Construction and Characterization of Two Bacterial Artificial Chromosome Libraries of Grass Carp

Abstract

Bacterial artificial chromosome (BAC) library is an important tool in genomic research. We constructed two libraries from the genomic DNA of grass carp (Ctenopharyngodon idellus) as a crucial part of the grass carp genome project. The libraries were constructed in the EcoRI and HindIII sites of the vector CopyControl pCC1BAC. The EcoRI library comprised 53,000 positive clones, and approximately 99.94% of the clones contained grass carp nuclear DNA inserts (average size, 139.7 kb) covering 7.4× haploid genome equivalents and 2% empty clones. Similarly, the HindIII library comprised 52,216 clones with approximately 99.82% probability of finding any genomic fragments containing single-copy genes; the average insert size was 121.5 kb with 2.8% insert-empty clones, thus providing genome coverage of 6.3× haploid genome equivalents of grass carp. We selected gene-specific probes for screening the target gene clones in the HindIII library. In all, we obtained 31 positive clones, which were identified for every gene, with an average of 6.2 BAC clones per gene probe. Thus, we succeeded in constructing the desired BAC libraries, which should provide an important foundation for future physical mapping and whole-genome sequencing in grass carp.

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References

  1. Baoprasertkul P, Xu P, Peatman E, Kucuktas H, Liu Z (2007) Divergent Toll-like receptors in catfish (Ictalurus punctatus): TLR5S, TLR20, TLR21. Fish Shellfish Immunol 23:1218–1230

    CAS  PubMed  Google Scholar 

  2. Cunningham C, Hikima J, Jenny MJ, Chapman RW, Fang GC, Saski C, Lundqvist ML, Wing RA, Cupit PM, Gross PS, Warr GW, Tomkins JP (2006) New resources for marine genomics: bacterial artificial chromosome libraries for the Eastern and Pacific oysters (Crassostrea virginica and C. gigas). Mar Biotechnol 8:521–533

    Article  CAS  PubMed  Google Scholar 

  3. Hirono I, Takami M, Miyata M, Miyazaki T, Han HJ, Takano T, Endo M, Aoki T (2004) Characterization of gene structure and expression of two toll-like receptors from Japanese flounder, Paralichthys olivaceus. Immunogenetics 56:38–46

    Article  CAS  PubMed  Google Scholar 

  4. Ishikawa Y (2000) Medakafish as a model system for vertebrate developmental genetics. Bioessays 22:487–495

    Article  CAS  PubMed  Google Scholar 

  5. Katagiri T, Asakawa S, Hirono I, Aoki T, Shimizu N (2000) Genomic bacterial artificial chromosome library of the Japanese flounder Paralichthys olivaceus. Mar Biotechnol 2:571–576

    Article  CAS  PubMed  Google Scholar 

  6. Katagiri T, Asakawa S, Minagawa S, Shimizu N, Hirono I, Aoki T (2001) Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim Genet 32:200–204

    Article  CAS  PubMed  Google Scholar 

  7. Katagiri T, Kidd C, Tomasino E, Davis JT, Wishon C, Stern JE, Carleton KL, Howe AE, Kocher TD (2005) A BAC-based physical map of the Nile tilapia genome. BMC Genom 6:89

    Article  Google Scholar 

  8. Li Y, Li H, Hong Y (1985) Studies on the karyotypes of Chinese cyprinid fishes VII. Acta Genetica Sin 12:367–372

    Google Scholar 

  9. Matsuo A, Oshiumi H, Tsujita T, Mitani H, Kasai H, Yoshimizu M, Matsumoto M, Seya T (2008) Teleost TLR22 recognizes RNA duplex to induce IFN and protect cells from birnaviruses. J Immunol 181:3474–3485

    CAS  PubMed  Google Scholar 

  10. Nandi S, Peatman E, Xu P, Wang S, Li P, Liu Z (2007) Repeat structure of the catfish genome: a genomic and transcriptomic assessment of Tc1-like transposon elements in channel catfish (Ictalurus punctatus). Genetics 131:81–90

    CAS  Google Scholar 

  11. Ng SH, Artieri CG, Bosdet IE, Chiu R, Danzmann RG, Davidson WS, Ferguson MM, Fjell CD, Hoyheim B, Jones SJ, de Jong PJ, Koop BF, Krzywinski MI, Lubieniecki K, Marra MA, Mitchel LA, Mathewson C, Osoegawa K, Parisotto SE, Phillips RB, Rise ML, von Schalburg KR, Schein JE, Shin H, Siddiqui A, Thorsen J, Wye N, Yang G, Zhu B (2005) A physical map of the genome of Atlantic salmon, Salmo salar. Genomics 86:396–404

    Article  CAS  PubMed  Google Scholar 

  12. O’Neill LA (2008) The interleukin-1 receptor/Toll-like receptor superfamily: 10 years of progress. Immunol Rev 226:10–18

