Publications

Genome size evolution- towards new model systems for old questions

Published in Proceedings of the Royal Society B: Biological Sciences, 2020

The amount of DNA in our cells (genome size) has intrigued biologists for many decades. Previously, it wasn’t understood why seemingly less-complex organisms (like onions) had more DNA than more complex organisms (like humans), but it was then found to be caused by non-coding DNA. Where does this extra DNA come from? And what are its other effects on the organism? In this review, I have discussed these issues and how we can combine new and old technologies to try to answer these questions. Hopefully this will lead to a deeper understanding of the evolutionary forces acting on non-coding DNA.

Recommended citation: Blommaert J.(2020). "Genome size evolution- towards new model systems for old questions." Proceedings of the Royal Society B: Biological Sciences https://royalsocietypublishing.org/doi/10.1098/rspb.2020.1441

The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

Published in BioArxiv, 2020

It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of 55% compared to the genome-wide density of 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesise that the avian W chromosome acts as a refugium for active ERVs, likely leading to female-biased mutational load that may influence female physiology similar to the "toxic-Y" effect in Drosophila. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage.

Recommended citation: Peona, V., Palacios-Gimenez, O.M., Blommaert, J. Liu, Jing., Haryoko, T., Jønsson, K.A., Irestedt, M., Zhou, Q., Jern, P., Suh, A. (2020). "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities ." BioRxiv https://www.biorxiv.org/content/10.1101/2020.07.31.230854v1

Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

Published in BMC Genomics, 2019

Here, we sequenced and analysed the genomes of four species of this complex with nuclear DNA contents spanning 110- 422 Mbp. To establish the likely mechanisms of genome size change, we analysed both sequencing read libraries and assemblies for signatures of polyploidy and repetitive element content. We also compared these genomes to that of B. calyciflorus, the closest relative with a sequenced genome (293 Mbp nuclear DNA content). Despite the very large differences in genome size, we saw no evidence of ploidy level changes across the B. plicatilis complex. However, repetitive element content explained a large portion of genome size variation (at least 54%). The species with the largest genome, B. asplanchnoidis, has a strikingly high 44% repetitive element content, while the smaller B. plicatilis genomes contain between 14% and 25% repetitive elements. According to our analyses, the B. calyciflorus genome contains 39% repetitive elements, which is substantially higher than previously reported (21%), and suggests that high repetitive element load could be widespread in monogonont rotifers.

Recommended citation: Blommaert J., Riss S., Heacox-Lea B., Mark-Welch D., Stelzer CP. (2019). "Small, but surprisingly repetitive genomes: Transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex ." BMC Genomics https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5859-y

The genomes of two key bumblebee species with primitive eusocial organization

Published in Genome Biology, 2015

These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Recommended citation: Sadd, Ben M, et al. (2015). "The genomes of two key bumblebee species with primitive eusocial organization." Genome Biology. 16(76). https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0623-3

Impacts of supernumerary genomic elements on hatching rate in a rotifer and implications for meiotic drive

Published in INPREP, 2000

This paper considers evidence for meiotic drive in rotifers by estimating proportions of genome sizes in haploid male rotifers and their eggs, compared to expected GS proportions in the absence of drive.

Recommended citation: Blommaert J., Stelzer CP. (in prep). "Impacts of supernumerary genomic elements on hatching rate in a rotifer and implications for meiotic drive ." in prep

Genomic causes of large intraspecific genome size variation in a species of rotifer

Published in INPREP, 2000

Here, we investigate the causes of large instraspecific genome size variation in Brachionus asplanchnoidis, a species within the B. plicatilis species complex. Previous work suggests this to be largely caused by B-chromosomes, here we analyse their number and content across a species

Recommended citation: Blommaert J., Heacox-Lea B., Mark-Welch D., Stelzer CP. (in prep). "Genomic causes of large intraspecific genome size variation in a species of rotifer." in prep