Mao Yunxiang

Bioinformatic analysis of expressed sequence tags from sporophyte of Porphyra yezoensis (Bagiaceae, Rhodophyta)∗

Abstract A total of 719 expressed sequence tags (EST) clustered into 329 non - redundant EST groups are obtained from the sporophte cDNA library of red alage, Porphyra yezoensis. Gene Ontology (GO) analysis is employed in characterizing 60 strictest annotatd unique genes out of the 329 EST groups and some domains such as COXI, Sod_Fe_C, GST_N, SHMT, and RNase_PH related to the enzymes and proteins functioning in cells have been identified by HMMPFAM search. As its leafy gametophyte, the similar codon usage with storong bias is found in P. yezoensis filamentous sporophyte, regardless of some differences found in given amino acids. The average GC content of the 329 unique genes is 53.0 %. In contrast, the third nucleotide of codon exhibits a higher GC content (72 %) than that of the first (58 % ) and the second (42 %) nucleotides. Similarity search of the present study shows a noves EST ratio of 60.2 % Which is against the Porphyra ESTs database, suggesting further investigations towards elucidating the cha...

Identification of phase and sex-related ISSR markers of red algaGracilaria lemaneiformis

Six ISSR primers are employed to display the polymorphism of different phases and sexes of red algaGracilaria lemaneiformis, and two of them, P1 and P3, amplified distinct band patterns. The ISSR pattern amplified by primer P1 of the female gametophyte is identical to that of tetrasporophyte, but distinct from that of male gametophyte. Of the bands produced by primer P3, one is specific to female gametophyte. Three morphologically similar fronds can be easily identified using ISSR technique. Two specific markers, SM1 and SF3, related to male gametophyte and female gametophyte, are cloned and sequenced. The homologous sequences of SM1 are found to encode a hypothetical protein. There is no homologous sequence of SF3 that can be found in GenBank.

In Silico Screening for Microsatellite Markers from Expressed Sequence Tags of Porphyra yezoensis （Bangiales,Rhodophyta）

The genomic resources of Porphyra yezoensis expressed sequence tags (ESTs) were utilized to identify simple sequence repeats (SSRs), or microsatellites. This method took the advantage of using ESTs and microsatellites either for the establishment of gene identities or for the acquisition of high polymorphism. The microsatellites can be used as gene markers when microsatellites are tagged to genes. Revealed by bioinformatics analysis, 1162 out of 21 954 ESTs contained microsatellites and cluster analysis indicated that 984 of these ESTs fell into 112 contigs, while the other 178 ESTs were singletons. A total of 290 unique SSR-containing genes were identified. The AAC SSRs were the most populous type of microsatellites. GC-rich microsatellites were predominant among all the microsatellites.

Construction and characterization of a fosmid library for pathogenic bacterium Vibrio anguillarum

Vibrio anguillarum is a common bacterial pathogen in fish. However, little is known about its pathogenic mechanism, in part, because the entire genome has not been completely sequenced. We constructed a fosmid library for V. anguillarum containing 960 clones with an average insert size of 37.7 kb and 8.6-fold genome coverage. We characterized the library by end-sequencing 50 randomly selected clones. This generated 93 sequences with a total length of 57 485 bp covering 1.4% of the whole genome. Of these sequences, 58 (62.4%) were homologous to known genes, 30 (32.3%) were genes with hypothetical functions, and the remaining 5 (5.3%) were unknown genes. We demonstrated the utility of this library by PCR screening of 10 genes. This resulted in an average of 6.2 fosmid clones per screening. This fosmid library offers a new tool for gene screening and cloning of V. anguillarum, and for comparative genomic studies among Vibrio species.