Julie Blommaert

Plant & Food Research

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Claus‐Peter Stelzer

Universität Innsbruck

B. Hecox-Lea

Marine Biological Laboratory

Alexander Suh

Institute for Biodiversity

Valentina Peona

Swiss Ornithological Institute

Martin Irestedt

Swedish Museum of Natural History

Knud A. Jønsson

Natural History Museum Aarhus

Patric Jern

Uppsala University

Qi Zhou

Zhejiang University

Octavio M. Palacios‐Gimenez

Uppsala University

Tri Haryoko

Indonesian Institute of Sciences

Cooperative Institutions

Baylor College of Medicine

Baylor Genetics

University of Illinois Urbana-Champaign

University of Queensland

University of Otago

Universidade de São Paulo

Google (United States)

Universidade de Ribeirão Preto

Commonwealth Scientific and Industrial Research Organisation

Heinrich Heine University Düsseldorf

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Growth and Survival of Elite Versus Unselected Snapper (Chrysophrys Auratus) in Land-Based and Ocean-Based Production Systems

Georgia Samuels Flavio F. Ribeiro David T. Ashton Sharon R. Ford Joshua Fantham

Elite

10.2139/ssrn.5056756

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

Research Square (Research Square) (2019)

Julie Blommaert Simone Riß B. Hecox-Lea David B. Mark-Welch Claus‐Peter Stelzer

Abstract Background: The causes and consequences of genome size variation across Eukaryotes, which spans five orders of magnitude, have been hotly debated since before the advent of genome sequencing. Previous studies have mostly examined variation among larger taxonomic units (e.g., orders, or genera), while comparisons among closely related species are rare. Rotifers of the Brachionus plicatilis species complex exhibit a seven-fold variation in genome size and thus represent a unique opportunity to study such changes on a relatively short evolutionary timescale. 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). Results summary: 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. Conclusions: Even though the genome sizes of these species are at the low end of the Metazoan spectrum, their genomes contain substantial amounts of repetitive elements. Polyploidy does not appear to play a role in genome size variations in these species, and these variations can be mostly explained by changes in repetitive element content. This contradicts the naïve expectation that small genomes are streamlined, or less complex, and that large variations in nuclear DNA content between closely related species are due to polyploidy.

Genome size

Brachionus calyciflorus

Repeated sequence

GC-content

10.21203/rs.2.9135/v3

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Generational breeding gains in a new species for aquaculture, the Australasian snapper (Chrysophrys auratus)

Aquaculture (2024)

Georgia Samuels Liam B. Hegarty Warren Fantham David T. Ashton Julie Blommaert

Broodstock

Selective breeding

Population bottleneck

10.1016/j.aquaculture.2024.740782

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Citations (3)

Supplementary Files S1 It contains the RepeatMasker annotation of the six avian genomes. from The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities

Figshare (2021)

Valentina Peona Octavio M. Palacios‐Gimenez Julie Blommaert Jing Liu Tri Haryoko

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 greater than 55% compared to the genome-wide density of less than 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 hypothesize 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.This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

10.6084/m9.figshare.14724652

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The genomes of two key bumblebee species with primitive eusocial organization

Genome Biology (2015)

Ben M. Sadd Seth M. Barribeau Guy Bloch Dirk C. de Graaf Peter K. Dearden

The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats.We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits.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.

Eusociality

Bumblebee

Bombus terrestris

10.1186/s13059-015-0623-3

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Citations (381)

Ten Simple Rules for Post-Pandemic Preprinting

Michele Avissar-Whiting Ramy K. Aziz Soham Bandyopadhyay Julie Blommaert Munyaradzi Dimairo

Preprints are research articles shared in the public domain before formal publication in an academic journal. They are housed in online repositories known as preprint servers, the largest and most well-established of which include arXiv (physical sciences), bioRxiv (biological sciences), SSRN (social sciences), and Research Square (multidisciplinary). In early 2020, preprint servers had to adjust to huge volumes of pandemic-related research submissions. Many preprint services adjusted their approach to screening and imposed new restrictions on the type of content they would agree to post. Some preprints became the focus of intense public scrutiny and were rapidly withdrawn. Some were misunderstood and exploited in the service of disinformation campaigns. The following is a list of ten simple rules for preparing a preprint submission, incorporating our learnings from more than 20 months of navigating rapid research dissemination in a global pandemic.

Preprint

Disinformation

Scrutiny

Pandemic

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10.31219/osf.io/vwtc4

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Additional file 6: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

Figshare (2019)

Julie Blommaert Simone Riß B. Hecox-Lea David B. Mark Welch Claus‐Peter Stelzer

File S2. A summary of log-likelihood scores from the nQuire programme, showing the percent of heterozygous sites retained after the denoise step, the score for the free, diploid, triploid, and tetraploid models, and the differences between the diploid, triploid, and tetraploid models and the free model. The “Allreads_nQuire” tab summarises the results for when all decontaminated reads were mapped back to the genome assemblies, “Repfree_selfmaps_nQuire” summarises the results for when repetitive reads were removed from the read libraries (all reads were mapped to the repeats assembled by dnaPipeTE, and read pairs where neither read mapped to the repeats were extracted and considered “repeat free”) and mapped back to the assemblies, and “Repfree_reads_BUSCO_nQuire” summarises the same repeat free mappings, but restricted only to the shared 740 BUSCO genes. (XLSX 12 kb)

Genome size

10.6084/m9.figshare.8245364

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

Research Square (Research Square) (2019)

Julie Blommaert Simone Riß B. Hecox-Lea David B. Mark-Welch Claus‐Peter Stelzer

Genome size

Brachionus calyciflorus

Repeated sequence

GC-content

Interspersed repeat

10.21203/rs.2.9135/v2

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Citations (2)

Additional file 5: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

Figshare (2019)

Julie Blommaert Simone Riß B. Hecox-Lea David B. Mark Welch Claus‐Peter Stelzer

File S1. A table of complete, duplicated, fragmented, and missing BUSCO genes for each of the genomes sequenced here and the average coverage of each of the shared BUSCO genes for each assembly. (XLSX 284 kb)

Genome size

10.6084/m9.figshare.8245361

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Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BMC Biology (2021)

Claus‐Peter Stelzer Julie Blommaert Ann‐Marie Waldvogel Maria Pichler B. Hecox-Lea

Abstract Background 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. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

Genome size

Comparative Genomics

Population genomics

Structural Variation

10.1186/s12915-021-01134-w

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Citations (11)