Taenia solium isolates from South and Central America, India, and Asia. Int J Parasitol, 2001, 31:1601-1607
[81]
74 Nakao M, Okamoto M, Sako Y, et al. A phylogenetic hypothesis for the distribution of two genotypes of the pig tapeworm Taenia soliumworldwide. Parasitology, 2002, 124: 657-662
[82]
75 Martinez-Hernandez F, Jimenez-Gonzalez D E, Chenillo P, et al. Geographical widespread of two lineages of Taenia solium due to humanmigrations: Can population genetic analysis strengthen this hypothesis? Infect Genet Evol, 2009, 9: 1108-1114
[83]
76 Zhan B, Li T, Zhang F, et al. Species-specific identification of human hookworms by PCR of the mitochondrial cytochrome oxidase I gene.J Parasitol, 2001, 87: 1227-1229
[84]
77 Ito A, Nakao M, Wandra T, et al. Taeniasis and cysticercosis in Asia and the Pacific: Present state of knowledge and perspectives. SoutheastAsian J Trop Med Public Health, 2005, 36: 123-130
[85]
78 Eom K S, Jeon H K, Kong Y, et al. Identification of Taenia asiatica in China: Molecular, morphological, and epidemiological analysis ofa Luzhai isolate. J Parasitol, 2002, 88: 758-764
[86]
84 Jeon H K, Chaib J Y, Kong Y, et al. Differential diagnosis of Taenia asiatica using multiplex PCR. Exp Parasitol, 2009, 121: 151-156??