Abstract
The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.
Highlights
Snakes are a fascinating and unique lineage of reptiles, and comprise a rich tapestry of species (~3889 sp.) with extensive phenotypic diversity, from the loss of limbs to the development of extra-long bodies [1,2]
Recent advances in genome sequencing technologies have facilitated the thoration in repeatomic contents, mainly between species of pythons and colubroids [131,132]
The increasing availability of genomic resources and the establishment of computational tools have enabled the production of high-quality snake genome assemblies
Summary
Snakes are a fascinating and unique lineage of reptiles, and comprise a rich tapestry of species (~3889 sp.) with extensive phenotypic diversity, from the loss of limbs to the development of extra-long bodies [1,2]. These W-linked BAC repeats include large amounts of long interspersed nuclear elements (LINEs) and long terminal repeats (LTRs), which share homology with squamate reptile chromosome 2 and the chicken Z chromosome [75,76,77,78] This multi-chromosome homology across diverse species suggests that snake sex chromosomes evolved as a result of repeat-mediated rearrangements [25,78], which drove genomic changes, such as chromosomal-scale variation and gene reshuffling, resulting in species-specific evolution and diversification at the individual or population level [27,28,91]. Comparative repeatomic landscapes and chromosomic analyses using snakes as model systems are key to elucidating the enigmas of sex chromosomes and microchromosomes
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