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Rob Waterhouse

@rmwaterhouse.bsky.social

Director, Environmental Bioinformatics Group at SIB Swiss Institute of Bioinformatics @sib.swiss. Chair, European Reference Genome Atlas (ERGA, @ergabiodiv.bsky.social). #biodiversity #genomics www.rmwaterhouse.org

1966 Posts2433 Follower1970 Folgt
Leibniz IPK@leibnizipk.bsky.social · 9h ago

We are delighted to announce the upcoming Gatersleben Research Conference “Genes, Chromosomes, and Genomes in Plants”, organized in partnership with the GPZ groups ‘Cytogenetics’ and ‘Genome Analysis’. When? November 3–5, 2027 Where? @leibnizipk.bsky.social, Germany Stay tuned for further updates!

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ERGA - European Reference Genome Atlas@ergabiodiv.bsky.social · last wk.

💡 #KnowledgeHighlight | Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step @galaxyproject.bsky.social 🔗 training.galaxyproject.org/training-mat... Explore more open-access training materials in the ERGA #KnowledgeHub ➡️ knowledge.erga-biodiversity.eu #GenomeAssembly

Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step / Hands-on: Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a 'Reference Sequence.'…

training.galaxyproject.org

Jamie Walters@bioboatr.bsky.social · last wk.

Comparing 6 independent assemblies, each W assembly is strikingly different, though the remainder of the genome is highly concordant. Presumably, these Ws are mis-assembled (again, this is HARD to do). If true in other species, it likely misleads comparative W analyses across Lepidoptera.

W chromosome alignment dotplots show striking differences between assemblies.
Jamie Walters@bioboatr.bsky.social · last wk.

Nonetheless, these assemblies seem to accurately capture strikingly reduced diversity of repeats on the W, compared to the remainder of the genome. We confirmed this by analyzing "raw" reads directly, thus the result is not an artifact of mis-assembly.

Plots showing that W chromosome has reduced diversity of repeats in silkworm. Repeat landscapes show substitution levels of W is about half that of autosomes or Z chromosomes. Scatterplot of cumulative repeat length versus number of repeat families per chromosome indicates W is a strong low outlier, with many fewer families than other chromosomes for the same amount of repetitive DNA.
Genome Biology and Evolution@genomebiolevol.bsky.social · 5d ago

@a-mack-s.bsky.social @evolvwing.bsky.social et al. generate deep-coverage PacBio long-read data from five Heliconius, recovering high genome contiguity, quality, and completeness scores. 🔗 doi.org/10.1093/gbe/evag171 #societyjournal #genome

de novo Assembly of five Highly Contiguous Heliconius Butterfly Genomes With Long-Read Sequencing Alone

Abstract. Rapidly decreasing costs of sequencing whole genomes have caused a boom in genomic resources for many species. However, many key nonmodel systems

doi.org

Bloodsucking Parasites@bloodsparasites.bsky.social · 11h ago

An improved chromosome-level genome resource for the sheep scab mite, Psoroptes ovis PubMed

An improved chromosome-level genome resource for the sheep scab mite, Psoroptes ovis

Sheep scab, caused by infestation with the ectoparasitic mite, Psoroptes ovis, represents a major welfare and economic challenge for the livestock industry. We present an updated 62.7 Mb genome assembly containing 10 chromosome-level scaffolds with 10,516 annotated protein-coding genes, which provides a useful resource for studies into resistance and control.

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ERGA - European Reference Genome Atlas@ergabiodiv.bsky.social · last wk.

#ERGAReads | ntSynt: multi-genome synteny detection using minimizer graph mappings link.springer.com/article/10.1... #genomes #synteny #graphmaps #genomeassemblies #assembly #BMCBiology

ntSynt: multi-genome synteny detection using minimizer graph mappings - BMC Biology

Background With the growing availability of reference-grade genome assemblies across diverse taxa, there is an increasing need for efficient and scalable tools for multi-species comparative genomics,…

link.springer.com

LIB@leibnizlib.bsky.social · last mo.

Every genome is a new window into biodiversity. Researchers generated a reference genome for Dailognatha quadricollis, an East Mediterranean darkling beetle, opening new opportunities to study evolution and adaptation. #LIBresearch © Bolanakis et al., CC BY | photo: Dr Apostolos Trichas 1/3

Dark beetle of the species Dailognatha quadricollis with four-segmented antennae and six legs, viewed from above on a light background.
ERGA - European Reference Genome Atlas@ergabiodiv.bsky.social · last mo.

