Transposable element annotation in non-model species: The benefits of species-specific repeat libraries using semi-automated EDTA and DeepTE de novo pipelines.

Transposable elements (TEs) are significant genomic components which can be detected either through sequence homology against existing databases or de novo, with the latter potentially reducing the risk of underestimating TE abundance. Here, we describe the semi-automated generation of a de novo TE library using the newly developed EDTA pipeline and DeepTE classifier in a non-model teleost (Corydoras fulleri). Using both genomic and transcriptomic data, we assess this de novo pipeline's performance across four TE based metrics: (i) abundance, (ii) composition, (iii) fragmentation, and (iv) age distributions. We then compare the results to those found when using a curated teleost library (Danio rerio). We identify quantitative differences in these metrics and highlight how TE library choice can have major impacts on TE-based estimates in non-model species.

Removal of beneficial insertion effects prevent the long-term persistence of transposable elements within simulated asexual populations.

BACKGROUND: Transposable elements are significant components of most organism's genomes, yet the reasons why their abundances vary significantly among species is poorly understood. A recent study has suggested that even in the absence of traditional molecular evolutionary explanations, transposon proliferation may occur through a process known as 'transposon engineering'. However, their model used a fixed beneficial transposon insertion frequency of 20%, which we believe to be unrealistically high. RESULTS: Reducing this beneficial insertion frequency, while keeping all other parameters identical, prevented transposon proliferation. CONCLUSIONS: We conclude that the author's original findings are better explained through the action of positive selection rather than 'transposon engineering', with beneficial insertion effects remaining important during transposon proliferation events.

Help or hindrance? The evolutionary impact of whole-genome duplication on immunogenetic diversity and parasite load.

Whole-genome duplication (WGD) events occur in all kingdoms and have been hypothesized to promote adaptability. WGDs identified in the early history of vertebrates, teleosts, and angiosperms have been linked to the large-scale diversification of these lineages. However, the mechanics and full outcomes of WGD regarding potential evolutionary impacts remain a topic of debate. The Corydoradinae are a diverse subfamily of Neotropical catfishes with over 170 species described and a history of WGDs. They are divided into nine mtDNA lineages, with species coexisting in sympatric-and often mimetic-communities containing representatives of two or more of the nine lineages. Given their similar life histories, coexisting species of Corydoras might be exposed to similar parasite loads and because of their different histories of WGD and genome size they provide a powerful system for investigating the impacts of WGD on immune diversity and function in an animal system. Here, we compared parasite counts and the diversity of the immune-related toll-like receptors (TLR) in two coexisting species of Corydoras catfish (C. maculifer and C. araguaiaensis), one diploid and one putative tetraploid. In the putative tetraploid C. araguaiaensis, we found significantly lower numbers of parasites and significantly higher diversity (measured by both synonymous and nonsynonymous SNP counts) in two TLR genes than in the diploid C. maculifer. These results provide insight into how WGD may impact evolution, in this case by providing greater immunogenetic diversity.