Please wait a minute...
Frontiers of Agriculture in China

ISSN 1673-7334

ISSN 1673-744X(Online)

CN 11-5729/S

Front. Agric. China    2010, Vol. 4 Issue (1) : 121-127     DOI: 10.1007/s11703-010-0101-3
Research articles |
Unigene derived SSR analysis for the Fugu rubripes and insights into the characteristics of EST-SSR distribution in tissues/organs
Jiaqing WANG1,Lin HOU2,
1.College of Ocean, Agricultural University of Hebei, Qinhuangdao 066003, China; 2.College of Life Sciences, Liaoning Normal University, Dalian 116029, China;
Download: PDF(133 KB)  
Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks
Abstract  A total of 11348 Unigene derived ESTs from five cDNA libraries corresponding to five different tissues/organs were screened for EST-SSR, and 1097 EST–SSRs (9.67%) were detected. There were considerable variations in the amount of EST-SSRs among the five tissues/organs. In all the tissues/organs, trinucleotide repeats (67.74%) were found to be most abundant. The trinucleotide repeats GCG were the most abundant in three tissues/organs that ranged from 80.2% in skin, 83.3% in gut, to 90.2% in fin. Dinucleotide was the second abundant repeat type (13.58%), followed by tetra-(12.38%), hexa-(5.34%), and penta-(0.96%) nucleotide repeats. Furthermore, the results of the present study also indicated that the EST-SSR motifs were not randomly distributed in tissues/organs of fugu, such as trinucleotide repeats were found to be strikingly abundant in fin, followed by skin and gut, tetra-nucleotide repeats were especially rich in muscle, while pentanucleotide repeats were less common in any tissue or organ. Most of the EST-SSRs in five tissues/organs that were assigned functions during the present study represent housekeeping genes.
Keywords Unigene      Fugu rubripes      EST-SSRs      tissues/organs      
Issue Date: 05 March 2010
URL:     OR
Bilgen M, Karaca M, Onus A N, Ince A G(2004). A software program combining sequence motif searches with keywordsfor finding repeats containing DNA sequences. Bioinformatics, 20: 3379―3386

doi: 10.1093/bioinformatics/bth410
Blair S H, Sudhir K, (2002). Vertebrategenomes compared. Science, 297: 1283―1285

doi: 10.1126/science.1076231
Cardle L, Ramsay L, Milbourne, D, Macaulay M, Marshall D, Waugh R(2002). Computational and experimental characterizationof physically clustered simple sequence repeats in plants. Genetics, 156: 847―854
Chin E C L(1996). Maize simple repetitive DNA sequences: abundance andallele variation. Genome, 39: 866―873

doi: 10.1139/g96-109
Heslop-Harrison J S(2003). Tandemly repeated DNA sequences and centromeric chromosomalregions of Arabidopsis species. Chromosome Res, 11: 241―253

doi: 10.1023/A:1022998709969
Ince A G, Onus A N, Elmasulu S Y, Bilgen M, Karaca M(2007). In silicodata mining for development of Capsicum microsatellites. Acta Horticulturae, 729: 123―127
Jeffreys A J, Wilson V, Thein S L(1985). Hypervariable minisatellite regionsin human DNA. Nature, 314: 67―73

doi: 10.1038/314067a0
Ju Z, Wells M C, Martinez A, Hazlewood L, Walter R B(2005). An insilico mining for simple sequence repeats from expressed sequencetags of zebrafish, medaka, Fundulus and Xiphophorus. In Silico Biol, 5: 439―463
Kantety R V, La R M, Matthews D E, Sorrells M E(2002). Data mining for simple sequence repeats in expressedsequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol, 48: 501―510

doi: 10.1023/A:1014875206165
Klintschar M, Wiegand P(2003). Polymeraseslippage in relation to the uniformity of tetrameric repeat stretches. Forensic Sci Int, 135: 163―166

doi: 10.1016/S0379-0738(03)00201-9
McMurray C T(1999). DNA secondary structure: a common and causative factorfor expansion in human disease. Proc NatlAcad Sci USA, 96: 1823―1825

doi: 10.1073/pnas.96.5.1823
Mehmet B, Mehmet K, Naci A O, Ays G I(2004). A software program combining sequence motif searches with keywordsfor finding repeats containing DNA sequences. Bioinformatics, 20: 3379―3386