We are very glad to hear that our coordination efforts for reference #genome production & use for #European #biodiversity is "changing how we do molecular evolution" 😀

Marc Robinson-Rechavi@marcrr.bsky.social · last mo.

My take-away from #SMBE2026 after 3 days: biodiversity genome projects such as Darwin Tree of Life @ergabiodiv.bsky.social @vertebrategenomes.bsky.social et al are no longer promises, but are changing how we do molecular evolution. I hope biodiversity gene expression will be next 😎 .

ORCID@orcid.org · yesterday

📣 Researchers, did you know your ORCID iD acts as a digital passport? When you sign into a manuscript submission system using your green iD icon, an authenticated "handshake" occurs. The system instantly verifies exactly who you are. 🛡️ See it visualized here:

What Your ORCID Record Can Do For You

Managing your research across different systems, institutions, and career stages can be exhausting. But is your ORCID iD just a required checkbox, or is it actually working for you? In this video, learn how to unlock the full potential of your record. Save Time by reducing manual data entry by seamlessly logging into systems, autofilling grant forms, and syncing your data across platforms. Build Trust through Trust Markers that signal your information has been verified and added directly by trusted institutions, funders, and employers. Stay in Control of how your data is shared, viewed, and managed with fully customizable visibility settings. The research ecosystem works best when everything connects. Explore your record today to see how much more your ORCID iD can do. 👉 Manage your record at orcid.org #ORCID #ResearchCommunity #OpenScience

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Genome Biology and Evolution@genomebiolevol.bsky.social · 6d ago

Castro-Nallar et al. report a chromosome-scale reference genome of the Antarctic Pearlwort (Caryophyllaceae), one of only two vascular plants native to Antarctica and a model species for studying adaptation to extreme environments. 🔗 doi.org/10.1093/gbe/evag182 #societyjournal #genome #PlantSky

A Chromosome-Scale Genome Assembly and Annotation of the Antarctic Pearlwort Colobanthus quitensis (Caryophyllaceae)

Abstract. Colobanthus quitensis (Caryophyllaceae) is one of only two vascular plants native to Antarctica and a model species for studying adaptation to ex

doi.org

Rob Waterhouse@rmwaterhouse.bsky.social · 6d ago

A wonderful escape to the mountains for our summer group outing ... hike up ⬆️⛰️, swim 🏊‍♂️, lunch 🧀🥪🥗, hike around the lake 🚶, swim 🏊, & hike down ⬇️⛰️

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Marc Robinson-Rechavi@marcrr.bsky.social · last wk.

New preprints! 2/3 Convergent gene family expansions and births with the evolution of metamorphosis in Pancrustacea. Led by Giulia Campli and @rmwaterhouse.bsky.social with @chipman-lab.bsky.social doi.org/10.64898/202...

Convergent gene family evolution underpins repeated transitions to metamorphic development across Pancrustacea

Arthropod developmental modes are highly diverse, ranging from direct development with little morphological change between moults to metamorphic life-stage progressions characterised by profound transformations. Metamorphosis can be defined as a post-embryonic life-stage progression event leading to adulthood that is characterised by major morphological changes and modifications of the adaptive landscape. Within this framework, we compare four independent evolutionary life history transitions to metamorphic development across Pancrustacea. Using a phylogenomic dataset of 54 species spanning 26 orders, we investigated gene family evolutionary dynamics associated with the inferred origins of metamorphosis in Insecta, Copepoda, Eucarida, and Thecostraca. Compared with non-metamorphic sister lineages as well as descendent and ancestral nodes, transitions to metamorphic development were consistently associated with elevated gene family births and expansions. Although these expansions predominantly involved different gene families in each lineage, they repeatedly converged on shared biological functions, particularly those related to embryonic and post-embryonic development, morphogenesis, nervous system differentiation, and other processes relevant to the biology and evolution of metamorphosis. Evolutionary modelling further identified a subset of gene families exhibiting adaptive, lineage-specific expansions, including genes implicated in neural and sensory development, segmentation, and moulting. Together, these findings support a model in which independent transitions to metamorphic development repeatedly recruited different components of a shared developmental toolkit, achieving functional convergence through distinct genetic trajectories. This reframes the arthropod moulting programme as an evolutionarily flexible developmental substrate whose repeated modification has facilitated the emergence of complex multi-phasic life histories and contributed to the extraordinary diversification of Pancrustacea. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, 198691

doi.org