Genome research profile of two Cordyceps sinensis cDNA libraries

Cordyceps sinensis (CS) is well known as an ancient Chinese herb. It is used to expand bronchial smooth muscles, inhibit tumor growth and decrease blood pressure. Cordyceps sinensis is composed of two parts. One is the dead larvae body; the other is the stroma like withered grass. Up to now, few genome database articles about Cordyceps sinensis have been reported. In this study, two cDNA libraries were constructed using the worm part and grass part respectively for the first time. 12192 and 15456 clones from the worm-part (CSCA) and grass-part (CSBA) library were respectively picked. Sequences derived from CSCA were clustered into 1333 contigs and 2469 singlets, while those from CSBA were clustered into 1297 contigs and 2875 singlets. These ESTs include sequences representing a significant portion of proteins encoding genes in cell signalling, metabolism, information storage and processing. Some enzymes encoding genes were also found and linked with CS’s physiology such as proteases, peptidases, lipases and chitinase. Pairwise comparison between the two cDNA libraries was also studied. Some ESTs were found only in CSCA and some only in CSBA. Finally, a comparative genomics research was performed with Fusarium graminearum, Aspergillus nidulans, Neurospora crassa and Saccharomyces bayanus. The results indicate that the fungus’ genes maybe have complicated variation at the nucleic acid level, but the proteins translated are still conservative.

Severe acute respiratory syndrome-associated coronavirus genotype and its characterization

Objective To study the severe acute respiratory syndrome (SARS) -associated coronavirus genotype and its characteristics.Methods A SARS-associated coronavirus isolate named ZJ01 was obtained from throat swab samples taken from a patient in Hangzhou, Zhejing province. The complete genome sequence of ZJ01 consisted of 29 715 bp (GenBank accession: AY297028, version; gi: 30910859). Seventeen SARS-associated coronavirus genome sequences in GenBank were compared to analyze the common sequence variations and the probability of co-occurrence of multiple polymorphisms or mutations. Phylogenetic analysis of those sequences was done.Results By bioinformatics processing and analysis, the 5 loci nucleotides at ZJ01 genome were found being T, T, G, T and T, respectively. Compared with other SARS-associated coronavirus genomes in the GenBank database, an A/G mutation was detected besides the other 4 mutation loci (C: G: C: C/T: T: T: T) involved in this genetic signature. Therefore a new definition was put forward according to the 5 mutation loci. SARS-associated coronavirus strains would be grouped into two genotypes (C: G: A: C: C/T: T: G: T: T), and abbreviated as SARS coronavirus C genotype and T genotype. On the basis of this new definition, the ZJ01 isolate belongs to SARS-associated coronavirus T genotype, first discovered and reported in China's Mainland. Phylogenetic analysis of the spike protein gene fragments of these SARS-associated coronavirus strains showed that the GZ01 isolate was phylogenetically distinct from other isolates, and compared with groups F1 and F2 of the T genotype, the isolates of BJ01 and CUHK-W1 were more closely related to the GZ01 isolate. It was interesting to find that two (A/G and C/T) of the five mutation loci occurred in the spike protein gene, which caused changes of Asp to Gly and Thr to He in the protein, respectively.Conclusion Attention should be paid to whether these genotype and mutation patterns are related to the virus' s biological activities, epidemic characteristics and host clinical symptoms.

Alternative Splicing and Expression Profile Analysis of Expressed Sequence Tags in Domestic Pig

Domestic pig （Sus scrofa domestica） is one of the most important mammals to humans. Alternative splicing is a cellular mechanism in eukaryotes that greatly increases the diversity of gene products. Expression sequence tags （ESTs） have been widely used for gene discovery, expression profile analysis, and alternative splicing detection. In this study, a total of 712,905 ESTs extracted from 101 different nonnormalized EST libraries of the domestic pig were analyzed. These EST libraries cover the nervous system, digestive system, immune system, and meat production related tissues from embryo, newborn, and adult pigs, making contributions to the analysis of alternative splicing variants as well as expression profiles in various stages of tissues. A modified approach was designed to cluster and assemble large EST datasets, aiming to detect alternative splicing together with EST abundance of each splicing variant. Much efforts were made to classify alternative splicing into different types and apply different filters to each type to get more reliable results. Finally, a total of 1,223 genes with average 2.8 splicing variants were detected among 16,540 unique genes. The overview of expression profiles would change when we take alternative splicing into account.