Comprehensive Analysis of Salmon DNA Transposons

The starting point for this in silico analysis were the sequences for the two known salmon DNA transposons SALT1 [Genbank:L22865] [19 (link)] and Tss [Genbank:L12207] [18 (link)], as well as an analysis of the sequence of the T-cell receptor alpha locus of Salmo salar by RepeatMasker [46 ]. These two transposons as well as the RepeatMasker data were used to find faint similarities which were used in turn to find a larger number of each family in approximately 3 Mbp of sequence. The Dotter program [47 (link)] was used extensively to find regions of similar sequence, which were extracted and stored in an SQL database. The length of the transposon sequences was determined by identifying the inverted terminal repeat sequences where possible. Sequence alignments were performed with ClustalW [48 (link)] and phylogenetic trees generated with MEGA3.1 [49 (link)] using the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), pairwise deletion, and a p-distance model. The entire alignment of the sequences was used in the phylogenetic reconstruction. Our salmon EST database was searched for the presence of sequences that are similar to the DNA transposon sequences that we found in salmon.
The following DNA sequences and BAC clones were used in this analysis. The Salmo salar TCRα locus [30 (link)], the major histocompatibility loci MHC class 1a and 1b [29 ], the growth hormone and interleukin loci (manuscripts in preparation), and zoneadhesin-like genes [Genbank:AY785950] and the Oncorhynchus mykiss sequences for the metallothionein gene [GENBANK:DQ156151], MHC1a [Genbank:AB162342] and MHC1b loci [Genbank:AB162343], and the IgH.A locus [Genbank:AY872256]. Genbank sequence entries were used in this study from a variety of other organisms (table 2): Oncorhynchus mykiss, Ictalurus punctatus, Esox lucius, Cyprinus carpio, Salvelinus namaycush, Salvelinus confluentus, Salvelinus fontinalis, Tanichthys albonus, Carassius auratus, Astatotilapia burtoni, Oryzias latipes, Petromyzon marinus, Danio rerio, Xenopus tropicalis, Xenopus laevis, Rana pipens, and Polypterus bichir. Sequences from Schistosoma japonicum EST Genbank data were found for transposon families as follows: DTSsa1 [Genbank:AY915112, AY809993], DTSsa2 [Genbank:AY816058, AY834394], DTSsa3 [Genbank:AY124772], DTSsa4 [Genbank:AY812589, AY915240], DTSsa5 [Genbank:AY813498], DTSsa6 [Genbank:AY813020], DTSsa7 [Genbank:AY813225, AY915121], SSTN1 [Genbank:AY809988, AY815476, AY915835], Tss [Genbank:AY915400, AY915891], and SALT1 [Genbank:AY223470, AY915102].
Representative sequences from all new families have been deposited in GenBank under accession numbers EF685954 – EF685960, EF685962 – EF685963, and EF685966 – EF685967.