Abstract
Reptiles are notable for the extensive genomic diversity and species richness among amniote classes, but there is nevertheless a need for detailed genome-scale studies. Although the monophyletic amniotes have recently been a focus of attention through an increasing number of genome sequencing projects, the abundant repetitive portion of the genome, termed the “repeatome”, remains poorly understood across different lineages. Consisting predominantly of transposable elements or mobile and satellite sequences, these repeat elements are considered crucial in causing chromosomal rearrangements that lead to genomic diversity and evolution. Here, we propose major repeat landscapes in representative reptilian species, highlighting their evolutionary dynamics and role in mediating chromosomal rearrangements. Distinct karyotype variability, which is typically a conspicuous feature of reptile genomes, is discussed, with a particular focus on rearrangements correlated with evolutionary reorganization of micro- and macrochromosomes and sex chromosomes. The exceptional karyotype variation and extreme genomic diversity of reptiles are used to test several hypotheses concerning genomic structure, function, and evolution.
Highlights
Over 150 years ago, Darwin and Wallace first proposed the theory of natural selection requiring variation among species individuals and stable inheritance from generation to generation [1,2].the mechanism of this variation remained unclear until Dobzhansky observed the occurrenceGenes 2020, 11, 827; doi:10.3390/genes11070827 www.mdpi.com/journal/genesGenes 2020, 11, 827 of chromosomal changes among species in a Drosophila lineage [3]
May 2020, the National Center of Biotechnology Information genome database included 64 publicly available assembled genomes, and this number is expected to rise rapidly. This advance has heralded renewed interest in several questions that link reptilian genomes and repeats, including (i) how does the proportion of repeats in the reptilian genome differ from that of other amniotes, (ii) in which specific genomic repeats do reptiles differ from other amniotes, (iii) how do genomic repeat contents differ among reptilian lineages, (iv) what potential mechanisms affect karyotypic evolution in reptiles through genomic repeats, and (v) is repeatomic diversity correlated with the extensive chromosomal variation seen in reptiles
The diversity of genomic structural and sequence composition indicates that the reptilian genome harbors an extreme and divergent landscape of repeats compared with other amniotes
Summary
Over 150 years ago, Darwin and Wallace first proposed the theory of natural selection requiring variation among species individuals and stable inheritance from generation to generation [1,2]. Evolutionary mechanisms include variation in chromosome size, composition, and number between and within species, which has been termed “stasipatric speciation” [5]. May 2020, the National Center of Biotechnology Information genome database included 64 publicly available assembled genomes (https://www.ncbi.nlm.nih.gov/genome/?term=reptiles), and this number is expected to rise rapidly This advance has heralded renewed interest in several questions that link reptilian genomes and repeats, including (i) how does the proportion of repeats in the reptilian genome differ from that of other amniotes, (ii) in which specific genomic repeats do reptiles differ from other amniotes, (iii) how do genomic repeat contents differ among reptilian lineages, (iv) what potential mechanisms affect karyotypic evolution in reptiles through genomic repeats, and (v) is repeatomic diversity correlated with the extensive chromosomal variation seen in reptiles. The dynamics of repeat-mediated rearrangements and their evolutionary impact on reptilian genome reorganization are discussed
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