ABSTRACT
DNA sequencing of randomly chosen clones from a cDNA library allows thousands of different transcripts to be identified. However, since the likelihood of observing a given transcript is proportional to the expression level of that transcript in the tissue from which the library is derived, often transcripts are represented by several EST sequences. An expressed sequence tags (EST) analysis was undertaken to identify the genes present in the leaves of Phyllanthus amarus, which is a small tropical, glabrous herb with several health benefits. Phyllanthin and hypophyllanthin, major bioactive components, present in highest amounts in the leaves, are of significant therapeutic importance like hepatoprotective, antioxidant, antiviral, hypoglycemic, etc. Taken together, sequencing of cDNA clones generated high-quality ESTs (Accession number: JK492908 to JK492964) with high similarities with genes from Ricinus communis, Onchocerca volvulus, Eucalyptus globules, Gossypium hirsutum, Nicotiana tabacum, Solanum spp. and many more. A BLASTN analysis along with BLASTX analysis of all the unique sequences was performed and was grouped according to the reported activities. Results represented here is the first reference collection of ESTs from this commercially important medicinal herb. This study indicated that the leaf transcriptome contains series of interesting sequences like ALBINO3, ribulose-1, 5 bisphosphate carboxylase/ oxygenase (RUBISCO), chloroplast photosystem II chlorophyll A/B-binding protein, stress-responsive proteins like methionine sulfoxide reductase type, etc.
ABSTRACT
OBJECTIVE: To investigate differential gene expression profiling of symbiotic germinated seeds of Dendrobium officinale. METHODS: cDNAs from 5-week symbiotic germinated seeds and 5-week aseptic cultivated seeds, taken as the tester and driver respectively, were used to construct a suppressive subtractive hybridization (SSH) cDNA library. RESULTS: By sequencing positive clones and BLASTx analysis against GenBank database, 100 expressed sequence tags (EST) homologous to plant known genes were obtained. Functional annotation revealed that they were grouped into serials of cellular processes including cell and chromosome structure, RNA synthesis, signal transduction, energy metabolism, protein synthesis and degradation, and cell defense, etc. Real-time quantitative RT-PCR analyses showed that the five randomly selected genes were all up-regulated in symbiotic germinated seeds. CONCLUSION: The symbiotic seed germination of D. officinale is involved in multiple pathways, and the results of this study will lay a foundation for further molecular elucidation of seed germination in Orchidaceae.
ABSTRACT
Objective To screen and identify the novel genes from the adult worm cDNA library of Schistosoma japonicum by the expressed sequence tags (EST) strategy.Methods The cDNA clones were selected randomly and the ESTs were obtained.The novel gene was searched for homologue identity with NCBI blast programmer.The homologue of the two sequences with a high identity was compared at amino acid and nucleotide level with the BLAST programmer,and the analysis of protein was carried out with the pcgene software. Results There was a novel gene of Schistosoma japonicum which included 1 677 bp coding for 424 amino acid residues, and it was given the accession number of sequence in Genbank(AY336497).The cDNA sequence was homologous to the known ornithine aminotransferase gene of Xenopus laevis. The identity of amino acid sequence was 66%. The academic pI was 8.52, and the antigen determinant was probably from 795 to 846 on the cDNA sequence. Conclusion EST strategy is an effective measure to discover new genes of Schistosoma japonicum. The novel gene is homologous to the ornithine aminotransferase gene of Xenopus laevis.This study is helpful to further sequential and functional search of the gene.[
ABSTRACT
Objective To construct a platform for in silico elongation and batch analysis of Schistosoma japonicum(Sj) ESTs, acquire the potential novel genes and research the expression profile of the genes. \ Methods\ On the basis of Linux operating system and local ESTs database of Sj, the BLAST and PHRAP softwares were used to construct a program to achieve the elongation of ESTs. Stand\|alone BLAST search against the nr database helped analyze the elongated sequence. After finishing the batch analysis script, the platform was used to research the Sj gene expression profile and acquire the potential novel genes. \ Results \ The platform showed satisfactory efficiency and fidelity. 487 elongated sequences obtained from 552 and 307 elongated sequences showed high homology within the nr database downloaded from NCBI. Furthermore, 104 elongated sequences displayed significant homology but showed no homology before elongated. 27 potential novel genes were filtered out. \ Conclusion \ An effective platform for Sj ESTs data mining was accomplished and further information on the potential novel genes was acquired.