Alejandro Manzano Marín
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amanzanom.bsky.social
Alejandro Manzano Marín
@amanzanom.bsky.social
1.9K followers 460 following 300 posts
Senior Scientist 👨🏽‍🔬 @dome-vienna.bsky.social, @univie.ac.at
🇲🇽🇪🇺(🇦🇹🇫🇷🇪🇸) Symbionts, bacteria, insects, leeches, viruses, bioinformatics, evolution, genomics. Opinions are my very own.

#SymbioSky

https://besymblab.univie.ac.at/
https://ecoevo.social/@amanzanom
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amanzanom.bsky.social
Alejandro Manzano Marín @amanzanom.bsky.social · Jan 13
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..
amanzanom.bsky.social
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
January 30, 2026 at 11:28 AM
Reposted by Alejandro Manzano Marín
lauriebelch.bsky.social
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)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Reposted by Alejandro Manzano Marín
hollybik.bsky.social
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
December 17, 2025 at 3:10 PM
Reposted by Alejandro Manzano Marín
jsantoyo.bsky.social
ChromoMapper: a new tool to quickly compare large genome assemblies. #GenomeAssembly #GenomeComparison #Bioinformatics #Genomics @bioinfoadv.bsky.social 🧪🧬 🖥️
academic.oup.com/bioinformati...
January 17, 2026 at 11:49 AM
amanzanom.bsky.social
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..
January 13, 2026 at 8:40 PM
Reposted by Alejandro Manzano Marín
ameliacervera.bsky.social
#TEsky #ViroSky #VirEvol
embojournal.org The EMBO Journal @embojournal.org · Jun 6
REFEREE 1: “I conclude with a simple, direct statement - this is the best paper I have read all year!”
#TransparentPeerReview

Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses
@juliusbrennecke.bsky.social et al

www.embopress.org/doi/full/10....
January 2, 2026 at 2:19 PM
Reposted by Alejandro Manzano Marín
molbioevol.bsky.social
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
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
doi.org
December 12, 2025 at 11:55 AM
Reposted by Alejandro Manzano Marín
willemsenanouk.bsky.social
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
December 10, 2025 at 11:06 AM
Reposted by Alejandro Manzano Marín
martasu.bsky.social
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.
December 8, 2025 at 9:31 AM
Reposted by Alejandro Manzano Marín
richardsever.bsky.social
Don’t say that! Every academic will start putting it on their CVs. 🤣
anaisbailles.bsky.social Anaïs Bailles @anaisbailles.bsky.social · Dec 4
And, do we even care about IQ? It is like the Impact Factor of intelligence...
December 5, 2025 at 12:29 PM
amanzanom.bsky.social
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
November 27, 2025 at 10:27 AM
amanzanom.bsky.social
Really cool #review

Natural and artificial variations of the standard #geneticCode

Of course with mention of #endosymbiont lineages

doi.org/10.1016/j.cu...
November 21, 2025 at 10:37 AM
Reposted by Alejandro Manzano Marín
probstlab.bsky.social
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!
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
doi.org
November 17, 2025 at 12:09 PM
Reposted by Alejandro Manzano Marín
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Alejandro Manzano Marín
danbrockington.bsky.social
Profits from scientific publishing are eye-watering, costing us billions. In ‘The Drain of Scientific Publishing’ (arxiv.org/abs/2511.04820), (building on ‘The Strain of Scientific Publishing’ doi.org/10.1162/qss_a_00327) we show how it is harmful – and unnecessary.
The Drain of Scientific Publishing
The domination of scientific publishing in the Global North by major commercial publishers is harmful to science. We need the most powerful members of the research community, funders, governments and ...
arxiv.org
November 12, 2025 at 11:41 AM
Reposted by Alejandro Manzano Marín
sullivan-lab.bsky.social
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)

vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.

🔗 Read the preprint: doi.org/10.1101/2025...

Improvements details below 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
amanzanom.bsky.social
.... 2nd work

2) Parallel #evolution of #Bacteroidota as Long-Term #endosymbionts of #insects

by Jinyeong Choi, Cong Liu, Pradeep Palanichamy, Yumiko Masukagami, Hirotaka Tanaka, Takumasa Kondo, Matthew E. Gruwell, @filiphusnik.bsky.social

doi.org/10.1101/2025...

#SymbioSky @oistedu.bsky.social
Parallel Evolution of Bacteroidota as Long-Term Endosymbionts of Insects
Symbiotic relationships transform diverse aspects of both symbiont and host biology. The most visible changes include a massive reduction of the endosymbiont genome and the development of novel host o...
doi.org
November 5, 2025 at 9:39 AM
amanzanom.bsky.social
Two great works by @filiphusnik.bsky.social group @oistedu.bsky.social on scale insect's #symbioses.

