Due to the relative scarcity of LTR elements, the number of regions with no LTR elements is approximately a magnitude higher than regions with no LINEs and SINEs regardless if 10 kbp or 20 kbp is used as a minimum size of regions (Figure 2).
Most of the reads mapped to unannotated regions 40-700%) probably due the scarcity of annotated elements for Anopheles gambiae.
The last worth mentioning feature that also contributed to small genome size (exclusively in Oikopleura) is the scarcity of transposable elements.
Scarcity of these elements that are essential in DNA synthesis favors the incorporation of an AT base-pair containing seven atoms of nitrogen, one less than a GC base-pair.
The opposite is true in the Late genes where late initiation of transcription (determined largely by loose promoter TFBS packing) is followed by slow termination (determined by scarcity of ARE elements in the 3′UTR).
This analysis demonstrated that large deletions occur much more often in stickleback than in humans and are sufficiently common to account for the extreme scarcity of ancient elements in the stickleback genome.
In addition, Oikopleura has undergone a severe process of genome reduction and compaction, a process that in part can be explained by the loss of some genes but in reality is largely due to other mechanisms such as shortening of intergenic distances, miniaturization of introns, and scarcity of mobile elements.
These species exhibit great genome plasticity and Oikopleura in particular has undergone a process of extreme genome reduction and compaction that can be explained in part by gene loss, but is mostly due to other mechanisms such as shortening of intergenic distances and introns, and scarcity of mobile elements.
The scarcity of FL elements in Anolis is similar to what was found in a study of teleost fish genomes that included zebrafish, Medaka, stickleback, and pufferfish (Basta et al. 2007), and their low frequencies in green anole is reminiscent of stickleback as well (Blass et al. 2012).
For instance, the sequencing and physical mapping of the chicken genome revealed the homology between bird and human chromosomes (Nanda et al. 2000; Schmid et al. 2000), and the high conservation of the avian genome previously attributed to the scarcity of repeat elements (Backstrom et al. 2008) was later confirmed by additional genome analyses (Dalloul et al. 2010; but see Griffin et al. 2007).
