Abstract:Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the… Show more
“…TEs are mobile DNA fragments that constitute a substantial albeit variable proportion of virtually all the genomes analyzed to date [13, 14]. TEs can create a variety of mutations from gene disruption to changes in gene expression and chromosome rearrangements [14, 15].…”
Section: Introductionmentioning
confidence: 99%
“…TEs are mobile DNA fragments that constitute a substantial albeit variable proportion of virtually all the genomes analyzed to date [13, 14]. TEs can create a variety of mutations from gene disruption to changes in gene expression and chromosome rearrangements [14, 15]. Although the majority of TE-induced mutations are deleterious or neutral, there are multiple instances in which individual TE insertions have been shown to play a role in adaptive evolution [10–12, 16].…”
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of
Drosophila melanogaster
, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
“…TEs are mobile DNA fragments that constitute a substantial albeit variable proportion of virtually all the genomes analyzed to date [13, 14]. TEs can create a variety of mutations from gene disruption to changes in gene expression and chromosome rearrangements [14, 15].…”
Section: Introductionmentioning
confidence: 99%
“…TEs are mobile DNA fragments that constitute a substantial albeit variable proportion of virtually all the genomes analyzed to date [13, 14]. TEs can create a variety of mutations from gene disruption to changes in gene expression and chromosome rearrangements [14, 15]. Although the majority of TE-induced mutations are deleterious or neutral, there are multiple instances in which individual TE insertions have been shown to play a role in adaptive evolution [10–12, 16].…”
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of
Drosophila melanogaster
, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Besides, we identified a set of 21 fixed TEs also likely to be adaptive. Indeed, we, and others, found evidence of selection for 84 of these reference TE insertions. The analysis of the genes located nearby these 84 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affects expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
“…Furthermore, the emergence of Bov-B LINE independently in snake lineages is suggested with large different sequence similarity between group. Although mutation rates of Bov-B LINE were indicated to be more rapid than those of COI and BDNF in snake lineages, Bov-B LINEs have evolved at a slow rate compared with other TEs [9,[83][84][85][86][87]. Average ratios of nonsynonymous to synonymous substitutions were generally less than one, which indicates that the RT genes evolved under purifying selection.…”
Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.
“…The TE‐mediated horizontal gene transfer process often involves element activation in one species and integration/transformation into a viral genome, then infection of another species by virus and subsequent activation of TEs with integration into the new host genome, completing the horizontal gene transfer cycle. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated (Gilbert & Feschotte, 2018; Guio & González, 2019). Finally, the phenomenon of horizontal gene transfer sheds new light on concepts such as common ancestor, synteny between genomes, phylogeny and the idea of species as a discrete unit. “If you know you are on the right track , if you have this inner knowledge , then nobody can turn you off…no matter what they say .…”
Transposable elements (TEs) are DNA sequences that can change their position within genomes. TEs are present in most organisms and can be an important genomic component. Their activities are manifold: restructuring of genome size, chromosomal rearrangements, induction of gene mutations, and alteration of gene activity by insertion near or within promoters, intronic regions, or enhancer. There are several examples of mutations and other genetic variations determined by the activity of TEs, associated with the evolution of prokaryotic and eukaryotic organisms and the domestication of plants. Generally, TE mobilization occurs when the organism is subjected to stress, which can include both biotic and abiotic stresses, polyploidy conditions, and interspecific hybridizations, very common events in plants. TEs are widely distributed among organisms. TEs also play essential roles in evolution, but most of them are either dormant or inactive. This is mainly determined by epigenetic silencing mechanisms, regulatory systems, and control systems that aim to limit its proliferation. Furthermore, the host has recruited many genes originated from TEs as transcriptional regulators, especially in defense against pathogens and invasive genetic elements; this phenomenon is called molecular domestication. Therefore, TEs are responsible for horizontal gene transfer and the movement of genetic material between organisms, even phylogenetically distant, with a consequent remixing of their gene pools.
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