African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12488

Full Length Research Paper

Expressed sequence tags (EST) analysis of a normalized full-length cDNA library from the pinewood nematode (Bursaphelenchus xylophilus)

Ha Young Chung†
  • Ha Young Chung†
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Man-Jung Kang†
  • Man-Jung Kang†
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Hye Rim Han
  • Hye Rim Han
  • Korea Forest Research Institute, Dongademun-gu, Seoul 130-712, Korea.
  • Google Scholar
Joon-Soo Sim
  • Joon-Soo Sim
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Byung-Ju Oh
  • Byung-Ju Oh
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Inchan Choi
  • Inchan Choi
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Chang-Muk Lee
  • Chang-Muk Lee
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Sang-Hong Yoon
  • Sang-Hong Yoon
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar
Bum-Soo Hahn*
  • Bum-Soo Hahn*
  • National Academy of Agricultural Science, Suwon 441-857, Korea.
  • Google Scholar


  •  Received: 15 May 2014
  •  Accepted: 21 July 2014
  •  Published: 13 August 2014

References

Abelleira A, Picoaga A, Mansilla JP, Aguin O (2011). Detection of Bursaphelenchus xylophilus, causal agent of pine wilt disease on Pinus pinaster in Northwestern Spain. Plant Dis. 95:776.
Crossref
 
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
Crossref
 
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, et al. (2001). The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29:37-40.
Crossref
 
Ashburner M, Lewis SE (2002). On ontologies for biologists: the Gene Ontology- uncoupling the web. Novartis Found Symp. 247: 66-80.
Crossref
 
Barker WC, Garavelli JS, Huang H, McGarvey PB, Orcutt BC, Srinivasarao GY, Xiao C, Yeh LS, Ledley RS, Janda JF, Pfeiffer F, Mewes HW, Tsugita A, Wu C (2000). The protein information resource (PIR). Nucleic Acids Res. 28:41-44.
Crossref
 
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002). The Pfam protein families database. Nucleic Acids Res. 30:276-280.
Crossref
 
Donald PA, Stamps WT, Linit MJ (2003). Pine wilt disease in APSnet plant disease lessons. The American Phytopathological Society, St. Paul, MN, USA.
 
Dubreuil G, Magliano M, Deleury E, Abad P, Rosso MN (2007). Transcriptome analysis of root knot nematode functions induced in the early stages of parasitism. N. Phytol. 176:426-436.
Crossref
 
Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A (2002). The PROSITE database, its status in 2002. Nucleic Acids Res. 30:235-238.
Crossref
 
Fan J, Kang L, Sun J (2007). Role of host volatiles in mate location by the Japanese pine sawyer, Monochamus alternatus Hope (Coleoptera: Cerambycidae). Environ. Entomol. 36:58-63.
Crossref
 
Fielding NJ, Evans HF (1996). The pine wood nematode Bursaphelenchus xylophilus (Steiner and Buhrer) Nickle (B. lignicolus Mamiya and Kiyohara): an assessment of the current position. For. 69:35-46.
 
Guda C (2006). pTARGET: a web server for predicting protein subcellular localization. Nucleic Acids Res. 34:W210-213.
Crossref
 
Henikoff S, Henikoff JG, Pietrokovski S (1999). Blocksþ: a nonredundant database of protein alignment blocks derived from multiple compilations. Bioinform. 15:471-479.
Crossref
 
Hofmann K, Stoffel W (1993). TMbase-A database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 374:166.
 
Kang JS, Lee H, Moon IS, Lee Y, Koh YH, Je YH, Lim KJ, Lee SH (2009). Construction and characterization of subtractive stage-specific expressed sequence tag (EST) libraries of the pinewood nematode Bursaphelenchus xylophilus. Genom. 1:70-77.
Crossref
 
Kang MJ, Kim YH, Hahn BS (2010). Expressed sequence tag analysis generated from a normalized full-length cDNA library of the root-knot nematode (Meloidogyne incognita). Genes Genom. 32:553-562.
Crossref
 
Kikuchi T, Aikawa T, Kosaka H, Pritchard L, Ogura N, Jones JT (2007). Expressed sequence tag (EST) analysis of the pine wood nematode Bursaphelenchus xylophilus and B. mucronatus. Mol. Biochem. Parasitol. 155:9-17.
Crossref
 
Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, Yokoi T, Larsson MC, Miwa J, Maule AG, Sahashi N, Jones JT, Berriman M (2011). Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog. 7:e1002219.
Crossref
 
Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J (2005). The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res. 1:D71-74.
 
