Dynamic Evolution of tRNA(Thr)-Derived HpaI SINEs and Effect on Genomes of Oncorhynchus 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 (genus Oncorhynchus). Experimental approaches and bioinformatics have been used to investigate the dynamic features and evolutionary impact of these SINEs. Four gene-related HpaI SINEs in the CD4L-2a, NOS, MHC and MB genes were identified by bioinformatics tool. To investigate these SINEs, PCR amplification and sequencing were performed on eight species of the genus Oncorhynchus and one of Salina Unexpectedly, the CD4L-2a, MHC and IL-1B gene loci proved to be dimorphic for the HpaI SINE insertion; this may be attributable to lineage sorting. Sequence transduction and horizontal transmission events also occurred in CD4L-2a. To elucidate the impact of HpaI 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 with HpaI 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.