High-efficiency thermal asymmetric interlaced PCR (hiTAIL-PCR) for determination of a highly degenerated prophage WO Genome in a Wolbachia strain infecting a fig wasp species

Applied and Environmental Microbiology

Volumn 79, Issue 23, 2013, Pages 7476-7481

  Wang, Guan Hong ^a,b   Xiao, Jin Hua ^a   Xiong, Tuan Lin ^a,b   Li, Zi ^a,b   Murphy, Robert W ^c,d   Huanga, Da Wei ^e  

^a INSTITUTE OF ZOOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c KUNMING INSTITUTE OF ZOOLOGY   (China)

^d DEPARTMENT OF NATURAL HISTORY   (Canada)

^e SHANDONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLETE GENOMES; GENOMIC STABILITY; HIGH-EFFICIENCY; INTRACELLULAR BACTERIA; LARGE REGIONS; MODEL SYSTEM; PARTIAL GENOMES; SINGLE NUCLEOTIDES;

GENE ENCODING; POLYMERASE CHAIN REACTION; VIRUSES;

BACTERIA;

BACTERIOPHAGE; BIODEGRADATION; DNA; ECOLOGICAL MODELING; EUKARYOTE; GENOME; POLYMERASE CHAIN REACTION; RECOMBINATION; TEMPERATURE EFFECT; VIRUS; WASP;

VIRUS DNA;

ANIMAL; ARTICLE; BACTERIOPHAGE; CHEMISTRY; DNA SEQUENCE; DNA VIRUS; FICUS; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PARASITOLOGY; POLYMERASE CHAIN REACTION; PROPHAGE; VIROLOGY; VIRUS GENOME; WASP; WOLBACHIA;

ANIMALS; BACTERIOPHAGES; DNA VIRUSES; DNA, VIRAL; FICUS; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; PROPHAGES; SEQUENCE ANALYSIS, DNA; WASPS; WOLBACHIA;

EID: 84888249956     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02261-13     Document Type: Article

References (45)

