Mining of EST-SSR markers in clam Meretrix meretrix larvae from 454 shotgun transcriptome

Genes and Genetic Systems

Volumn 86, Issue 3, 2011, Pages 197-205

  Wang, Hongxia ^a   Huan, Pin ^a   Lu, Xia ^a   Liu, Baozhong ^a  

^a INSTITUTE OF OCEANOLOGY   (China)

Author keywords

Developmental stages; EST SSR; High throughput marker identification; Meretrix meretrix

Indexed keywords

TRANSCRIPTOME;

ARTICLE; CLAM; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DINUCLEOTIDE REPEAT; DNA FLANKING REGION; EXPRESSED SEQUENCE TAG; LARVAL STAGE; MERETRIX MERETRIX; MICROSATELLITE MARKER; MOLLUSC LARVA; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PENTANUCLEOTIDE REPEAT; POLYMERASE CHAIN REACTION; SIMPLE SEQUENCE REPEAT; TETRANUCLEOTIDE REPEAT; TRINUCLEOTIDE REPEAT;

ANIMALS; BASE SEQUENCE; BIVALVIA; DNA PRIMERS; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENETIC VARIATION; LIFE CYCLE STAGES; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

BIVALVIA; MERETRIX MERETRIX;

EID: 80053314292     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.86.197     Document Type: Article

References (35)

