Sub-thread 5: Like prokaryotes, ONT long reads facilitate far enhanced recovery of marine vMAGs. Some marine Crassvirales clades are low-GC and present from Antarctica to the GBR, some appear to be higher GC and more warm adapted.

bsky.app/profile/stev...

At the same time, many of the GBR reps fall into a separate sub-clade characterized by much higher GC than the rest of the Crassvirales (~44% GC). This is actually quite interesting as, given genome streamlining theory and reefs being quite low-nutirent environments, I would have expected...

So now that we have some Crassvirales from coral reefs, where do they place? Piedade identified 4 marine clades, C1-C4. All from the GBR fell into a single large marine-only clade that coalesces the Piedade C1 and C2 clades and contains both Antarctic and tropical coral reef reps (panel 4B above).

Secondly, a lot about this paper refers back to GC bias. Most Crassvirales have low GC (~35%), so Illumina would strongly bias against them. Their abundance in Illumina data is surely lower than their actual abundance (refer to discussion of GC/pMAG recovery). This will apply to all low-GC microbes.

So we moved forward with our true Crassvirales contigs, made sure they had all the right Crassvirales core genes, and had a look at their taxonomy, incorporating several recently published Antarctic marine sequences from @goncalopiedade.bsky.social et al (2024).

pmc.ncbi.nlm.nih.gov/articles/PMC...

We started out with 312 contigs >20kb classified by geNomad as putative Crassvirales (cool!), but once we placed them into a TerL tree we realized that 93% of them were actually Pachyviridae and Pervagoviridae, completely different order than the Crassvirales.

In recovering vMAGs from the GBR-MGD, we noticed firstly that viral classification is really hard, but also that what we could classify was often labeled as marine Crassvirales. Non-gut Crassvirales were known to exist already, but are criminally understudied nonetheless. So we looked into ours! A 🧵

I’ve written threads about the GBR-MGDs pMAGs, but it also contains viruses (vMAGs), including a monophyletic clade of marine Crassvirales, chromosome-level eukaryote eMAGs, and putative plasmids. We wanted a holistic DB.

One problem: some key software appear to break with long reads. A 🦠 🧵.

Considering the massive benefit using Nanopore provided for building the GBR-MGD—HQ/complete Pelagibacter, SAR86, Prochlorococcus, etc pMAGs+ chromosome-level picoeukaryote eMAGs + HQ Crassvirales vMAGs—seems fitting to share this preprint during London Calling.

@nanoporetech.com #nanoporeconf

We found new #Crassvirales clades on #Antarctica (prospective families): @goncalopiedade.bsky.social's new paper on the viruses in Antarctic waters is out! Check out the manuscript (www.nature.com/articles/s41...) and Gonçalo's "Behind the Paper": communities.springernature.com/posts/unveil...