Phylogenetic reconstruction using secondary structures and sequence motifs of ITS2 rDNA of Paragonimus westermani (Kerbert, 1878) Braun, 1899 (Digenea: Paragonimidae) and related species

BMC Genomics

Volumn 10, Issue SUPPL. 3, 2009, Pages

  Prasad, Pramod K ^a   Tandon, Veena ^a   Biswal, Devendra K ^a   Goswami, Lalit M ^a   Chatterjee, Anupam ^a  

^a NORTH EASTERN HILL UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME DNA;

ARTICLE; DIGENEA; DNA SEQUENCE; DNA STRUCTURE; MORPHOMETRICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAGONIMIDAE; PARAGONIMUS BANGKOKENSIS; PARAGONIMUS HARINASUTAI; PARAGONIMUS HETEROTREMUS; PARAGONIMUS PROLIFERUS; PARAGONIMUS SIAMENSIS; PARAGONIMUS SKRJABINI; PARAGONIMUS WESTERMANI; PHYLOGENY; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES IDENTIFICATION; TREMATODE; ANIMAL; CHEMISTRY; CONFORMATION; GENETICS; MOLECULAR GENETICS;

CANCER PAGURUS; DIGENEA (FLUKES); PARAGONIMIDAE; PARAGONIMUS; PARAGONIMUS HARINASUTAI; PARAGONIMUS HETEROTREMUS; PARAGONIMUS SIAMENSIS; PARAGONIMUS SKRJABINI; PARAGONIMUS WESTERMANI; TREMATODA;

ANIMALS; BASE SEQUENCE; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PARAGONIMUS WESTERMANI; PHYLOGENY;

BAYESIAN ANALYSIS; COMBINED ANALYSIS; DATA PARTITION; IN-SILICO; MOLECULAR PHYLOGENY; MORPHOMETRICS; MOUNTAIN STREAMS; MOUNTAINOUS REGIONS; NEW SPECIES; NORTHEASTERN INDIA; PHYLOGENETIC RECONSTRUCTION; PHYLOGENETIC RELATIONSHIPS; PHYLOGENETIC STUDIES; PRIMARY SEQUENCES; RIBOSOMAL DNA; RNA SECONDARY STRUCTURES; SECONDARY STRUCTURES; SEQUENCE ANALYSIS; SEQUENCE MOTIFS; SPECIES IDENTIFICATION; THAILAND;

BIOLOGICAL ORGANS; BIOLOGY; RNA; TOPOLOGY;

BIOINFORMATICS;

EID: 71549165131     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-S3-S25     Document Type: Article

References (28)

