Depending upon whether they contain long terminal repeats (LTRs), retrotransposons are classified into LTR elements (human endogenous retroviruses, HERVs), non-LTR elements (long interspersed elements, LINE-1 or L1 elements), and short interspersed elements (SVA and Alu elements).
Among the retro-TEs, Copia-like and Gypsy-like long terminal repeat (LTR) elements are abundant in angiosperms, whereas Long Interspersed Elements (LINEs) and Short Interspersed Elements (SINEs), that are prominent in mammalian genomes, are less common.
Over more than one hundred and sixty million years, mammals have accumulated elements from four major classes of transposons, Long INterspersed Elements (LINEs), Short INterspersed Elements (SINEs), retrovirus-like Long Terminal Repeats (LTRs), and DNA transposons [ 4].
Alu elements are short (~300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition.
Repetitive elements, such as LINEs (Long interspersed elements), SINEs (Short interspersed nuclear elements) and LTRs (Long terminal repeats), can lead to erroneous assembly of sequences.
Concerning the activity of LINEs, the second most represented interspersed elements, the InterProScan analysis identified amino acidic domains linked to these autonomous retrotransposons.
The complex repeats include DNA elements as well as very few LINEs (Long Interspersed Elements), SINEs (Short Interspersed Elements) and LTR (Long Terminal Repeat) elements.
The data analyses show that, relative to other ruminantian species, the lesser kudu genome has seen an expansion of BovB Long INterspersed Elements (LINEs) and BovB related Short INterspersed Elements (SINEs) like BOVA2.
Compared to sole sequence data, mobile elements such as Short Interspersed Elements (SINEs) and Long Interspersed Elements (LINEs) exhibit advantages which make them ideal markers for phylogenetic reconstructions (for review see [ 24- 30]).
This step eliminated transcripts with large (large) introns but kept retroelements, such as Long Interspersed Elements (LINEs) (∼6 kb) and Short Interspersed Elements (SINEs) (<1 kb), that are frequently inserted inside retrocopied loci.
Long Interspersed Elements (L1 elements) are biologically active retrotransposons that are capable of autonomous replication using their own reverse transcriptase (RT) enzyme.
