Transposable elements (TEs) are mobilegenetic elements that have the ability to propagate themselves within thegenome, causing deleterious, neutral and sometimes advantageous effect to thehost genome due to the genomic instability caused by the increased in TE numbers(Cordaux andBatzer 2009).
TEs exhibit a broad range of transpositionsmechanisms, and are subdivided into two main classes, according to their majortransposition strategy, including subclasses that show transpositionintermediates. Class I TEs are theretrotransposons or “copy and paste” elements, which are characterized byutilizing an RNA intermediate to insert themselves into new locations in the genome,LINEs and SINEs and examples of retrotransposons. Class II are the DNA transposonsor “cut and paste” elements, these utilize a transposase enzyme to recognize TEsand excise and reinserted themselves in different genomic locations. Example ofclass II elements includes hAT, piggyBac and TcMariner (Wicker, Sabotet al.
2007)TEs have been considered as one of thefactors that underline evolutionary processes (Abrusan andKrambeck 2006). TEs occupy large portions of the eukaryoticgenome (Sundaram,Cheng et al. 2014), constitute over half of the DNA in manyhigher eukaryotes (Fedoroff 2012) and they influence their host’s evolution indifferent ways, including but not limited to gene function alteration viainsertion, chromosomal rearrangements and insertion of genetic material thatallows the emergence of genetic novelty (new genes and regulatory sequences)(Feschotte andPritham 2007). TEs have been associated with genomeexpansion and genome evolution (SanMiguel,Gaut et al. 1998), therefor they account for a large fractionof the genomes in most vertebrates, such as elephants (57.6% of the genome areTE derived sequences) Opossum (56.5%) and zebrafish (52.
6 %), it has beenhypothesis that the C-value enigma, the lack correspondence between genome sizeand morphological and physiological complexity of an organism, may be explainedby the differential amplification and proliferation of TEs in different genomes(Hawkins, Kimet al. 2006, Freeling, Xu et al. 2015). Therefore, a proper understanding ofaccumulation patterns is needed. Overall a general increase in genome size hasbeen identified in the evolution of vertebrate genomes, suggesting that TEsaccumulation increases linearly in amount with total genome size. (Hancock 2002, Vieira, Nardon etal. 2002, Chalopin, Fanet al. 2014)Fishesare the most diverse group of living vertebrates (Amores, Force et al.
1998); Cartilaginous fishes represent themost basal group of jawed vertebrates (gnathostomes) that are composed of twogroups, the elasmobranchs (sharks, rays and skates) and the holocephalians(chimera). These two groups diverged approximately 374 million years ago (Ravi, Lam et al. 2009). Due to their phylogenetic positioncartilaginous fishes are considered critical tool for the better understanding ofvertebrate evolution. The Australian ghostshark (Callorhinchus milii), a holocephalian cartilaginous fish, wassequenced in 2007 (Venkatesh, Kirkness et al. 2007) and whole genome analysis of saidgenome yield that the C.
milii proteincoding-genes have evolved slower when compared to other vertebrates, includingcoelacanth (Venkatesh, Lee et al. 2014). The C.milii genome is one of the least derived among vertebrates,making it a good model for inferring the ancestral state of vertebrate genomes.Dueto both the significant impact that TEs have in genome evolution and the largeportion of TEs in genomes, comprehensive annotation of TEs in newly sequencedgenomes is imperative.
The majority of genome projects identify and annotateTEs utilizing homology methods (Hoen, Hickey et al. 2015), but the most accurate assessment ofTE landscape is by using a combination of homology based repeat identificationin conjunction with an additional manual curation step (Permal, Flutre et al. 2012). Previous studies have attempted toannotate the TE accumulation in the Australian Ghostshark (Venkatesh,Kirkness et al.
2007, Chalopin, Naville et al. 2015) however, it is our believe that they havewrongly estimate the amount of TE accumulated in the C.milii genome. To obtain an accurate history of the transposableelement accumulation in the Australian Ghostshark genome we both investigatedthe general accumulation of TEs and the patters of insertion of SINE2. SINEinsertions may impact the genome by inducing structural variations and modifygenomic variations.
We also examine all vertebrate genomes available, that haveTE annotations and analyzed the contribution of transposable elements to theirgenome size.