Transposable processes (Abrusan and Krambeck 2006). TEs occupy large

Transposable elements (TEs) are mobile
genetic elements that have the ability to propagate themselves within the
genome, causing deleterious, neutral and sometimes advantageous effect to the
host genome due to the genomic instability caused by the increased in TE numbers
(Cordaux and
Batzer 2009). TEs exhibit a broad range of transpositions
mechanisms, and are subdivided into two main classes, according to their major
transposition strategy, including subclasses that show transposition
intermediates.  Class I TEs are the
retrotransposons or “copy and paste” elements, which are characterized by
utilizing an RNA intermediate to insert themselves into new locations in the genome,
LINEs and SINEs and examples of retrotransposons. Class II are the DNA transposons
or “cut and paste” elements, these utilize a transposase enzyme to recognize TEs
and excise and reinserted themselves in different genomic locations. Example of
class II elements includes hAT, piggyBac and TcMariner (Wicker, Sabot
et al. 2007)

TEs have been considered as one of the
factors that underline evolutionary processes (Abrusan and
Krambeck 2006). TEs occupy large portions of the eukaryotic
genome (Sundaram,
Cheng et al. 2014), constitute over half of the DNA in many
higher eukaryotes (Fedoroff 2012) and they influence their host’s evolution in
different ways, including but not limited to gene function alteration via
insertion, chromosomal rearrangements and insertion of genetic material that
allows the emergence of genetic novelty (new genes and regulatory sequences)(Feschotte and
Pritham 2007). TEs have been associated with genome
expansion and genome evolution (SanMiguel,
Gaut et al. 1998), therefor they account for a large fraction
of the genomes in most vertebrates, such as elephants (57.6% of the genome are
TE derived sequences) Opossum (56.5%) and zebrafish (52.6 %), it has been
hypothesis that the C-value enigma, the lack correspondence between genome size
and morphological and physiological complexity of an organism, may be explained
by the differential amplification and proliferation of TEs in different genomes
(Hawkins, Kim
et al. 2006, Freeling, Xu et al. 2015). Therefore, a proper understanding of
accumulation patterns is needed. Overall a general increase in genome size has
been identified in the evolution of vertebrate genomes, suggesting that TEs
accumulation increases linearly in amount with total genome size. (Hancock 2002, Vieira, Nardon et
al. 2002, Chalopin, Fan
et al. 2014)

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Fishes
are the most diverse group of living vertebrates (Amores, Force et al. 1998); Cartilaginous fishes represent the
most basal group of jawed vertebrates (gnathostomes) that are composed of two
groups, 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 position
cartilaginous fishes are considered critical tool for the better understanding of
vertebrate evolution. The Australian ghostshark (Callorhinchus milii), a holocephalian cartilaginous fish, was
sequenced in 2007 (Venkatesh, Kirkness et al. 2007) and whole genome analysis of said
genome yield that the C.milii protein
coding-genes have evolved slower when compared to other vertebrates, including
coelacanth (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.

Due
to both the significant impact that TEs have in genome evolution and the large
portion of TEs in genomes, comprehensive annotation of TEs in newly sequenced
genomes is imperative. The majority of genome projects identify and annotate
TEs utilizing homology methods (Hoen, Hickey et al. 2015), but the most accurate assessment of
TE landscape is by using a combination of homology based repeat identification
in conjunction with an additional manual curation step (Permal, Flutre et al. 2012). Previous studies have attempted to
annotate the TE accumulation in the Australian Ghostshark (Venkatesh,
Kirkness et al. 2007, Chalopin, Naville et al. 2015) however, it is our believe that they have
wrongly estimate the amount of TE accumulated in the C.milii genome. To obtain an accurate history of the transposable
element accumulation in the Australian Ghostshark genome we both investigated
the general accumulation of TEs and the patters of insertion of SINE2. SINE
insertions may impact the genome by inducing structural variations and modify
genomic variations. We also examine all vertebrate genomes available, that have
TE annotations and analyzed the contribution of transposable elements to their
genome size.