Expressed sequence tag

Development and validation of single nucleotide polymorphism markers in Odontobutis potamophila from transcriptomic sequencing

H. W. Zhang, Yin, S. W., Zhang, L. J., Hou, X. Y., Wang, Y. Y., and Zhang, G. S., Development and validation of single nucleotide polymorphism markers in Odontobutis potamophila from transcriptomic sequencing, vol. 14, pp. 2080-2085, 2015.

Transcriptome sequencing technology has been applied in the development and discovery of single nucleotide polymorphism (SNP) markers in fish. In this study, a panel of 120 expressed sequence tag (EST)-derived SNPs was selected by several selection filters from the resultant EST library of Odontobutis potamophila using Illumina Sequencing. In total, 37 SNPs from 120 putative SNPs were considered as the true SNPs using Sanger sequencing. For each SNP locus of 30 individuals of one wild population of O.

Isolation and characterization of novel EST-SSRs in the showy dendrobium, Dendrobium nobile (Orchidaceae)

J. J. Lu, Kang, J. Y., Ye, S. R., and Wang, H. Z., Isolation and characterization of novel EST-SSRs in the showy dendrobium, Dendrobium nobile (Orchidaceae), vol. 13, pp. 986-991, 2014.

Expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers could enrich the current resource of molecular markers. In this study, microsatellite markers were developed for Dendrobium nobile Lindl. by mining the ESTs. Twenty-eight EST-SSRs amplified 2 to 6 nucleotide repeats with a mean number of 2.82 alleles per locus. The observed and expected heterozygosities per locus ranged from 0.158 to 0.579 and 0.422 to 0.752, respectively.

Development and characterization of single nucleotide polymorphism markers in Camellia sinensis (Theaceae)

C. C. Zhang, Wang, L. Y., Wei, K., and Cheng, H., Development and characterization of single nucleotide polymorphism markers in Camellia sinensis (Theaceae), vol. 13, pp. 5822-5831, 2014.

Tea is the second most popular non-alcoholic beverage in the world. In recent years, several molecular markers have been used in genetic studies of the tea plant. Yet, only a few single nucleotide polymorphisms (SNPs) have been reported. Here, we identified 818 putative SNPs from expressed sequence tag (EST) databases for the tea plant, which produced a frequency of 1 SNP/170 bp. A direct sequencing method was then used to verify 253 putative SNPs in genome DNA of 17 tea varieties. Fifty (20%) candidate and 299 new SNPs were identified.

CoffeebEST: an integrated resource for Coffea spp expressed sequence tags

A. R. Paschoal, Fernandes, E. D. M., Silva, J. C., Lopes, F. M., Pereira, L. F. P., and Domingues, D. S., CoffeebEST: an integrated resource for Coffea spp expressed sequence tags, vol. 13, pp. 10913-10920, 2014.

Coffee is one of the most important commodities in the world, and its production relies mainly on two species, Coffea arabica and Coffea canephora. Although there are diverse transcriptome datasets available for coffee trees, few research groups have exploited the potential knowledge contained in these data, especially with respect to fruit and seed development.

Mining SNPs from EST sequences using filters and ensemble classifiers

J. Wang, Zou, Q., and Guo, M. Z., Mining SNPs from EST sequences using filters and ensemble classifiers, vol. 9, pp. 820-834, 2010.

Abundant single nucleotide polymorphisms (SNPs) provide the most complete information for genome-wide association studies. However, due to the bottleneck of manual discovery of putative SNPs and the inaccessibility of the original sequencing reads, it is essential to develop a more efficient and accurate computational method for automated SNP detection. We propose a novel computational method to rapidly find true SNPs in public-available EST (expressed sequence tag) databases; this method is implemented as SNPDigger. EST sequences are clustered and aligned.

Understanding bamboo flowering based on large-scale analysis of expressed sequence tags

X. C. Lin, Chow, T. Y., Chen, H. H., Liu, C. C., Chou, S. J., Huang, B. L., Kuo, C. I., Wen, C. K., Huang, L. C., and Fang, W., Understanding bamboo flowering based on large-scale analysis of expressed sequence tags, vol. 9, pp. 1085-1093, 2010.

Unlike other plants, bamboo (Bambusoideae) flowering is an elusive physiological phenomena, because it is unpredictable, long-periodic, gregarious, and uncontrollable; also, bamboo plants usually die after flowering. The flowering mechanism in Arabidopsis thaliana, a eudicot model species, is well established, but it remains unknown in bamboo species. We found 4470 and 3878 expressed sequence tags in the flower bud and vegetative shoot cDNA libraries, respectively, of the bamboo species, Bambusa oldhamii.

Generation of a preliminary bovine gene atlas, using expression clustering to annotate gene function

O. M. Keane, Maqbool, N., McCulloch, A. F., McEwan, J. C., and Dodds, K. G., Generation of a preliminary bovine gene atlas, using expression clustering to annotate gene function, vol. 8, pp. 1013-1027, 2009.

Genes whose products function in a common biological process are often co-regulated. When regulation occurs at the transcriptional level, co-expressed genes can be detected globally by expression arrays or by sequencing non-normalized cDNA libraries. We examined bovine gene expression in 27 tissues using non-normalized cDNA library sequencing. Contigs were generated from expressed sequence tags whose sequences overlapped.

Paracoccidioides brasiliensis RNA biogenesis apparatus revealed by functional genome analysis

P. Albuquerque, Baptista, A. J., Derengowsky, Lda Silveir, Procópio, L., Nicola, A. Moraes, Arraes, F. B. M., de Souza, D. Paulo, Kyaw, C. Maria, and Silva-Pereira, I., Paracoccidioides brasiliensis RNA biogenesis apparatus revealed by functional genome analysis, vol. 4, pp. 251-272, 2005.

The RNA biogenesis machinery of Paracoccidioides brasiliensis was assessed by comparative analyses of PbAESTs (P. brasiliensis assembled expressed sequence tags (ESTs)) with sequences from Saccharomyces cerevisiae MIPS database. PbAESTs related to almost all categories of S. cerevisiae RNA biogenesis were found. Two of the 12 S.

Analysis of slipped sequences in EST projects

C. Baudet and Dias, Z., Analysis of slipped sequences in EST projects, vol. 5, pp. 169-181, 2006.

Slippage is an important sequencing problem that can occur in EST projects. However, very few studies have addressed this. We propose three new methods to detect slippage artifacts: arithmetic mean method, geometric mean method, and echo coverage method. Each method is simple and has two different strategies for processing sequences: suffix and subsequence. Using the 291,689 EST sequences produced in the SUCEST project, we performed comparative tests between our proposed methods and the SUCEST method.

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