1. Toscano C, Yu SH, Nunn P, Mott KE. Paragonimiasis and tuberculosis, diagnostic confusion: a review of the literature. Trop Disease Bulletin 1995, 92:R1-R26.
2. Bunnag D, Harinasuta T. Opisthorchiasis, clonorchiasis and paragonimiasis. Tropical and Geographical Medicine 1985, 461-470. New York: McGraw-Hill Iac, Warren KS, Mahmoud AAF.
3. Kusner DJ, King CH. Cerebral paragonimiasis. Seminars in Neurology 1993, 13:201-208. 10.1055/s-2008-1041126, 8356355.
4. Kerbert C. Zur Trematoden-Kenntnis. Zoologischer Anzeiger 1878, 1:271-273.
5. Blair D, Xu ZB, Agatsuma T. Paragonimiasis and the Genus Paragonimus (Review). Adv Parasitol 1999, 42:113-222. full_text, 10050273.
6. Razaque MA, Mutum SS, Singh TS. Recurrent haemoptysis? Think of Paragonimiasis. Trop Doct 1991, 21:153-155.
7. Singh TS, Mutum S, Razaque MA, Singh YI, Singh EY. Paragonimiasis in Manipur. Indian J Med Res 1993, 97:247-252.
8. Singh TS. Occurrence of the lung fluke Paragonimus hueitungensis in Manipur, India. Zhonghua Yi Xue Za Zhi (Taipei) 2002, 65:426-429.
9. Narain K, Devi KR, Mahanta J. Paragonimus and paragonimiasis - A new focus in Arunachal Pradesh, India. Curr Sci 2003, 84:985-987.
10. Blair D, Wu B, Chang ZS, Gong X, Agatsuma T, Zhang YN, Chen SH, Lin JX, Chen MG, Waikagui J, Guevara AG, Feng Z, David GM. A molecular perspective on the genera Paragonimus Braun, Euparagonimus Chen and Pagumogonimus Chen. J Helminthol 1999, 73:295-299.
11. Leon-Regagnon V, Brooks DR, Perez-Ponce de Leon G. Differentiation of Mexican species of Haematoloechus Looss, 1899 (Digenea: Plagiorchiformes): Molecular and morphological evidence. J Parasitol 1999, 85:935-946. 10.2307/3285832, 10577731.
12. Iwagami M, Lo Y, Su K, Lai PF, Fukushima M, Nakano M, Blair D, Kawashima K, Agatsuma T. Molecular phylogeographic studies on Paragonimus westermani in Asia. J Helminthol 2000, 74:315-322.
13. Blair D, Campos A, Cummings MP, Laclette JP. Evolutionary biology of parasitic platyhelminths: the role of molecular phylogenetics. Parasitol Today 1996, 12:66-71. 10.1016/0169-4758(96)80657-0, 15275257.
14. Blair D, Agatsuma T, Watanobe T, Okamoto M, Ito A. Geographical genetic structure within the human lung fluke, Paragonimus westermani, detected from DNA sequences. Parasitology 1997, 115:411-417. 10.1017/S0031182097001534, 9364568.
15. Caetano-Anolles G. Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res 2002, 30:2575-2587. 10.1093/nar/30.11.2575, 117177, 12034847.
16. Billoud B, Guerrucci MA, Masselot M, Deutsch JS. Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol 2000, 17:1435-1445.
17. Zwieb C, Glotz C, Brimacombe R. Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species. Nucleic Acids Res 1981, 9:3621-3640. 10.1093/nar/9.15.3621, 327379, 7024918.
18. Schultz J, Maisel S, Gerlach D, Müller T, Wolf M. A common core of secondary structure of the internal transcribed spacer 2(ITS2) throughout the Eukaryota. RNA 2005, 11:361-364. 10.1261/rna.7204505, 1370725, 15769870.
19. Grajales A, Aguilar C, Sánchez JA. Phylogenetic reconstruction using secondary structures of Internal Transcribed Spacer 2 (ITS2, rDNA): finding the molecular and morphological gap in Caribbean gorgonian corals. BMC Evol Biol 2007, 7:90. 10.1186/1471-2148-7-90, 1913914, 17562014.
20. Bowles J, Blair D, McManus DP. A molecular phylogeny of the human schistosomes. Mol Phylogenet Evol 1995, 4:103-109. 10.1006/mpev.1995.1011, 7663756.
21. Prasad PK, Tandon V, Chatterjee A, Bandyopadhyay S. PCR-based determination of internal transcribed spacer (ITS) regions of ribosomal DNA of giant intestinal fluke, Fasciolopsis buski (Lankester, 1857) Looss, 1899. Parasitol Res 2007, 101:1581-1587. 10.1007/s00436-007-0680-y, 17712571.
22. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 2007, 24:1596-1599. 10.1093/molbev/msm092, 17488738.
23. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analsysis program for Windows 95/98/NT. Nucl Acids Symp 1999, 41:95-98.
24. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acids Res 2003, 31:3406-3415. 10.1093/nar/gkg595, 169194, 12824337.
25. Bailey TL, Elkan C. Fitting a mixure model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology 1994, 28-36. AAAI Press, Menlo Park, California.
26. Zuker M. Prediction of RNA secondary structure by energy minimization. Methods Mol Biol 1994, 25:267-294.
27. Shapiro BA. An algorithm for comparing multiple RNA secondary structures. Comput Appl Biosci 1998, 4:387-393.
28. Blair D, Zhengshan C, Minggang C, Aili C, Bo W, Agatsuma T, Iwagami M, Corlis D, Chengbin F, Ximei Z. Paragonimus skrjabini Chen, 1959 (Digenea: Paragonimidae) and related species in eastern Asia: a combined molecular and morphological approach to identification and taxonomy. Syst Parasitol 2005, 60:1-21. 10.1007/s11230-004-1378-5, 15791397.