Julie Blommaert

Julie Blommaert

Postdoc - Genomics and evolution

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Posts

Blog Post number 4

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Blog Post number 2

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Blog Post number 1

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portfolio

publications

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

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

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 Philosophical Transactions of the Royal Society B, 2021

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. (2021). "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities ." Philosophical Transactions of the Royal Society B https://royalsocietypublishing.org/doi/full/10.1098/rstb.2020.0186

Genome structure of Brachionus asplanchnoidis, a Eukaryote with intrapopulation variation in genome size

Published in BMC Biology, 2021

Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population.

Recommended citation: Stelzer, CP., Blommaert, J., Waldvogel, AM., Pichler, M., Hecox-Lea, B., Mark-Welch, D. (2021). "Genome structure of Brachionus asplanchnoidis, a Eukaryote with intrapopulation variation in genome size." BMC Biology https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01134-w

talks

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

Published in 5th meeting of Fresh Blood for FreshWater, 2017

Rotifers are an important part of freshwater ecosystems. The Brachionus plicatilis species complex inhabits a wide range of freshwater habitats worldwide. This complex of at least 15 species is morphologically diverse, both within and between species, and likely inhabits many different niches within these ecosystems. As well as this range of morphologies, B. plicatilis spp. exhibits genome size variations up to 8-fold. This dramatic change in genome size across the species complex is likely the largest observed in such closely related animals. The consequences of such variation, on both the structure and composition of genome, and the biology of the species complex is unknown. One species in this complex, Brachionus asplanchnoidis, has genome sizes ranging from 205Mbp to 271Mbp. Genome sequencing and analysis of different populations from this species are the first step in understanding such large genome size changes on short evolutionary time-scales. These data can then be related to biological and ecological outcomes. Often, in similar cases of genome size variation in plants, these changes are largely driven by non-coding DNA. Initial analyses of B. asplanchnoidis genomes indicate that repetitive DNA sequences are partly responsible for a large part of the observed genome size variation. The identity and distribution of these repetitive sequences shed light on the influence of such sequences not only on genome size evolution, but also on rotifer biology. 

Intraspecific Genome Size Variation: If it’s not transposable elements, what is it?

Published in Martiniplaza, 2017

I presented this poster at the 2017 Congress of the European Society for Evolutionary Biology (ESEB) in Groningen. The poster focused on ongoing comparative genomics of 14 rotifer genomes, taking a mostly coverage-based approach to identify genomic regions potentially contributing to genome size change in the Brachionus plicatilis species complex.

Rotifers of unusual (genome) size: rotifer genomes are many things, none of them logical

Published in Uppsala University, 2019

I gave this talk at the 3rd annual Uppsala Transposon Symposium, covering most of my PhD work on B. plicatilis genome size variation. This covered the genomic causes of interspecific genome size variation (mostly transposons), genomic causes of intraspecific genome size variation (annotating B chromosomes), and some analyses of meiotic behaviour of B chromosomes.

teaching

CELS191- Cell and Molecular Biology

Published in University of Otago, Department of Zoology, 2010

- In this course, which takes place in the first semester of each year, I helped teach over 350 students, in four rotations over two weeks, different aspects of cellular and molecular biology laboratory work. The skills taught included microscopy, pipetting, PCR, and data collection and analysis.

BIOL112- Animal Biology

Published in University of Otago, Department of Zoology, 2010

- I helped teach the lab portion of the Animal Biology undergraduate course for two years. This course takes place in the second semester of teaching and I helped teach around 20 students per week, helping with dissections, setting up experiments, collecting and analysing data, and performing other lab tasks.

Genome Evolution

Published in University of Innsbruck, Department of Limnology, 2018

- I helped teach the computer-based and lab-based practical elements of this two-week course for students studying towards a Bachelor of Biology at the University of Innsbruck. I assisted with prokaryotic and eukaryotic bioinformatics, as well as flow cytometry to measure genome size of various fish species.