Computational prediction of amphioxus microRNA genes and their targets

Using a homology search based on genomic survey sequence analysis and microRNA (miRNA) secondary structure, a total of 51 miRNA genes encoding 30 amphioxus miRNAs were identified. These amphioxus miRNAs belong to 27 miRNA families. Many miRNA genes were found in multiple locations and in more than one genomic context. Analysis of amphioxus miRNA genes revealed nearly 50% miRNA genes identified positioning within introns of protein-coding genes. MicroRNA genes were also positioned intergenically between known protein-coding genes. MicroRNA genes were also clustered throughout the genome, indicating the potential for the cotranscription and coordinate expression of miRNAs located in a given cluster. Cross-species comparison indicates that of the 27 miRNA families, 17 families are shared by both protostomia and deuterostomia, and 2, 3 and 5 families are protostome-specific, deuterostome invertebrate-specific and chordate-specific, respectively. Computational predictions of amphioxus miRNA targets, taking into account the relationship between miRNA target genes and their host genes/neighboring genes, show that 49 target sites for 34 potential target genes were complementary to 19 miRNAs. For the intronic miRNA genes co-expressed with the host gene, they may not be involved in the regulation of the host gene expression. However, some intergenic miRNAs could participate in the modulation of their neighboring gene expression.