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

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, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. 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

The genomes of two key bumblebee species with primitive eusocial organization

Background: 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. Results: 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. Conclusions: 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

The swan genome and transcriptome, its not all black and white

BACKGROUND: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. RESULTS: Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. CONCLUSION: Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-022-02838-0

The swan genome and transcriptome, it is not all black and white

Background: The Australian black swan (Cygnus atratus) is an iconic species with contrasting plumage to that of the closely related northern hemisphere white swans. The relative geographic isolation of the black swan may have resulted in a limited immune repertoire and increased susceptibility to infectious diseases, notably infectious diseases from which Australia has been largely shielded. Unlike mallard ducks and the mute swan (Cygnus olor), the black swan is extremely sensitive to highly pathogenic avian influenza. Understanding this susceptibility has been impaired by the absence of any available swan genome and transcriptome information. Results: Here, we generate the first chromosome-length black and mute swan genomes annotated with transcriptome data, all using long-read based pipelines generated for vertebrate species. We use these genomes and transcriptomes to show that unlike other wild waterfowl, black swans lack an expanded immune gene repertoire, lack a key viral pattern-recognition receptor in endothelial cells and mount a poorly controlled inflammatory response to highly pathogenic avian influenza. We also implicate genetic differences in SLC45A2 gene in the iconic plumage of the black swan. Conclusion: Together, these data suggest that the immune system of the black swan is such that should any avian viral infection become established in its native habitat, the black swan would be in a significant peril

