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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

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

Published in , 2018

Here, we investigate the causes of large instraspecific genome size variation in Brachionus asplanchnoidis, a species within the B. plicatilis species complex. The analysis is almost completed and hopefully the results will be publishable soon!

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

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

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

Published in Target journal: Ecology and Evolution, 2019

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 ."

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.

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.