The Mobilome of Reptiles: Evolution, Structure, and Function

Abstract

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

Consequence of Paradigm Shift with Repeat Landscapes in Reptiles: Powerful Facilitators of Chromosomal Rearrangements for Diversity and Evolution

“…Reptile genomes show great considerable TE diversity, with TE family abundance ranging from 23% to 53% within species [ 49 , 61 ] ( Figure 1 b). The anole lizard mobilome displays extraordinarily diversified TE families annotated as young copies of ancient elements [ 52 , 64 , 86 ] ( Figure 3 b).…”

“…The correlation between repeats and chromosomal rearrangements must be investigated in the context of the diversity and evolution of reptilian lineages. To date, genome-wide characterization of repeats (‘repeatomics’) has focused on certain animal groups, such as mammals [ 47 , 48 ], with scant attention given to reptilian genomes [ 49 ]. Following completion of the first two mammalian genome sequencing projects involving mouse and humans [ 50 , 51 ], a decade passed before publication of the first reptilian genome, that of the green anole ( Anolis carolinensis ) in 2011 [ 52 ].…”

“…In this modern era of next generation sequencing (NGS), the number of sequenced mammalian genomes is considerably greater than that of reptiles, although the total number of reptilian species is almost four times higher than that of mammalian species [ 53 ]. However, genomic assemblies for several reptiles are in progress, which will provide novel resources for high-throughput repeatomic analyses of diverse lineages [ 49 ]. As of May 2020, the National Center of Biotechnology Information genome database included 64 publicly available assembled genomes ( ), and this number is expected to rise rapidly.…”

Comparative Cytogenetics of Four Sea Turtle Species (Cheloniidae): G-Banding Pattern and in situ Localization of Repetitive DNA Units

“…The use of repetitive DNAs as chromosomal markers in reptiles has not yet been thoroughly explored. Usually, studies applying repetitive DNAs in turtles involve chromosomal localization of multigene families [Badenhorst et al, 2015;Cavalcante et al, 2018Cavalcante et al, , 2020aMatsubara et al, 2019] and in situ localization of satellite DNA sequences or transposable elements, restricted to a few groups [Badenhorst et al, 2015;Boissinot et al, 2019;Cavalcante et al, 2020b]. However, chromosomal painting and BAC-FISH for detecting single-copy genes has proven useful for identifying chromosomal rearrangements in reptiles in cytogenetic studies [Young et al, 2013;Badenhorst et al, 2015;Iannucci et al, 2019;Lee et al, 2019;Lisachov et al, 2019].…”

Transposons Continue the Amaze

“…For example, TEs have been shown to silence or alter expression of genes adjacent to insertion sites, contribute to chromosomal rearrangements via recombination, epigenetically alter regional methylation patterns, and provide template sequences for RNA interference (Feschotte et al, 2002;Bennetzen, 2005;Morgante et al, 2007;Weil and Martienssen, 2008;Slotkin et al, 2012;Lerat et al, 2019). This diverse functional impacts of TEs, and their intrinsic contribution to genomic plasticity suggest that these elements play a major role in molecular diversification, and ultimately, species divergence (Schrader and Schmitz, 2019;Dupeyron et al, 2019;Boissinot et al, 2019). This review article covers a short overview of TEs classification, transposition mechanisms, their effects on gene expression and evolutionary processesand even importance and usage of transposons for different purposes such as transposon markers, transposomics, and .…”