Dynamic evolution of tRNAThr-derivedHpaI SINEs and effect on genomes ofOncorhynchus species

Abstract

Short interspersed nuclear elements (SINEs) are the most abundant non-autonomous retroelements in many vertebrate genomes. The events that led to their integration may have had marked effects on the evolution of host genomes. One well-investigated SINE lineage is in the pacific salmon (genusOncorhynchus). Experimental approaches and bioinformatics have been used to investigate the dynamic features and evolutionary impact of these SINEs. Four gene-relatedHpaI SINEs in theCD4L-2a, NOS, MHC andIL1B genes were identified by bioinformatics tool. To investigate these SINEs, PCR amplification and sequencing were performed on eight species of the genusOncorhynchus and one ofSalmo. Unexpectedly, theCD4L-2a, MHC andIL-1B gene loci proved to be dimorphic for theHpaI SINE insertion; this may be attributable to lineage sorting. Sequence transduction and horizontal transmission events also occurred inCD4L-2a. To elucidate the impact ofHpaI SINEs on pacific salmon genomes and the diversity of transcriptomes, 243,668 mRNA sequences from the GenBank database were analyzed. A total of 163 mRNA sequences were identified as fused withHpaI SINEs. Among these, 87 ESTs were annotated into 41 functional genes. Our data suggest that SINEs could contribute to the genomic diversity of the pacific salmon by exonization and could move more dynamically within this genome by lineage sorting, sequence transduction and horizontal transmission.