1) Genomic diversity and functional potential of facultative bacterial #symbionts across #scaleInsects

by Pradeep Palanichamy, Jinyeong Choi, Arno Hagenbeek

doi.org/10.1101/2025...

#SymbioSky
Genomic diversity and functional potential of facultative bacterial symbionts across scale insects
Microbial symbionts play pivotal roles in the physiology, ecology, and evolution of insects. While obligate symbionts have been extensively characterized in insects feeding on nutritionally poor diets...
doi.org
November 5, 2025 at 9:34 AM
Reposted by Alejandro Manzano Marín
chaintist.bsky.social
Had to draw a cartoon for this fascinating finding!
Defensive fungal symbiosis on insect hindlegs: www.science.org/doi/10.1126/...
#SymbioSky
A cartoon/ digital drawing summarising the findings of the paper "Defensive fungal symbiosis on insect hindlegs" by T. Nishino et al published in 2025. On the top left, a female Megymenum gracilicorne bug shows off symbiotic organs on the hind legs where she carries Ascomycota fungi. These were previously assumed to be Tympanal organs in these bugs but only females had them?; that didnt make a whole lot of sense to the authors...To the right of the bug is a row of eggs lying side by side. The paper shows that the bugs deposit the symbiotic fungi on the egg surface after egg-laying. Next on the image, fungal conidia grow on the egg surface. The eggs are pinkish in colour. A few fungi wear sunglasses like they are body guards. The paper shows that they protect the eggs from Trissolcus brevinotaulus, a parasitoid wasp, that likes to lay its eggs inside the developing bug's eggs. There are two wasps in this cartoon "eyeing" the fungi and looking frustrated. Eggs turn from whitish to pinkish within 10-days because they are reflecting the body colour of the nymph within the eggs.
November 1, 2025 at 4:59 PM
Reposted by Alejandro Manzano Marín
hansonmark.bsky.social
PhD studentship for interested chinese nationals funded by the China Scholarship Council!

Come work with us to investigate how innate immunity works in an important agricultural pest, and disentangle how the immune system evolves. 🇬🇧🇨🇳

For more info, see: bit.ly/4ntrsEe
#Drosophila #Aphid #Immunity
An advertisement for a PhD doing aphid immunity work
October 28, 2025 at 1:44 PM
Reposted by Alejandro Manzano Marín
jsantoyo.bsky.social
Commentary: a review of technical considerations for planning an RNA-Sequencing experiment. #RNAseq #TechnicalConsidertions #ExperimentDesign #LibraryPrep #DataAnalysis #BMCgenomics 🧪🧬 🖥️
bmcgenomics.biomedcentral.com/articles/10....
October 27, 2025 at 3:31 PM
amanzanom.bsky.social
The Endosymbiont consortia of two #Cixiidae #Planthoppers reveal an ancient #Symbiosis with ‘Candidatus #Mirabilia symbiotica’

#SymbioSky

doi.org/10.1111/1758...
The Endosymbiont Consortia of Two Cixiidae Planthoppers Reveal an Ancient Symbiosis With ‘Candidatus Mirabilia Symbiotica’
Many insects harbour ancient beneficial endosymbionts that produce essential nutrients. Two planthopper species from the Cixiidae family harbour different tripartite endosymbiont consortia, including...
doi.org
October 16, 2025 at 12:43 PM
Reposted by Alejandro Manzano Marín
meehubs.bsky.social
We’re back! ✨ The next #MeeHubs26 is coming with 7 hubs across the globe and incredible lineups at each. Can’t wait to share more soon! meehubs.org
Home
meehubs.org
October 7, 2025 at 2:30 PM
Reposted by Alejandro Manzano Marín
rodai.bsky.social
Viral AlphaFold Database (VAD) is live in Science Advances

~27,000 predicted viral protein monomers & homodimers

Conserved folds across bacteria, archaea & eukaryotic viruses

New toxin–antitoxin system KreTA uncovered

Vast “functional darkness” remains uncharted

www.science.org/doi/10.1126/...
The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes
VAD is a Viral AlphaFold Database of protein monomers and homodimers from viruses infecting hosts across the tree of life.
www.science.org
October 2, 2025 at 8:48 AM
Reposted by Alejandro Manzano Marín
jack-tamisiea.bsky.social
437 million years ago in what is now Wisconsin, the earliest known leeches were terrorizing trilobites. Instead of sucking blood, these critters were likely engulfing invertebrates whole or vacuuming out their insides!

Latest for @nytimes.com on a fantastic #fossil: www.nytimes.com/2025/10/01/s...
This Leech Had an Appetite for Something Other Than Blood
www.nytimes.com
October 1, 2025 at 8:00 PM