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.
Expressed sequence tag
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.
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.
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.
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.
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.
The technology of mRNA-based differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR) was used to detect a 246-bp differentially expressed fragment from the nematophagous fungus Arthrobotrys oviformis when young mycelia were induced with the round worm Haemonchus contortus. The fragment was converted into an expressed sequence tag (EST) through characterization at the molecular level.
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.
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.
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.