doi: 10.1093/bioinformatics/bth410
Metzgar D, Bytof J, Wills C(2000). Selection against frameshift mutationslimits microsatellite expansion in coding DNA. Genome Res, 10: 72―80
Muragaki Y, Mundlos S, Upton J, Olsen B R(1996). Altered growth and branching patterns in synpolydactyly caused bymutations in HOXD13. Science, 272: 548―551

doi: 10.1126/science.272.5261.548
Perez F, Ortiz J, Zhinaula M, Gonzabay C, Calderon J, Volckaert F A(2005). Development of EST-SSR markers bydata mining in three species of shrimp, Litopenaeusvannamei, Litopenaeus stylirostris and Trachypenaeus birdy. MarineBiotechnol, 7: 554―569

doi: 10.1007/s10126-004-5099-1
Reddy P S, Housman D E(1997). The complexpathology of trinucleotide repeats. CurrOpin Cell Biol, 9: 364―372

doi: 10.1016/S0955-0674(97)80009-9
Riley D E, Krieger J N(2004). Shorttandem repeats are associated with diverse mRNAs encoding membrane-targetedproteins. Bioassays, 26: 434―444

doi: 10.1002/bies.20001
Rohrer G A, Fahrenkrug S C, Nonneman D, Tao N, Warren W C(2002). Mapping microsatellitemarkers identified in porcine EST sequences. Anim Genet, 33: 372―376

doi: 10.1046/j.1365-2052.2002.00880.x
Saha S, Karaca M, Jenkins J N, Zipf A E, Reddy O U K, Pepper A E, Kantety R(2003). Simplesequence repeats as useful resources to study transcribed genes ofcotton. Euphytica, 130: 355―364

doi: 10.1023/A:1023077209170
Schlotterer C, Wiehe T(1999). Microsatellites,a neutral marker to infer selective sweeps. In: Goldstein D B, Schlstterer C, eds. Microsatellites: Evolution and Applications. Oxford: Oxford University Press, 238―247
Serapion J, Kucuktas H, Feng J, Liu Z(2004). Bioinformatic mining of type I microsatellites from expressed sequencetags of channel catfish (Ictalurus punctatus). J Mar Biotechnol, 6: 364―377

doi: 10.1007/s10126-003-0039-z
Timchenko L T, Caskey C T(1999). Tripletrepeat disorders: discussion of molecular mechanisms. Cell Mol Life Sci, 55: 1432―1447

doi: 10.1007/s000180050383
Toth G, Gaspari Z, Jurka J(2000). Microsatellites in different eukaryoticgenome, survey and analysis. Genome Res, 10: 1967―1981

doi: 10.1101/gr.10.7.967
Tu M, Lu B R, Zhu Y Y, Wang Y Y(2007). Abundant within-varietal genetic diversity in rice germplasm fromYunnan Province of China revealed by SSR fingerprints. Biochemical Genetics, 45: 789―801

doi: 10.1007/s10528-007-9118-6
Varshney R K, Thiel T, Stein N, Langridge P, Graner A(2002). In silicoanalysis on frequency and distribution of microsatellites in ESTsof some cereal species. Cell Mol Biol Lett, 7: 537―546
Wang D, Liao X, Cheng L, Yu X, Tong J(2007). Development of novelEST-SSR markers in common carp by data mining from public EST sequences. Aquaculture, 271: 558―574

doi: 10.1016/j.aquaculture.2007.06.001
Wierdl M, Dominska M, Petes T D(1997). Microsatellite instability in yeast,dependence on the length of the microsatellite. Genetics, 146: 769―779
Yu X M, Zhou Q, Qian Z Q, Li S, Zhao G F(2006). Analysis of geneticdiversity and population differentiation of Larix potaninii var. chinensis using microsatellite DNA. BiochemicalGenetics, 44: 483―493

doi: 10.1007/s10528-006-9049-7
Zhuchenko O, Bailey J, Bonnen P, Ashizawa T, Stockton D W, Amos C, Dobyns W B, Subramony S H, Zoghbi H Y, Lee C C(1997). Autosomal dominant cerebellar ataxia (SCA6) associated with smallpolyglutamine expansions in the α1A-voltage-dependent calciumchannel. Nature Genet, 15: 62―69

doi: 10.1038/ng0197-62
No related articles found!
Full text