Transposable Elements in Reptilian and Avian (Sauropsida) Genomes

Abstract

Transposable elements (TEs) have profound effects on the structure, function and evolution of their host genomes. Our knowledge about these agents of genomic change in sauropsids, a sister group of mammals that includes all extant reptiles and birds, is still very limited. Invaluable information concerning the diversity, activity and repetitive landscapes in sauropsids has recently emerged from analyses of the draft genomes of chicken and Anolis and other preliminary reptilian genome sequencing projects. Avian and reptilian genomes differ significantly in the classes of TEs present, their fractional representation in the genome and by the level of TE activity. While lepidosaurian genomes contain many young, active TE families, the extant avian genomes have very few active TE lineages. Most reptilian genomes possess quite rich TE repertoires that differ considerably from those of birds and mammals, being more similar in diversity to that of lower vertebrates. The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context.

The transposable element profile of the Anolis genome

“…A large number of active families of class I elements (i.e., elements that require an RNA intermediate for their mobilization or retrotransposons) were recovered from the anole genome. [25][26][27] Anolis retrotransposons are extremely diverse and representative of the two main categories of these elements-those with Long-Terminal Repeats (LTRs) and those that lack LTRs-were found to be active. Within the non-LTR retrotransposons alone, 43 distinct families, belonging to five clades (L1, L2, RTE, CR1 and R4), show sign of recent activity.…”

“…In particular, two SINEs have amplified to extremely large copy number: 27 Sauria SINE which is mobilized by an RTE retrotransposon (>200,000 copies) and Anolis SINE2 which is mobilized by a LINE-2 element (~140,000 copies). LTR-retrotransposons are also very diverse in the Anolis genome, as representatives of the four major groups of LTR elements (Metaviridae, Pseudoviridae, BEL/Pao and Retroviridae) have been identified 25,27 and appear to be represented by multiple, highly conserved copies, suggestive of their recent activity. 25,27 Interestingly, it was observed in a recent study of BEL/Pao that Anolis contains the highest copy number (397) of these elements across metazoans.…”

“…LTR-retrotransposons are also very diverse in the Anolis genome, as representatives of the four major groups of LTR elements (Metaviridae, Pseudoviridae, BEL/Pao and Retroviridae) have been identified 25,27 and appear to be represented by multiple, highly conserved copies, suggestive of their recent activity. 25,27 Interestingly, it was observed in a recent study of BEL/Pao that Anolis contains the highest copy number (397) of these elements across metazoans. 31 The transition from the relatively small but diverse genomes of teleostean fish to the large, L1-dominated genomes of mammals is one of the most important, yet poorly understood, transitions in the evolution of vertebrates.…”

Evolutionary history of the mariner element galluhop in avian genomes

“…Although TEs are currently recognized as major players in genome evolution, in some taxa such as birds, knowledge of TEs is limited [24,25]. One of the reasons for this gap has been the scarcity of available genome sequences, but since 2014, more than 70 draft whole genome sequences have become available [26].…”

“…Among the few studies focusing on TEs in bird genomes, a reduction in repetitive DNA was detected in sauropsids, perhaps due to the purifying selection pressure acting on metabolism optimization [25,27,28]. In particular, Class II TEs, which are abundant in other eukaryotic species, appear to show limited diversity in the few avian genomes studied so far: the chicken Gallus gallus and the wild turkey Meleagris gallopavo [24,29].…”