Do larger genomes contain more diverse transposable elements?

Abstract

BackgroundThe genomes of eukaryotes vary enormously in size, with much of this diversity driven by differences in the abundances of transposable elements (TEs). There is also substantial structural and phylogenetic diversity among TEs, such that they can be classified into distinct classes, superfamilies, and families. Possible relationships between TE diversity (and not just abundance) and genome size have not been investigated to date, though there are reasons to expect either a positive or a negative correlation. This study compares data from 257 species of animals, plants, fungi, and “protists” to determine whether TE diversity at the superfamily level is related to genome size.ResultsNo simple relationship was found between TE diversity and genome size. There is no significant correlation across all eukaryotes, but there is a positive correlation for genomes below 500Mbp and a negative correlation among land plants. No relationships were found across animals or within vertebrates. Some TE superfamilies tend to be present across all major groups of eukaryotes, but there is considerable variance in TE diversity in different taxa.ConclusionsDifferences in genome size are thought to arise primarily through accumulation of TEs, but beyond a certain point (~500 Mbp), TE diversity does not increase with genome size. Several possible explanations for these complex patterns are discussed, and recommendations to facilitate future analyses are provided.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0339-8) contains supplementary material, which is available to authorized users.

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

“…For example, the pufferfish genome contains far more types of TEs than the human genome, despite being only one-tenth as large [9]. However, a recent large-scale comparison by the present authors revealed that any relationship between genome size and TE diversity is much more complex [47]. The results of that analysis suggest that there is an increase in TE diversity with genome size up to a point (approx.…”

“…Raw data exist for many additional species, but it was not possible to include them in the format of the present analysis simply because the publications reporting the genome sequencing project results do not provide the basic summary required. This issue had previously been noted as particularly problematic when it comes to reporting details of TE content (both abundance and diversity [47]). This study has revealed that a similar issue pertains to other types of genomic sequences, including coding regions and introns.…”

Abstracts of the 75th Scientific Conference of the University of Latvia

“…These elements consist of two constant Long Terminal Repeats from each side and two GAG and POL coding regions in the middle. The principle of this structure and produced proteins, such as Gag capsid-like proteins, reverse transcriptase, protease and integrase, allow integrating their own copies into host DNA using retrovirus-like "copy-and-paste" mechanism (Elliott, Gregory 2015;Pachulska-Wieczorek et al 2016). Each place of integration can be used to calculate the number of polymorphic loci and unique alleles within populations and genetic distances between them.…”

Similar ratios of introns to intergenic sequence across animal genomes

“…In regards to eukaroytes, some patterns in genome size have been discussed (Lynch and Conery 2003;Daubin and Moran 2004;Lynch 2004). Additionally, a handful of studies have analyzed genome size in connection to other parameters such as indels (Pettersson et al 2009), transposon content (Kidwell 2002;Elliott and Gregory 2015a;Canapa et al 2016), average intron length (Deutsch and Long 1999;Zhu et al 2009) or total intron length (Elliott and Gregory 2015b). Despite these advances, none of these studies have estimated the amount of the genome that is genic (exonic plus intronic, including noncoding) based on independent examination of single genomes and without averaging over a whole kingdom.…”