Abstract
Half-smooth tongue sole (Cynoglossus semilaevis: Pleuronectiformes) is a commercially important cultured marine flatfish in China and forms an important fishery resource, but the research of its genome is underdeveloped. In this study, we constructed a female C. semilaevis fosmid library and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of 49,920 clones with an average insert size of about 39 kb, amounting to 3.23 genome equivalents. Fosmid stability assays indicate that female C. semilaevis DNA was stable during propagation in the fosmid system. Library screening with eight microsatellite markers yielded between two and five positive clones, and none of those tested was absent from the library. End-sequencing of both 5′ and 3′ ends of 1,152 individual clones generated 2,247 sequences after trimming, with an average sequence length of 855 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 259 (11.53%) and 287 (12.77%) significant hits (E < e −5), respectively. Repetitive sequences analysis resulted in 5.23% of base pairs masked using both the Fugu and Danio databases, repetitive elements were composed of retroelements, DNA transposons, satellites, simple repeats, and low-complexity sequences. The fosmid library, in conjunction with the fosmid end sequences, will serve as a useful resource for large-scale genome sequencing, physical mapping, and positional cloning, and provide a better understanding of female C. semilaevis genome.
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References
Birren BW, Tachi-iri Y, Kim UJ, Nguyen M, Shizuya H, Korenberg J, Simon MI (1996) A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 34:97–106
Chen S, Li J, Deng S, Tian Y, Wang Q, Zhuang Z, Sha Z, Xu J (2007) Isolation of female-specific AFLP markers and molecular identification of genetic sex in half-smooth tongue sole (Cynoglossus semilaevis). Mar Biotechnol 9:273–280
De Smet WHO (1981) The nuclear Feulgen-DNA content of the vertebrates (especially reptiles), as measured by fluorescence cytophotometry, with notes on the cell and chromosome size. Acta Zool Pathol Antverp 76:119–167
De Tomaso AW, Weissman IL (2003) Construction and characterization of large-insert genomic libraries (BAC and fosmid) from the ascidian Botryllus schlosseri and initial physical mapping of a histocompatibility locus. Mar Biotechnol 5:103–115
Dolezel J, Bartos H, Voglmayr J, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry 51:127–128
Fitz-Gibbon S, Choi AJ, Miller JH, Stetter KO, Simon MI, Swanson R, Kim U (1997) A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum. Extremophiles 1:36–51
Hardie DC, Hebert PDN (2003) The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes. Genome 46:683–706
Hardie DC, Hebert PDN (2004) Genome-size evolution in fishes. Can J Fish Aquat Sci 61:1636–1646
Hinegardner R (1968) Evolution of cellular DNA content in teleost fishes. Am Nat 102:517–523
Hinegardner R, Rosen DE (1972) Cellular DNA content and the evolution of teleostean fishes. Am Nat 106:621–644
Kim C-G, Fujiyama A, Saitou N (2003) Construction of a gorilla fosmid library and its PCR screening system. Genomics 82:571–575
Kim UJ, Shizuya H, de Jong PJ, Birren B, Simon MI (1992) Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res 20:1083–1085
Larkin DM, Everts-van der Wind A, Rebeiz M, Schweitzer PA, Bachman S, Green C, Wright CL, Campos EJ, Benson LD, Edwards J, Liu L, Osoegawa K, Womack JE, de Jong PE, Lewin HA (2003) A cattle–human comparative map built with cattle BAC-ends and human genome sequence. Genome Res 13:1966–1972
Liao X, Shao C, Tian Y, Chen S (2007) Polymorphic dinucleotide microsatellites in tongue sole (Cynoglossus semilaevis). Mol Ecol Resources 7:1147–1149
Liu W, Zhang Y, Liu Z, Guo L, Wang X, Fei J, Feng J, Zhao R, Hu X, Li N (2006) A five-fold pig bacterial artificial chromosome library: a resource for positional cloning and physical mapping. Prog Nat Sci 16:889–892
Liu Y, Sun X, Gao H, Liu L (2007) Microsatellite markers from an expressed sequence tag library of half-smooth tongue sole (Cynoglossus semilaevis) and their application in other related fish species. Mol Ecol Resources 7:1242–1244
Liu Y, Bao B, Liu L, Wang L, Lin H (2008) Isolation and characterization of polymorphic microsatellite loci from RAPD product in half-smooth tongue sole (Cynoglossus semilaevis) and a test of cross-species amplification. Mol Ecol Resources 8:202–204
Magrini V, Warren WC, Wallis J, Goldman WE, Xu J, Mardis ER, Mcpherson JD (2004) Fosmid-based physical mapping of the Histoplasma capsulatum genome. Genome Res 14:1603–1609
Moon DA, Magor KE (2004) Construction and characterization of a fosmid library for comparative analysis of the duck genome. Anim Genet 35:417–418
Ohno S, Atkin NB (1966) Comparative DNA values and chromosome complements of eight species of fishes. Chromosoma 18:455–466
Ojima Y, Yamamoto K (1990) Cellular DNA contents of fishes determined by flow cytometry. La Kromosomo II 57:1871–1888
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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
Zhang Q, Katsutoshi A (1996) Flow cytometry for DNA contents of somatic cells and spermatozoa in the progeny of natural tetraploid loach. Fish Sci 62(6):870–877
Zhang L, Bao Z, Cheng J, Li H, Huang X, Wang S, Zhang C, Hu J (2007) Fosmid library construction and initial analysis of end sequences in zhikong scallop (Chlamys farreri). Mar Biotechnol 9:606–612
Zhao S, Shatsman S, Ayodeji B, Geer K, Tsegaye G, Krol M, Gebregeorgis E, Shvartsbeyn A, Russell D, Overton L, Jiang L, Dimitrov G, Tran K, Shetty J, Malek JA, Feldblyum T, Nierman WC, Fraser CM (2001) Mouse BAC ends quality assessment and sequence analyses. Genome Res 11:1736–1745
Zhuang Z, Wu D, Zhang S, Pang Q, Wang C, Wan R (2006) G-banding patterns of the chromosomes of tonguefish Cynoglossus semilaevis Günther, 1873. J Appl Ichthyol 22:437–440
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This work was supported by ‘863’ Hi-Tech Research and Development Program of China (2006AA10A404).
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Wang, X., Zhang, Q., Sun, X. et al. Fosmid Library Construction and Initial Analysis of End Sequences in Female Half-smooth Tongue Sole (Cynoglossus semilaevis). Mar Biotechnol 11, 236–242 (2009). https://doi.org/10.1007/s10126-008-9137-2
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DOI: https://doi.org/10.1007/s10126-008-9137-2