Lilley CJ, Atkinson HJ, Urwin PE (2005). Molecular aspects of cyst nematodes. Mol. Plant Pathol. 6:577-588.
Crossref
 
Linit MJ (1988). Nemtaode-vector relationships in the pine wilt disease system. J. Nematol. 20:227-235.
Pubmed
 
Lupas A, Van Dyke M, Stock J (1991). Predicting coiled coils from protein sequences. Sci. 24:1162-4116.
Crossref
 
Martin DM, Berriman M, Barton GJ (2004). GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinform. 5:178.
Crossref
 
Maruyama K, Sugano S (1994). Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138:171-174.
Crossref
 
Menon R, Garg G, Gasser RB, Ranganathan S (2012). TranSeqAnnotator: large-scale analysis of transcriptomic data. BMC Bioinformatics 13(Suppl 17):S24.
Pubmed
 
Mota M, Vieira P (2008). Pine wilt disease: a worldwide threat to forest ecosystems. Springer XVIII, 406 p., ISBN: 978-1-4020-8454-6
 
Mota MM, Braasch H, Bravo MA, Penas AC, Burgermeister W, Metge K, Sousa E (1999). First report of Bursaphelenchus xylophilus in Portugal and in Europe. Nematology 1: 727-734.
Crossref
 
Myers RF (1988). Pathogenesis in pine wilt caused by pinewood nematode, Bursaphelenchus xylophilus. J. Nematol. 20:236-244.
Pubmed
 
Nagaraj SH, Gasser RB, Ranganathan S (2008). Needles in the EST Haystack: Large-Scale Identification and Analysis of Excretory-Secretory (ES) Proteins in Parasitic Nematodes Using Expressed Sequence Tags (ESTs). PLoS Negl. Trop. Dis. 2:e301.
Crossref
 
Oh JH, Kim YS, Kim NS (2003). An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material. Exp. Mol. Med. 35:586-590.
Crossref
 
Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Schmid R, Hall N, Barrell B, Waterston RH, McCarter JP, Blaxter ML (2004). A transcriptomic analysis of the phylum Nematoda. Nat. Genet. 36:1259-1267.
Crossref
 
Rensing SA, Lang D, Reski R (2003). In silico prediction of UTR repeats using clustered EST data. Proceed. German Conference Bioinform. 117-122.
 
Rosso MN, Jones JT, Abad P (2008). RNAi and functional genomics in plant parasitic nematodes. Annu. Rev. Phytopathol. 47:207-232.
Crossref
 
Sakai M, Yamasaki T (1990). (+)-Juniperol and (+)-pimaral: Attractants for the cerambycid beetle, Monochamus alternatus Hope. J. Chem. Eco. 16:3383-3392.
Crossref
 
Scholl EH, Thorne JL, McCarter JP, Bird DM (2003). Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol. 4:R39.
Crossref
 
Shen YQ, Burger G (2007). 'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools. BMC Bioinform. 8:420.
Crossref
 
Shibata E (1987). Oviposition schedules, survivorship curves, and mortality factors within trees of two cerambycid beetles (Coleoptera: Cerambycidae), the Japanese pine sawyer, Monochamus alternatus hope, and sugi bark borer, Semanotus japonicus lacordaire. Res. Population Ecol. 29:347-367.
Crossref
 
Sriwati R, Takemoto S, Futai K (2007). Cohabitation of the pine wood nematode, Bursaphelenchus xylophilus, and fungal species in pine trees inoculated with B. xylophilus. Nematol. 9:77-86.
Crossref
 
Steiner G, Buhrer EM (1934). Aphelenchoides xylophilus n. sp. a nematode associated with bluestain and other fungi in timber. J. Agric. Res. 48:949-951.
 
Sultana T, Kim J, Lee SH, Han H, Kim S, Min GS, Nadler SA, Park JK (2013). Comparative analysis of complete mitochondrial genome sequences confirms independent origins of plant-parasitic nematodes. BMC Evol. Biol. 13:12.
Crossref
 
Tae H, Ryu D, Sureshchandra S, Choi JH (2012). ESTclean: A Cleaning Tool for Next-Gen Transcriptome Shotgun Sequencing. BMC Bioinform. 13:247.
Crossref
 
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001). The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
Crossref
 
Vieira J, Messing J (1987). Production of single-stranded plasmid DNA. Methods Enzymol. 153:3-11.
Crossref
 
Wootton JC, Federhen S (1993). Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17:149-163.
Crossref
 
Xie G, Chain PS, Lo CC, Liu KL, Gans J, Merritt J, Qi F (2010). Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Mol. Oral Microbiol. 25:391-405.
Pubmed
 
Yan X, Cheng XY, Wang YS, Luo J, Mao ZC, Ferris VR, Xie BY (2012). Comparative transcriptomics of two pathogenic pinewood nematodes yields insights into parasitic adaptation to life on pine hosts. Gene 505:81-90.
Crossref
 
Yang F, Xu B, Zhao S, Li J, Yang Y, Tang X, Wang F, Peng M, Huang Z (2012). De novo sequencing and analysis of the termite mushroom (Termitomyces albuminosus) transcriptome to discover putative genes involved in bioactive component biosynthesis. J. Biosci. Bioeng. 4:228-231.
Crossref