1. Abdelkrim, J., Robertson, B. C., Stanton, Jo-Ann., L., and Gemmell, N. J. (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Bio Techniques 46, 185-192.
2. Cardle, L., Ramsay, L., Milbourne, D., Macaulay, M., Marshall, D., and Waugh, R. (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156, 847-854.
3. Castoe, T. A., Polle, A. W., Gu, W., de Koning, A. P. J., Daza, J. M., Smith, E. N., and Pollock, D. D. (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix)microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources 10, 341-347.
4. Coleman, T. P., and Roesser, J. R. (1998) RNA secondary structure: an important cis-element in rat calcitonin/CGRP pre-messenger RNA splicing. Biochemistry 37, 15941-15950.
5. Cruz, F., Pérez, M., and Presa, P. (2005) Distribution and abundance of microsatellites in the genome of bivalves. Gene 346, 241-247.
6. Edwards, Y. J., Elgar, G., Clark, M. S., and Bishop, M. J. (1998) The identification and characterization of microsatellites in the compact genome of the Japanese pufferfish, Fugu rubripes: perspectives in functional and comparative genomic analysis. Journal of Molecular Biology 278, 843-854.
7. Eujayl, I., Sorrells, M. E., Baum, M., Wolters, P., and Powell, W. (2002) Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat. Theoretical and Applied Genetics 104, 399-407.
8. Frank, M. Y., Huo, N., Gu, Y. Q., Luo, M., Ma, Y., Hane, D., Lazo, G. R., Dvorak, J., and Anderson, O. D. (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9, 253, doi:10.1186/1471-2105-9-253.
9. Huan, P., Wang, H., and Liu, B. (2011) Transcriptomic analysis of the clam Meretrix meretrix on different larval stages. Marine Biotechnology doi: 10.1007/s10126-011-9389-0.
10. Jurka, J., and Pethiyagoda, C. (1995) Simple repetitive DNA sequences from primates: compilation and analysis. Journal of Molecular Evolution 40, 120-126.
11. Karsi, A., Cao, D., Li, P., Patterson, A., Kocabas, A., Feng, J., Ju, Z., Mickett, K. D., and Liu, Z. (2002) Transcriptome analysis of channel catfish (Ictalums punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene 285, 157-168.
12. Katti, M. V., Ranjekar, P. K., and Gupta, V. S. (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Molecular Biology and Evolution 18, 1161-1167.
13. Kenneson, A., Zhang, F. P., Hagedorn, C. H., and Warren, S. T. (2001) Reduced FMRP and increased FMR1 transcription is proportionally associated with CGG repeat number in intermediate-length and premutation carriers. Human Molecular Genetics 10, 1449-1454.
14. Kumpatla, S. P., and Mukhopadhyay, S. (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48, 985-998.
15. Lawson, M. J., and Zhang, L. (2008) Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5'-UTR region. Gene 407, 54-62.
16. Li, H., Liu, W., Gao, X., Zhu, D., Wang, J., Li, Y., and He, C. (2010) Identification of host-defense genes and development of microsatellite markers from ESTs of hard clam Meretrix meretrix. Molecular Biology Reports doi: 10.1007/s11033-010-0165-4.
17. Li, Y. C., Korol, A. B., Fahima, T., and Nevo, E. (2004) Microsatellites within genes: structure, function, and evolution. Molecular Biology and Evolution 21, 991-1007.
18. Liu, Z., Karsi, A., and Dunham, R. A. (1999) Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Marine Biotechnology 1, 437-447.
19. Lu, X., Wang, H., Dai, P., and Liu, B. (2011) Characterization of EST-SSR and genomic-SSR markers in the clam, Meretrix meretrix. Conservation Genetics Resources doi: 10.1007/s12686-011-9426-3.
20. Moran, C. (1993) Microsatellite repeats in pig (Sus domestica) and chicken (Gallus domesticus) genomes. Journal of Heredity 84, 274-280.
21. Pérez, F., Ortiz, J., Zhinaula, M., Gonzabay, C., Calderón, J., and Volckaert, F. A. M. J. (2005) Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Marine Biotechnology 7, 554-569.
22. Persico, A. M., Levitt, P., and Pimenta, A. F. (2006) Polymorphic GGC repeat differentially regulates human reelin gene expression levels. Journal of Neural Transmission 113, 1373-1382.
23. Sharma, P. C., Grover, A., and Kahl, G. (2007) Mining microsatellites in eukaryotic genomes. Trends in Biotechnology 25, 490-498.
24. Sithichoke, T., Prakit, S., Pichahpuk, U., Juntima, C., Duangjai, S., Worapa, S., Warunee, S., Somvong, T., and Peerasak, S. (2009) Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata(L.) Wilczek). BMC Plant Biology 9: 137, doi: 10.1186/1471-2229-9-137.
25. Tang, B. J., Liu, B. Z., Wang, G. D., Zhang, T., and Xiang, J. H. (2005) Effects of various algal diets and starvation on larval growth and survival of Meretrix meretrix. Aquaculture 254, 526-533.
26. Tanguy, A., Bierne, N., Saavedra, C., Pina, B., Bachère, E., Kube, M., Bazin, E., Bonhomme, F., Boudry, P., and Boulo, V., et al. (2008) Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution. Gene 408, 27-36.
27. Temnykh, S., Park, W. D., Ayres, N., Cartinhour, S., Hauck, N., Lipovich, L., Cho, Y. G., Ishii, T., and McCouch, S. R. (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics 100, 697-712.
28. Toth, G., Gaspari, Z., and Jurka, J. (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research 10, 967-981.
29. Toutenhoofd, S. L., Garcia, F., Zacharias, D. A., Wilson, R. A., and Strehler, E. E. (1998) Minimum CAG repeat in the human calmodulin-1 gene 5'untranslated region is required for full expression. Biochimica et Biophysica Acta-Gene Structure and Expression 1398, 315-320.
30. Varshney, R. K., Thiel, T., Stein, N., Langridge, P., and Graner, A. (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cellular & Molecular Biology Letters 7, 537-546.
31. Wang, H., Chai, X., and Liu, B. (2011) Estimation of genetic parameters for growth traits in cultured clam Meretrix meretrix (Bivalvia: Veneridae) using the Bayesian method based on Gibbs sampling. Aquaculture Research 42, 240-247.
32. Wang, Z., Weber, J. L., Zhong, G., and Tanksley, S. D. (1994) Survey of plant short tandem repeats. Theoretical and Applied Genetics 88, 1-6.
33. Weber, J. L. (1990) Informativeness of human (dC-dA) n(dG-dT)n polymorphisms. Genomics 7, 524-530.
34. Whan, V. A., Wilson, K. J., and Moore, S. S. (2000) Two polymorphic microsatellite markers from novel Penaeus monodon ESTs. Animal Genetics 31, 143-144.
35. Zeng, S., Xiao, G., Guo, J., Fei, Z., Xu, Y., Roe, B. A., and Wang, Y. (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC genomics 11: 94, doi:10.1186/1471-2164-11-94.