MBE Advance Access published online on April 29, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm083
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Research Article |
Novel SINE Families from Salmons Validate Parahucho (Salmonidae) as a Distinct Genus and Evidence that SINEs Can Incorporate LINE-related 3'-Tails of Other SINEs
Tokyo Institute of Technology, Yokohama, Japan
* Faculty of Bioscience and Biotechnology, Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Kanagawa-ken, Japan
Correspondence to N. Okada: Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan, Tel.: +81 45 924 5742, Fax: +81 45 924 5835, E-mail: nokada{at}bio.titech.ac.jp
Received for publication February 9, 2007. Revision received April 11, 2007. Revision received April 17, 2007. Accepted for publication April 18, 2007.
Short interspersed elements (SINEs) constitute a group of retroposons propagating in the genome via mechanism of reverse transcription, in which they depend on the enzymatic machinery of long retroposons (LINEs). Over 70 SINE families have been described to date from the genomes of various eukaryotes. Here, we characterize two novel SINEs from salmons (Actinopterygii: Salmonoidei). The first family, termed SlmI, was shown to be widespread among all genera of the suborder. These SINEs have a tRNALeu-related promoter region at their 5'-end, a unique central conserved domain with subfamily-specific region and end with RSg-1-LINE-derived 3'-terminus preceding the A/T-rich tail. The same LINE-related segment is also shared by two other salmonid SINEs: HpaI and OS-SINE1. The structural peculiarities and overall sequence identity of SlmI 3'-terminus suggest that it has been acquired from HpaI SINEs, but not directly from the partner LINE. This region plays a crucial role in the process of retrotransposition of short interspersed elements, and the case of its SINE-to-SINE transmission is the first recorded to date. Possible scenarios and potential evolutionary implications of the observed interaction between short retroposons are discussed. Apart from the above, we found a copy of SlmI SINE in the GenBank entry for blood fluke, Schistosoma japonicum (Trematoda: Strigeiformes) – a trematode causing one of the most important human helminth infections, with its genome known to host other groups of salmonid retroposons. In the present paper, we suggest our views in regards to possible ways of such intensive horizontal transfer of salmonid retroposons to schistosomal genome. The second novel SINE family, termed SlmII, originates from one of SlmI subfamilies, with which it shares the same tRNA-related region, central domain and a part of RSg-1-derived segment, but has a different 3'-tail of unidentified origin. Its distribution among salmonids validates Parahucho (Japanese huchen) as a distinct monotypic genus.
Key Words: Slm SINEs • Parahucho perryi • salmon • 3'-tail • horizontal transfer • Schistosoma