    Article  PubMed  Google Scholar 

  13. Oshiumi H, Matsuo A, Matsumoto M, Seya T (2008) Pan-vertebrate toll-like receptors during evolution. Curr Genom 9:488–493

    Article  CAS  Google Scholar 

  14. Osoegawa K, Woon PY, Zhao B, Frengen E, Tateno M, Catanese JJ, de Jong PJ (1998) An improved approach for construction of bacterial artificial chromosome libraries. Genomics 52:1–8

    Article  CAS  PubMed  Google Scholar 

  15. Postlethwait JH, Johnson SL, Midson CN, Talbot WS, Gates M, Ballinger EW, Africa D, Andrews R, Carl T, Eisen JS et al (1994) A genetic linkage map for the zebrafish. Science 264:699–703

    Article  CAS  PubMed  Google Scholar 

  16. Quiniou SM, Katagiri T, Miller NW, Wilson M, Wolters WR, Waldbieser GC (2003) Construction and characterization of a BAC library from a gynogenetic channel catfish Ictalurus punctatus. Genet Sel Evol 35:673–683

    Article  CAS  PubMed  Google Scholar 

  17. Sepulcre MP, Alcaraz-Pérez F, López-Muñoz A, Roca FJ, Meseguer J, Cayuela ML, Mulero V (2009) Evolution of lipopolysaccharide (LPS) recognition and signaling: fish TLR4 does not recognize LPS and negatively regulates NF-kappaB activation. J Immunol 182:1836–1845

    Article  CAS  PubMed  Google Scholar 

  18. Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797

    Article  CAS  PubMed  Google Scholar 

  19. Strong SJ, Ohta Y, Litman GW, Amemiya CT (1997) Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res 25:3959–3961

    Article  CAS  PubMed  Google Scholar 

  20. Tao Q, Chang YL, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang HB (2001) Bacterial artificial chromosome-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711–1724

    CAS  PubMed  Google Scholar 

  21. Thorsen J, Zhu B, Frengen E, Osoegawa K, de Jong PJ, Koop BF, Davidson WS, Hoyheim B (2005) A highly redundant BAC library of Atlantic salmon (Salmo salar): an important tool for salmon projects. BMC Genom 6:50

    Article  Google Scholar 

  22. Tsujita T, Tsukada H, Nakao M, Oshiumi H, Matsumoto M, Seya T (2004) Sensing bacterial flagellin by membrane and soluble orthologs of Toll-like receptor 5 in rainbow trout (Onchorhynchus mikiss). J Biol Chem 279:48588–48597

    Article  CAS  PubMed  Google Scholar 

  23. Wang S, Xu P, Thorsen J, Zhu B, deJong PJ, Waldbieser G, Kucuktas H, Liu Z (2007) Characterization of a BAC library from channel catfish Ictalurus punctatus: indications of high levels of chromosomal reshuffling among teleost genomes. Mar Biotechnol 9:701–711

    Article  CAS  PubMed  Google Scholar 

  24. Whitaker HA, McAndrew BJ, Taggart JB (2006) Construction and characterization of a BAC library for the European seabass Dicentrarchus labrax. Anim Genet 37:526

    Article  CAS  PubMed  Google Scholar 

  25. Xu P, Wang S, Liu L, Peatman E, Somridhivej B, Thimmapuram J, Gong G, Liu Z (2006) Channel catfish BAC-end sequences for marker development and assessment of syntenic conservation with other fish species. Anim Genet 37:321–326

    Article  CAS  PubMed  Google Scholar 

  26. Xu P, Wang S, Liu L, Thorsen J, Kucuktas H, Liu Z (2007) A BAC-based physical map of the channel catfish genome. Genomics 90:380–388

    Article  CAS  PubMed  Google Scholar 

  27. Zhang X, Zhang Y, Scheuring C, Zhang HB, Huan P, Wang B, Liu C, Li F, Liu B, Xiang J (2010) Construction and characterization of a Bacterial Artificial Chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei. Mar Biotechnol 12:141–149

    Google Scholar 

  28. Zhang Y, Zhang X, Scheuring CF, Zhang HB, Huan P, Li F, Xiang J (2008) Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system. Mar Biotechnol 10:358–365

    Article  PubMed  Google Scholar 

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Acknowledgments

This study was financially supported by the Development Plan of the State Key Fundamental Research of China (Grant No. 2009CB118701), and the National Natural Science Foundation of China (Grant No. 30540084). We also thank Professor Runlin Ma for his enthusiastic help in the experiment.

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Correspondence to Yaping Wang.

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Jang, S., Liu, H., Su, J. et al. Construction and Characterization of Two Bacterial Artificial Chromosome Libraries of Grass Carp. Mar Biotechnol 12, 261–266 (2010). https://doi.org/10.1007/s10126-010-9268-0

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Keywords

  • Bacterial artificial chromosome
  • Grass carp
  • Gene-specific hybridization