Mechanisms and significance of genome size variation in rotifers

Die Genomgröße variiert bei Eukaryonten über mindestens fünf Größenordnungen, obwohl sie innerhalb einer Spezies tendenziell ein stabiles Merkmal ist. Diese Variation korreliert in der Regel nicht mit der Komplexität eines Organismus, was allgemein als "C-value enigma" bezeichnet wird. Die evolutionären Ursachen und Folgen von Genomgrößenänderungen sind Gegenstand vieler fachlicher Diskussionen. Die Genomgröße könnte ein adaptives Merkmal sein, die neutrale Theorie der Evolution bietet jedoch eine alternative Erklärung. Laut neutralen evolutionären Theorien ist die Genomgröße hauptsächlich ein Produkt genetischen Drifts. Selektive Hypothesen betonen dagegen, dass die Genomgröße ein Ziel der natürlichen Selektion über phänotypische Merkmale wie Körpergröße, Entwicklungszeit und andere zellgrößenbezogene Effekte sein könnte. Es gibt verschiedene Belege für beide Theorien, obwohl sie sich hauptsächlich auf interspezifische Vergleiche über große phylogenetische Distanzen stützen. Da die genomische Basis der Genomgrößenvariation den Phänotyp beeinflussen kann, ist das Verständnis auf einer intraspezifischen Ebene entscheidend, um diese evolutionären Hypothesen robust zu testen. Genomgrößenvariation kann durch verschiedene Mechanismen bedingt sein. Die Genomgröße kann durch Ereignisse wie Polyploidisierung (d.h. eine vollständige Genomduplikation) oder andere Duplikationsereignisse zunehmen. Weitere Beispiele für Auswirkungen auf der Ebene von Chromosomen sind zusätzliche Chromosomen (oder B- Chromosomen) und heterochromatin knobs‘. Eher graduelle Veränderungen der Genomgröße können durch die Amplifikation repetitiver Elemente einschließlich einfacher Wiederholungssequenzen oder Transposons verursacht wertden. Rädertiere aus dem Brachionus plicatilis Artenkomplex enthalten viele Variationen in Genomongröße. Über den gesamten Artenkomplex hinweg variiert die Genomgröße bis zu 7- fach. Darüber hinaus variiert die Größe des Genoms innerhalb einer Spezies in diesem Komplex, B. asplanchnoidis, um das Doppelte, wahrscheinlich verursacht durch überzählige genomische Elemente wie B-Chromosomen oder heterochromatin knobs‘. Mit diesen Variationen, innerhalb und zwischen den Arten, können wir evolutionäre Hypothesen über die Genomgröße testen. Aber um potenzielle evolutionäre Ergebnisse vollständig zu verstehen, muss die genomische Grundlage solcher Veränderungen vollständig verstanden werden. Hier haben wir durch Genomsequenzierung und -analyse festgestellt, dass interspezifische Genomgrößenunterschiede bei B. plicatilis hauptsächlich durch den Anteil vonrepetitivetiver DNA erklärt werden können. Darüber hinaus wurde festgestellt, dass dieser Artenkomplex einen bemerkenswert hohen Anteil an repetitiven Sequenzen für Genome dieser Größenordnung aufweist. Durch die Generierung und Annotation eines hochwertigen Referenzgenoms und den Vergleich von Variationen der ‚Coverage‘ zwischen verschiedenen Rädertierklonen derselben Art konnten wir lange, repetitive, genarme Teile im Genomidentifizieren, die fast die gesamte Variation der Genomgröße innerhalb von B. asplanchnoidis erklären. Wir haben festgestellt, dass diese überzähligen Elemente einige Anzeichen eines ‚meiotic drive‘ aufweisen, wobei verschiedene evolutionäre Kräfte diesem ‚meiotic drive‘ entgegenwirken werden können. Die in dieser Arbeit charakterisierten Mechanismen der innerartlichen Genomgrößenvariation bilden die Grundlage für zukünftige Untersuchungen zu den evolutionären Folgen solcher Genomgrößen-Veränderungen sowie Fragen zu Umweltwechselwirkungen mit der Genomgröße und möglichen Auswirkungen auf ‚Life history‘ Merkmale.Genome size varies tremendously across eukaryotes, at least five orders of magnitude, though it tends to be a stable trait within a species. This variation is not correlated with measures of organismal complexity, and is a phenomenon generally referred to as the “C- value enigma”. The evolutionary causes and consequences of genome size change are widely- discussed, but contentious. Some argue that genome size is an adaptive trait, while others prefer a more neutral theory behind genome size evolution. The neutral evolutionary theories of genome size argue that genome size is mainly a product of genetic drift. The selective hypotheses suggest that genome size is target of natural selection via phenotypic traits such as body size, developmental time, and other cell-size related effects. There is varying evidence supporting theories in either of these schools of thought, though it relies mostly on interspecific comparisons across large phylogenetic distances. Since the genomic basis of genome size variation can influence the phenotype, understanding this at an intraspecific level is vital to testing these evolutionary hypotheses robustly. Various mechanisms have been found which explain genome size variation. Genome size can increase by dramatic events such as polyploidisation (i.e. a whole genome duplication) or other duplication events. Other examples of chromosome level impacts on genome size include supernumerary chromosomes (or B-chromosomes) and heterochromatic knobs. More gradual genome size changes can often be put down to amplification of repetitive elements, including both simple repeat sequences and transposons. It is clear that many different types of genomic changes can underlie genome size changes, each of which has particular evolutionary consequences, and often these different genomic causes interact. The rotifer species complex, Brachionus plicatilis, harbours large variations in genome size, both within and between species. Across the species complex, genome size has been found to vary up to 7-fold. Additionally, within one species in this complex, B. asplanchnoidis, genome size varies up to two-fold, likely caused by supernumerary genomic elements such as B chromosomes or heterochromatic knobs. These variations, both within and between species provide an ideal platform for testing evolutionary hypotheses about genome size. But, to fully understand potential evolutionary outcomes, the genomic basis of such changes must be fully understood. Here, through genome sequencing and analysis, we established that interspecific genome size changes in B. plicatilis are caused by expansions of repetitive DNA. Additionally, this species complex was found to have remarkably high repeat content compared to similar-sised genomes. By generating and annotating a high-quality reference genome and comparing coverage variations between rotifer clones, we could identify long, repeat-rich, gene-poor genomic tracts which account for almost all of the genome size variation within B. asplanchnoidis. We also found, by examining genome size and hatching rate of haploid male rotifers, that these supernumerary elements exhibited some signs of meiotic drive, though these may be counteracted by different evolutionary forces. This thesis analysed genome sequencing data to dissect the causes of genome size variation at inter- and intra-specific levels, and begins to probe the consequences of this via examining evidence for meiotic drive in haploid males. This lays the ground-work for future investigations into evolutionary consequences of such genome expansions, as well as questions around environmental interactions with genome size, and possible impacts on life- history traits such as reproductive mode.by Julie BlommaertKumulative Dissertation aus drei ArtikelnZusammenfassung in deutscher SpracheUniversity of Innsbruck, Dissertation, 2019(VLID)436602

Ten Simple Rules for Post-Pandemic Preprinting

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

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Background: 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. Results: 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. Conclusions: 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

RAD tag (SgrAI) derived SNPs from Bombus impatiens

RAD tag (SgrAI) derived SNPs from Bombus impatiens from Sadd et al. (2015) "The genomes of two key bumblebee species with primitive eusocial organisation