Alejandro Manzano Marín

Leeches are so cool! 🤩 We had a special speaker today at @i2sysbio.es , Alejandro Manzano Marin @amanzanom.bsky.social . I have known him since my PhD and I'm really amazed by his research line about symbionts of leeches
#symbiosis #microsky

... or, maybe the transcriptional slippage correction is already a feature that is found early in these pseudogenisation process and they just end up getting fixed at the long term in x or y genes (maybe related to expression levels, as some of these are very "essential" genes)....

Several/Many of these HP-tract-containing genes have evolved repeatedly in independent lineages. So, I immediately wondered whether or not these pop out in your dataset. Maybe there is some specific tolerance for HP tracts and bias of correction at the transcription level in those genes...

While the first category I have commonly analysed more in small to tiny genomes, the second category I have commonly found also in "early" endosymbionts. Anyways, things that popped into my mind checking out your paper. I'm really into pseudogenes..... and your dataset is pretty cool

Also, I imagine another fraction might be those that have recorded homologues that can function in large to severely truncated forms (e.g. doi.org/10.1038/srep...). This paper includes just some of them, but I keep an extensive collection of these references in my Zotero library (I can share it...).

I especially wondered this in light of the very few proteins you detect from genes classified as pseudogenes. I imagine a fraction of these are homopolymeric frameshifted ones. You should be able to easily pinpoint them by identifying transcripts where the frameshift is corrected (transcr. slippage)

Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts | PNAS Among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smalle...

Sorry, copied it wrong
doi.org/10.1073/pnas...

Very cool work! I wonder though, as (I think) it is not mentioned in the paper: Do pseudogenes with polyA/T/etc tracts end up more commonly transcribed and/or translated? Thinking about 👇🏼

doi.org/10.1073/pnas... &
doi.org/10.1093/molb...

Does this start early or is is a late-symbiont thing only...

Regardless from the cut-offs, which can be affected by the amount of applications and the percentage of reviewers that are aware that if they want a certain grant funded, they should provide a (nearly) perfect score, let's not forget that those ridiculous comments come from fellow "scientists" 🫠

Yba3 (sorry, SyeA) was one of those enigmatic Buchnera proteins: (almost) always there, but who knows what it did.... Now we know! SyeA is "secreted and homologous to secreted effectors of bacterial pathogens AND is essential for Buchnera transmission"!

Really cool work!

(image: Ext. Data Fig 2.)

This is a really cool study on one of my favourite obligate symbiotic systems: Aphid + Buchnera by @jerrymaeda.bsky.social, @nancy-moran.bsky.social, & co.

A secreted #endosymbiont protein (SyeA, formally Yba3) essential for colonizing host cells

doi.org/10.1101/2025...

#SymbioSky

Calling all OrthoFinder users!

We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.

GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...

(1/10)

Announcing our next #NSFfunded workshop on "Telling Stories Through Data", co-lead by myself + @vgwschutte.bsky.social! It’s half bioinformatics data viz & half #SciComm - this year’s focus is host-associated microbiome datasets. Apply here to join us (form closes 1/10) bit.ly/TSTD2026 #symbiosky

ChromoMapper: a new tool to quickly compare large genome assemblies. #GenomeAssembly #GenomeComparison #Bioinformatics #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...

.... of course, it would not be entirely "me" if I missed the "symbiont part", which is certainly under work and you can expect some cool (in my not-so-humble opinion) work to see the light of day soon.... #SymbioSky

This specific #leech was collected in Vienna, where it should not naturally occur, likely representing an historical introduction into an artificial pond. This so-called "medicinal" leech was erroneously treated for a long time as H. medicinalis, but now is one of several recognised European species

After a long(ish) while, the reference genome for the #leech #Hirudo verbana is officially out!

doi.org/10.12688/ope...

w/@ergabiodiv.bsky.social, @biogeneurope.bsky.social, @leibnizlib.bsky.social, & @sangerinstitute.bsky.social

@dome-vienna.bsky.social, @cemess.bsky.social, @univie.ac.at

1/3..

#TEsky #ViroSky #VirEvol

Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids Abstract. Gene duplication and transposable elements (TEs) are major drivers of genomic innovation that can fuel adaptation. While the roles of duplication

Olvera-Vazquez, @cornilleamand.bsky.social et al. analyzed olfactory and gustatory receptor genes in 12 aphid genomes with varying host plant ranges. Aphid lineages with broader host ranges exhibited higher evolutionary rates.

🔗 doi.org/10.1093/molbev/msaf238

#evobio #molbio

Last week we wrapped up the first edition of the Virus evolution and ecology course under the umbrella of the brand new Master in Microbiome Science offered @univie.ac.at. We learned about viruses, their evolution, and their ecological impact across different ecosystems. 1/2

#VirEvol

It’s exciting to see converging evidence across systems! 😀
Alongside the new work on gutless worms, our study shows that organosulfur cycling is also essential in lucinid holobionts. Lucinid host provides DMSP to its symbionts, sulphur-oxidising Thiodiazotropha and, a new member, Endozoicomonas.

Don’t say that! Every academic will start putting it on their CVs. 🤣

We have #leech #cocoons!

The hard work of @pegah-kalatehjari.bsky.social already paying off. Soon to come, baby leeches @dome-vienna.bsky.social

@fwf-at.bsky.social @univie.ac.at

Yes! mites overall are cool. And certainly quite crazy mitochondrial genomes (like those split ones!)

mmmmmm tRNAs....

Really cool #review

Natural and artificial variations of the standard #geneticCode

Of course with mention of #endosymbiont lineages

doi.org/10.1016/j.cu...

There is also the case of the A. vulgare mt-genome, where many tRNAs are overlapping mRNAs, and I suspect some missing ones might actually be there, overlapping... they also fix tRNAs missing large parts of the main structure 🤯. Mitochondria are crazy, tRNAs are cool... Really into tRNAs these days

I wonder how many evolved from a single ancestral tRNA locus... Not sure if there are enough mt-genomes from mites to figure it out..... I like the term mirror tRNA, sounds like from a 90's sci-fi series...

Cool. Reminds me of mite mitochondrial genomes which also have some loco tRNAs (coded in two different pieces, lacking arms) and also largely overlapping reduced ones, sometimes in the same sense. Proper annotations of many of these are missing (Maybe not too hard to figure out bioinformatically..)

Acquisition of Spacers from Foreign Prokaryotic Genomes by CRISPR-Cas Systems in Natural Environments Abstract. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems of bacteria and archaea provide immunities

We are excited to share @probstlab.bsky.social's latest publication on the diversity of CRISPR-Cas spacers, led by @katharinasures.bsky.social !! 🧬

Have a read!! ➡️ doi.org/10.1093/gbe/...

@emilruff.bsky.social @alexjaffe.bsky.social @geomicrosoares.bsky.social & others not in Bluesky!