iiinova — where your digital self keeps evolving

Erich M. Schwarz @erichmschwarz.bsky.social · 03/08/2025

Thanks! I was recruited to this project in ~2015. I expected it to be very straightforward -- making a perfect isogenic copy of the N2 genome. I didn't expect to have an extra 2 Mb by 2019, and absolutely didn't expect getting all extra 6 Mb to take until 2025...

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Erich M. Schwarz @erichmschwarz.bsky.social · 03/08/2025

Good question! We don't know. Generally, my hope is that this new genome will motivate people to look at a lot of phenomena that were harder to study in the N2 genome assembly because it necessarily lacked that extra 6.0 Mb of difficult sequences.

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Erich M. Schwarz @erichmschwarz.bsky.social · 01/08/2025

After 10 years of work, a complete telomere-to-telomere gap-free genome for C. elegans finally exists: it has 106 Mb rather than the textbook 100.3 Mb, and up to 366 additional genes. genome.cshlp.org/content/35/8...

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Erich M. Schwarz @erichmschwarz.bsky.social · 05/02/2025

Protein categories we talk a great deal about in the paper: 1. A complex palette of possible immunomodulators -- some of whose genes transcriptionally upregulate when the worm encounters a functional host immune system. 2. Anticoagulants! Which are unfashionable, but were first seen in 1903.

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Erich M. Schwarz @erichmschwarz.bsky.social · 05/02/2025

Thanks! We do cite extracellular vesicles at one point, to explain a phenomenon that's been known for many years but not discussed much: in our data, and in several other parasitic nematodes, roughly one-third of excreted/secreted proteins lack N-term signals.

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Erich M. Schwarz @erichmschwarz.bsky.social · 05/02/2025

This is the first time in my life where I wrote a paper, found out that I couldn't preprint or publish that paper until I got a provisional patent application filed, and spent one year fighting in all directions to indeed get it filed. While the paper sat on my desk. Never again, I hope.

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Erich M. Schwarz @erichmschwarz.bsky.social · 05/02/2025

Finally got this preprinted: "...immunoregulation was observed primarily in mature adult hookworm intestine directly exposed to host blood; it may include hookworm genes activated in response to the host immune system in order to neutralize the host immune system." www.biorxiv.org/content/10.1...

biorxiv.org

Hookworm genes encoding intestinal excreted-secreted proteins are transcriptionally upregulated in response to the host’s immune system

Hookworms are intestinal parasitic nematodes that chronically infect ∼500 million people, with reinfection common even after clearance by drugs. How infecting hookworms successfully overcome host prot...

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Reposted by Erich M. Schwarz

Erin Young @erinyoung.bsky.social · 19/12/2024

I just realized there was a new canu release, and its the last one: """ Goodbye. Do not expect another release. This is it, folks. The sequencing technology has moved on and Canu is all but obsolete now. Thanks for all the feedback, citations and bug reports. """ 🧬🖥️🦠

github.com

Release Canu v2.3 · marbl/canu

These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...

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Erich M. Schwarz @erichmschwarz.bsky.social · 20/12/2024

"...self-fertility not only required mutations that activated the spermatogenesis program in XX germ lines, but prior to these there must have been mutations that decanalized the sex-determination process, allowing for subsequent changes to germ cell fates." academic.oup.com/genetics/adv...

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Erich M. Schwarz @erichmschwarz.bsky.social · 17/12/2024

"...active development of WormBase ParaSite is temporarily on hold, due to a break in funding, and are currently unable to load new datasets." Not good news for anybody analyzing any worm genome, outside of a small set of C. elegans-adjacent nematode species. wbparasite.wordpress.com/2024/12/12/t...

wbparasite.wordpress.com

Temporary break in service

We are sorry to announce that active development of WormBase ParaSite is temporarily on hold, due to a break in funding, and are currently unable to load new datasets. We remain committed to our go…

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Erich M. Schwarz @erichmschwarz.bsky.social · 11/12/2024

Yes. The preprint is an exact copy of what we're submitting to a journal for publication, so, the text you see ("this genome is already available") is what we hope will be in print not *too* many months from now... We'll definitely make the data files go live before then!

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Erich M. Schwarz @erichmschwarz.bsky.social · 10/12/2024

That being said, if not having immediate access is going to cost you an R01 application or something, e-mail me at ems394@cornell.edu, and I'll try to get you immediate help!

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Erich M. Schwarz @erichmschwarz.bsky.social · 10/12/2024

WormBase has been given a heads-up on this and they are thinking through their strategy for how to do a migration, which as you can imagine will not be trivial. What they may do is build up CGC1 on their site incrementally, then migrate. OSF.io files will be available ASAP, though.

osf.io

OSF

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Erich M. Schwarz @erichmschwarz.bsky.social · 10/12/2024

At the request of my coauthors, I've held off on making the assembly publicly available (one of them was burned in the past by sharing data plus Reviewer Number Three feeling no urgency to stop acting out). But as soon as all authors feel OK, all files will be posted to osf.io for immediate use.

osf.io

OSF

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Erich M. Schwarz @erichmschwarz.bsky.social · 06/12/2024

After 5 years, our team has a new telomere-to-telomere gap-free reference genome for C. elegans. We published our first results in 2019; I thought we'd have our loose ends wrapped up by spring 2020. That prediction was ... slightly off. But here's the genome now! www.biorxiv.org/content/10.1...

biorxiv.org

CGC1, a new reference genome for Caenorhabditis elegans

The original 100.3 Mb reference genome for Caenorhabditis elegans , generated from the wild-type laboratory strain N2, has been crucial for analysis of C. elegans since 1998 and has been considered co...

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