One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential.
www.biorxiv.org/content/10.1...
Check out our paper in Evolution Letters!
We used D. melanogaster pigmentation as a focal trait to explore parallelism in phenotypic and genomic responses to environmental change - read more at the link below 👇
Drosophila picticornis, a Hawaiian fly with patterned wings
Wish I could be at #Evol2025 this year! I’ll be starting a new lab at NYU this fall, and will be recruiting at all levels. Please spread the word if you know anyone who wants to work on evo. genomics, phylogenies, and comparative development of inverts (like Hawaiian Drosophila!) shchurch.github.io
Huge congrats and see you soon on the East Coast!
I am delighted to be starting as an assistant professor in the Department of Molecular Genetics & Microbiology at the University of Florida in January 2026. The lab is broadly interested in the functional, developmental, and evolutionary genetics of cell types and organs across flies and beyond 🪰🧬
Cool paper, congrats Jun!
Super excited to share my latest preprint with @klohmueller.bsky.social! Here we leverage the unique signature that recessive deleterious variants can lead to an increase in archaic ancestry to tackle a classic question - the dominance distribution on the human genome www.biorxiv.org/content/10.1...
Excited to share the first manuscript from my PhD in which we leveraged ultra-long Nanopore sequencing, D. melanogaster inbred lines, and a ton of manual validation to investigate the effects of long-read length on population-level structural variant (SV) calling accuracy! doi.org/10.1101/2025...
To my fellow #Drosophila colleagues & friends...
As you know @flybase.bsky.social has been under financial pressure due to #NIH cuts for several years.
With the threats Harvard is currently facing, supporting FlyBase is even more essential. If you have the means, make a tax-deductible donation.
Note that this approach uses public data and comparative annotation, but no new transcriptome data. New RNA-seq data for select key taxa is in the works but will take some time to complete.
A lot of folks have asked about gene annotations for the Drosophila genome data. @pankajd.bsky.social and @darrenobbard.bsky.social have something for you!
I know you like #Drosophila and I know you like #Genomes - but do you also like #Genes? Coding DNA annotation of 304 species of Drosophilidae! www.biorxiv.org/content/10.1...
Preprint alert: FlyCADD! 🧬
Excited to share FlyCADD: impact prediction tool scoring the functional impact of any single nucleotide variant across the entire Drosophila melanogaster genome, to distinguish causal from neutral SNPs
www.biorxiv.org/content/10.1...
Please share! In addition an important resource for improving human health, it will grow to be an incredible resource for science. E.g. we envision layering population genomic data across all species and connecting to other insect systems. There are so many cool questions to ask w/this kind of data.
How is functional variation at large-effect loci maintained in natural populations?
Thrilled to share our work showing how beneficial dominance reversal helps fruit flies maintain a resistance polymorphism as selection varies in their environment! A thread 🧵 1/n
www.biorxiv.org/content/10.1...
Hello Bluesky friends! I am a #newPI starting at UC Irvine in April, interested in gene regulation and functional genomics in stem cell models of development (esp neural crest). We are hiring at all levels – please reach out/spread the word! sskimlab.org
Ha, thank you! You might also be interested to know that these patterns are correlated with function too.
Much credit and thanks to all of the wonderful co-authors who make this kind of work possible!
We’re particularly excited this as a framework for connecting micro- to macro-evolution in this group. One early look at a fascinating result: a 2400 residue protein where polymorphism across ~30spp matches substitutions (neutral evolution) across ~30 million years. More soon!
We have more coming in the near future, including a comprehensive Drosophilidae Tree of Life integrating whole-genome data (pictured phylogeny) with classic markers (not shown), RNA-seq for annotation, and population genomic data for >100 species.
This effort is being managed as an open science, community resource. Data are on NCBI, containerized+Snakemake pipelines on GitHub, public protocols, and a 298-way Cactus alignment is available for download. Please see the preprint for more details on accessing these resources.
We are continuing our sequencing with the goal of hitting 1,000 drosophilid genomes by the end of next year. Please reach out if you are interested in collaborating on genomes: no cost to you and the only stipulation is open data.
We are ironing out some issues with shorter (~1kbp N50) ONT sequencing runs that might be related to the recent light issue.
This approach also worked surprisingly well for ethanol-preserved specimens, opening up older collections to genomic study and helping us add many esoteric taxa to the tree.
We’ve done lots of fresh collections of wild flies over the last couple years: across the Hawaiian Islands, the Western US (CA, OR, WA, MT, ID, CO), the Midwest (MI, OH), Europe (UK) and were able to assemble single-fly genomes for every species we collected.
The genomes are obviously more fragmented but surprisingly high quality in many/most cases: >1Mb N50, >QV40, 98-99% BUSCO, etc. Our benchmarking with D. mel suggests minimal benefit from Illumina polishing, but we do it sequence because it’s so cheap and convenient assembly QC.
One of the most underrated aspects of R10.4.1 chemistry is the 10-fold increase in sensitivity which has allowed us to prep libraries (5-10 kbp N50) with as little as 30 ng gDNA as input (e.g. the pictured sample)! I’m also sure we could go lower.
But with improvements brought to our hands by R10.4.1 and P2, we’ve been able to assemble Nanopore based hybrid genomes from single flies with no amplification, just a slightly modified LSK114 workflow. Cost is about $150 per fly at 40X ONT and 40X Illumina coverage.
Long-read sequencing is promising but protocols seem to require a lot more gDNA than can be obtained from a single fly, and while single-fly methods work they add logistical complexity, labor, and cost to the process - i.e. difficult to scale to thousands of species.
This means we’re missing out on large sections of interesting biodiversity, for example, the radiation of possibly up to 1,000 species on the Hawaiian Islands. doi.org/10.1093/molb...
