Transcriptome-wide Comparative Analyses Based On Amphioxus(Branchiostoma Floridae) ESTs And Its EST Database

The cephalochordate amphioxus has been widely regarded as an important model organism which is the clostest living invertebrate relative to the vertebrates.However, some recent studies demonstrated that urochordate sea squirt is the sister group of vertebrates instead of cephalochordates.In order to further elucidate the relationship in cephalochordates,urochordates and vertebrates and therefore,it is very essential for carting through transcriptome-wide analysis of amphioxus(Branchiostoma floridae)and comparating with sea Urchin and sea squirt.In addition,it would also provide an important foundation for further annotating and assembling of the forthcomingly publicized amphioxus genome.In this paper,using bioinformatical tools,amphioxus ESTs of five differential developmental stages were clustered,assembled,gene annotion,gene function classification,microRNA target prediction and comparative analysis etc.We used gene expression profile and GO functional expression profile which were derived from the result of amphioxus EST analysis to do the Transcriptome-wide Analysis of Amphioxus and Comparison with Sea Urchin and Ciona intestinalis.Amphioxus EST database have been built based on all the above result data by using Apache,php,MySQL under the windows operation system.The result shows as follows:1.The 277539 amphioxus ESTs were clustered to 15778 clusters,ssembled to roughly 19875 contigs and 18414 singlets,of which approximately 81.9%have a high confidence match to UniProt.Approximately206 dismatched the nucleic acid database,they were predicted to be new gene or the gene with unknown function.2.Using the result by blastx,an inferred putative GO annotion was found for 48%of unique sequence set.24%of sequences were categorized to the cellular components,39% of the sequences were assigned molecular function annotation.In the biological process, 37%of the sequences were correlated to a GO term.3.There wre 1736304 microRNA targets in the 3' UTR region.The types of these target from different developmental stages were nearly the same,approximately 2625 kinds,902 microRNA families.The numbers of predicted targets and the initial EST counts of different transcriptomes revealed positive correlation.However,several targets were identified that displayed significant differences of appearenced frequency and types between larval stage and others. 4.In the five diffent developmental stages,the expression number of neurula is the highest, but the least could be annotationed.The EST composing density per contig was growing large according to developmental order.5.In the five diffent developmental stages,the stage-specific expression level of C,F,P was more than the persistent expression separately.The expression correlate with molecular function and biological process had distinct differences between specific expression and persistent expression.6.The larva-specific expression level of the function correlated to celluar components was the highest.The highest specific expression level of molecular function was appeared at neurula stage.A lot of functional specific expression about biological process was also appeared at neurula stage.7.The result showed that the pearson correlation coefficient was 0.896 compared between the sea urchin and Ciona savignyi.The pearson correlation coefficient was 0.682 of the comparision between the sea urchin and amphioxus.So it have added significant weight to the argument of the developmental position of amphioxus,which was the clostest invertebrate relative to the vertebrates.8.The EST database of amphioxus was addressed at http: //amphioxus.lnnu.edu.cn/homepage.php.