Centromeric enrichment of LINE-1 retrotransposons and its significance for the chromosome evolution of Phyllostomid bats

Abstract

Despite their ubiquitous incidence, little is known about the chromosomal distribution of long interspersed elements (LINEs) in mammalian genomes. Phyllostomid bats, characterized by lineages with distinct trends of chromosomal evolution coupled with remarkable ecological and taxonomic diversity, represent good models to understand how these repetitive sequences contribute to the evolution of genome architecture and its link to lineage diversification. To test the hypothesis that LINE-1 sequences were important modifiers of bat genome architecture, we characterized the distribution of LINE-1-derived sequences on genomes of 13 phyllostomid species within a phylogenetic framework. We found massive accumulation of LINE-1 elements in the centromeres of most species: a rare phenomenon on mammalian genomes. We hypothesize that expansion of these elements has occurred early in the radiation of phyllostomids and recurred episodically. LINE-1 expansions on centromeric heterochromatin probably spurred chromosomal change before the radiation of phyllostomids into the extant 11 subfamilies and contributed to the high degree of karyotypic variation observed among different lineages. Understanding centromere architecture in a variety of taxa promises to explain how lineage-specific changes on centromere structure can contribute to karyotypic diversity while not disrupting functional constraints for proper cell division.

Poly-Enrich: Count-based Methods for Gene Set Enrichment Testing with Genomic Regions

“…Interesting additional findings are that L1 elements are enriched in chemical stimulus detection such as “detection of chemical stimulus” and “sensory perception of chemical stimulus”, while Alu elements are depleted in the genes in these processes. We also find that both Alu and L1 are enriched in centrosome-related GO terms, which were only made possible with recent advancements in genome mapping near the centromeres [21], and is consistent with previous findings [22]. Finally, both Alu and L1 elements are significantly depleted in genes in GO terms relating to development and morphogenesis.…”

Islands of retroelements are the major components ofDrosophilacentromeres

“…However, retroelements are also abundant and widespread at the centromeres of plants such as maize [39] and rice [40,41]. Retroelements are also found at the centromeres of fungi [42], humans [43], marsupials [44], bats [45], and gibbons [46], suggesting that they are pervasive centromeric features ( Fig. 7B).…”

“…The approximate satellite size estimates are based on Jagannathan et al [37]. B) Phylogenetic tree showing that centromere-associated retroelements are common across highly diverged lineages: Gossypium hirsutum (cotton) [71], Zea mays mays (maize) [9,39], Oryza sativa (rice) [40,41,72], Triticum boeoticum (wild wheat) [73], Cryptococcus [42], Phyllostomid (bat) [45], Hoolock leuconedys (gibbon) [46], Homo sapiens (human) [43] and a human neo-centromere [49], Macropus eugenii (tammar wallaby) [74][75][76], Phascolarctos cinereus (koala) [77], Drosophila melanogaster (this paper). The Phylogeny was constructed using TimeTree [78].…”

Decoding the Role of Satellite DNA in Genome Architecture and Plasticity—An Evolutionary and Clinical Affair

“…Several studies document the presence of TEs intermingled with centromeric satDNA [127,128], in some cases forming complex structures [24,[129][130][131]. TEs are highly represented in some vertebrate species, making up to 60% or more of their genomes.…”

“…TEs are highly represented in some vertebrate species, making up to 60% or more of their genomes. They are characterized by their mobility within genomes using either a direct cut-and-paste mechanism to alter their position (transposons) or requiring an RNA intermediate (retrotransposons) [127,132]. This intrinsic feature makes them active elements of the genome and has been associated with genomic instability.…”