Transcriptome Assembly, Annotation And Development Of Molecular Marks Of Tedania Sp. And Mycale Phyllophila

As the most primitive multicellular organism, sponge (Phylum:Porifera) has been on the earth for at least600million years and has been playing an important role in the ecosystem ever since its emergence. In the past a few decades, sponge has been extensively studied as an important resource for biologically active products. Besides, the characteristics and biomineralization mechanisms of sponge spicules are also an active research area. Being generally recognized as the oldest surviving metazoan phyletic lineage, sponges have a critical role in the search for the origins of metazaoan multicellular process. Despite the high value of sponge utility, the basic research on sponge is still a weak point.With the rapid growth of sequencing technology, transcriptomics has been applied to many research projects as a powerful tool. There are two transcriptome studies about sponge available at present. These two studies focused on the genes which are closely related to the life cycle of sponge. Transcriptome can be used not only to discover genes that are responsible for particular physiological status, but also to develope new genetic markers. Single Nucleotide polymorphisms (SNP), a third-generation molecular markers, are single base pair positions in genomic DNA at which different sequence alternatives (alleles) exist in normal individuals in some population(s). Analysing the ratio of non-synonymous (amino acid changing) substitutions per non-synonymous site to synonymous (silent) substitutions per synonymous site caused by SNP helps to understand the evolution of genes with different functions.This study aimed at determining the landscape of nucleotide polymorphism across the transcriptomes of Tedania sp. and Mycale phyllophila to provide a broad view of their distributions across the spectrum of GO terms and to pick up genes which were under the positive selection. The transcritpomes of Tedania sp. and M. phyllophila were first assembled after being sequenced by Illumina Hiseq2000. The assemblies were then annotated by the SwissProt database and protein database of Amphimedon queenslandica whose genome is currently available. GO annotation were performed for transcriptomes of Tedania sp., M. phyllophila, A. queenslandica and Crella elegans. Comparison of GO annotation among these transcrtiptomes revealed a similar transcriptome organization in terms of GO terms and their relative frequencies.36ortholgs were determined from the four sponge transcriptomes which could be classified into8categories. These orthologous genes could be further developed into new genetic markers which can be applied to the study of evolutionary relationship across Deospongiae. SNP abundance and SNP A/S were calculated for the transcriptome of Tedania sp. and M. phyllophila. In order to evaluate the nature selection from different environment on sponges, we also analysed the SNP for the transcriptome of C. elegans which lives in the western Mediterranean. Among these three sponges, the SNP abundance of M. phyllophila was the largest and that of C. elegans was the smallest, indicating that the population of M. phyllophila was the largest or that its speciation time has been the longest. The average SNP A/S of C. elegans was larger than that of Tedania sp. and M. phyllophila, suggesting that C. elegans suffered less negative selection than Tedania sp. and M. phyllophila. The averages SNP A/S of Tedania sp. and M. phyllophila were similar. This may be due to the fact that they live in the same area and suffer a similar natural selection. Among genes with SNP A/S>1, sequences involved in immunity were identified for all three sponges, indicating a positive selection on these genes.8genes originated from virus were also identified for Tedania sp. among genes whose SNP A/S was larger than1. About one third of the sequences under positive selection for the three sponges were related to multicellular process. This was the first time for sponges to compare on transcriptome level and the first analysis of sponge SNP on such a large scale, revealing the evolutionary history of sponge genes with different functions. This will certainly provide a solid foundation for the future study on gene evolutionary rate of sponges.