1. Kent BN, Bordenstein SR. 2010. Phage WO of Wolbachia: lambda of the endosymbiont world. Trends Microbiol. 18:173-181.
2. Werren JH, Baldo L, Clark ME. 2008. Wolbachia: master manipulators of invertebrate biology. Nat. Rev. Microbiol. 6:741-751.
3. Geniez S, Foster JM, Kumar S, Moumen B, LeProust E, Hardy O, Guadalupe M, Thomas SJ, Boone B, Hendrickson C. 2012. Targeted genome enrichment for efficient purification of endosymbiontDNAfrom host DNA. Symbiosis 58:201-207.
4. Kent BN, Salichos L, Gibbons JG, Rokas A, Newton ILG, Clark ME, Bordenstein SR. 2011. Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol. Evol. 3:209. doi:10.1093/gbe/evr007.
5. Melnikov A, Galinsky K, Rogov P, Fennell T, Van Tyne D, Russ C, Daniels R, Barnes KG, Bochicchio J, Ndiaye D. 2011. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol. 12:R73. doi:10.1186/gb-2011-12-8-r73.
6. Metcalf JA, Bordenstein SR. 2012. The complexity of virus systems: the case of endosymbionts. Curr. Opin. Microbiol. 15:546-552.
7. Fujii Y, Kubo T, Ishikawa H, Sasaki T. 2004. Isolation and characterization of the bacteriophageWOfrom Wolbachia, an arthropod endosymbiont. Biochem. Biophys. Res. Commun. 317:1183-1188.
8. Wright JD, Sjostrand FS, Portaro JK, Barr AR. 1978. The ultrastructure of the rickettsia-like microorganism Wolbachia pipientis and associated virus-like bodies in the mosquito Culex pipiens. J. Ultrastruct. Res. 63:79-85.
9. Masui S, Kamoda S, Sasaki T, Ishikawa H. 2000. Distribution and evolution of bacteriophage WO in Wolbachia, the endosymbiont causing sexual alterations in arthropods. J. Mol. Evol. 51:491-497.
10. Klasson L, Walker T, Sebaihia M, Sanders MJ, Quail MA, Lord A, Sanders S, Earl J, O'Neill SL, Thomson N. 2008. Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Mol. Biol. Evol. 25: 1877-1887.
11. Wu M, Sun LV, Vamathevan J, Riegler M, Deboy R, Brownlie JC, McGraw EA, Martin W, Esser C, Ahmadinejad N. 2004. Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements. PLoS Biol. 2:e69. doi:10.1371/journal.pbio.0020069.
12. Tanaka K, Furukawa S, Nikoh N, Sasaki T, Fukatsu T. 2009. Complete WO phage sequences reveal their dynamic evolutionary trajectories and putative functional elements required for integration into the Wolbachia genome. Appl. Environ. Microbiol. 75:5676-5686.
13. Klasson L, Westberg J, Sapountzis P, Näslund K, Lutnaes Y, Darby AC, Veneti Z, Chen L, Braig HR, Garrett R. 2009. The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans. Proc. Natl. Acad. Sci. U. S. A. 106:5725-5730.
14. Liu Y-G, Chen Y. 2007. High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences. Biotechniques 43: 649-656.
15. Triglia T, Peterson MG, Kemp DJ. 1988. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acids Res. 16:8186. doi:10.1093/nar/16.16.8186.
16. Ochman H, Gerber AS, Hartl DL. 1988. Genetic applications of an inverse polymerase chain reaction. Genetics 120:621-623.
17. Silver J, Keerikatte V. 1989. Novel use of polymerase chain reaction to amplify cellular DNA adjacent to an integrated provirus. J. Virol. 63: 1924-1928.
18. Mueller PR, Wold B. 1989. In vivo footprinting of a muscle specific enhancer by ligation mediated PCR. Science 246:780. doi:10.1126/science.2814500.
19. Riley J, Butler R, Ogilvie D, Finniear R, Jenner D, Powell S, Anand R, Smith J, Markham A. 1990. A novel, rapid method for the isolation of terminal sequences from yeast artificial chromosome (YAC) clones. Nucleic Acids Res. 18:2887-2890.
20. Rosenthal A, Jones D. 1990. Genomic walking and sequencing by oligocassette mediated polymerase chain reaction. Nucleic Acids Res. 18: 3095.
21. Frohman MA, Dush MK, Martin GR. 1988. Rapid production of fulllength cDNAs from rare transcripts: amplification using a single genespecific oligonucleotide primer. Proc. Natl. Acad. Sci. U. S. A. 85:8998-9002.
22. Ohara O, Dorit RL, Gilbert W. 1989. One-sided polymerase chain reaction: the amplification of cDNA. Proc. Natl. Acad. Sci. U. S. A. 86:5673-5677.
23. Liu YG, Whittier RF. 1995. Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert end fragments from P1 and YAC clones for chromosome walking. Genomics 25:674-681.
24. Liu YG, Mitsukawa N, Oosumi T, Whittier RF. 1995. Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetric interlaced PCR. Plant J. 8:457-463.
25. Ellegaard KM, Klasson L, Näslund K, Bourtzis K, Andersson SG.2013. Comparative genomics of Wolbachia and the bacterial species concept. PLoS Genet. 9:e1003381. doi:10.1371/journal.pgen.1003381.
26. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol. 3:294-299.
27. Zhou W, Rousset F, O'Neill S. 1998. Phylogeny and PCR-based classification of Wolbachia strains using wsp gene sequences. Proc. Biol. Sci. 265: 509-515.
28. O'Neill SL, Giordano R, Colbert A, Karr TL, Robertson HM. 1992. 16S rRNA phylogenetic analysis of the bacterial endosymbionts associated with cytoplasmic incompatibility in insects. Proc. Natl. Acad. Sci. U. S. A. 89:2699-2702.
29. Jeyaprakash A, Hoy M. 2000. Long PCR improves Wolbachia DNA amplification: wsp sequences found in 76% of sixty-three arthropod species. Insect Mol. Biol. 9:393-405.
30. Zhang Z, Ye G-Y, Cai J, Hu C. 2005. Comparative venom toxicity between Pteromalus puparum and Nasonia vitripennis (Hymenoptera: Pteromalidae) toward the hemocytes of their natural hosts, non-target insects and cultured insect cells. Toxicon 46:337-349.
31. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
32. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32:11-16.
33. Galtier N, Gouy M, Gautier C. 1996. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12:543-548.
34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
35. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321.
36. Darriba D, Taboada GL, Doallo R, Posada D. 2011. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164-1165.
37. Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest 2: more models, new heuristics and parallel computing. Nat. Methods 9:772. doi: 10.1038/nmeth.2109.
38. Xiao JH, Wang NX, Murphy RW, Cook J, Jia LY, Huang DW. 2012. Wolbachia infection and dramatic intraspecific mitochondrial DNA divergence in a fig wasp. Evolution 66:1907-1916.
39. Kent BN, Funkhouser LJ, Setia S, Bordenstein SR. 2011. Evolutionary genomics of a temperate bacteriophage in an obligate intracellular bacteria [sic] (Wolbachia). PLoS One 6:e24984. doi:10.1371/journal.pone.0024984.
40. Baldo L, Dunning Hotopp JC, Jolley KA, Bordenstein SR, Biber SA, Choudhury RR, Hayashi C, Maiden MC, Tettelin H, Werren JH. 2006. Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Appl. Environ. Microbiol. 72:7098-7110.
41. Katoh K, Kuma K-I, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518.
42. Nash HA. 1996. Site-specific recombination: integration, excision, resolution, and inversion of definedDNAsegments, p 2363-2376. In Neidhardt FC, Curtiss R, Ingraham JL, Lin ECC, Low KB, Magasanik B, ReznikoffWS, Riley M, Schaechter M, Umbarger H (ed), Escherichia coli and Salmonella: cellular and molecular biology. ASM Press, Washington, DC.
43. Stark WM, Boocock MR, Sherratt DJ. 1992. Catalysis by site-specific recombinases. Trends Genet. 8:432-439.
44. Bordenstein SR, Wernegreen JJ. 2004. Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates. Mol. Biol. Evol. 21:1981-1991.
45. Gavotte L, Henri H, Stouthamer R, Charif D, Charlat S, Bouletreau M, Vavre F. 2007. A survey of the bacteriophage WO in the endosymbiotic bacteria [sic] Wolbachia. Mol. Biol. Evol. 24:427-435.