KamilSJaron.bsky.social

@kamilsjaron

Biodiversity genomics; reproduction; k-mers; Evolution of species with weird genomes; frequently featuring diptera and collembola; group leader at the Tree of Life, Wellcome Sanger Institute; dysorthographic

381 Siguiendo516 Seguidores162 Publicaciones

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KamilSJaron.bsky.social@kamilsjaron· 20d

Comparing genome evolution in beetles with flies (doi.org/10.64898/202...) and butterflies/moths (doi.org/10.1038/s415...). Showing 1. Beetles how much greater variation in rearrangement rates than either of the two orders featuring both ancient and recent rearrangement events.

Distinct patterns of chromosomal evolution across three major insect orders. (A) Cross-painting of ancestral elements among coleopteran ALGs, dipteran ALGs, and lepidopteran ALGs. Each coloured box represents an ancestral element, and each line represents an orthologous gene linking its assignments across orders. The thickness of the ribbons connecting elements is therefore proportional to the number of orthologous genes shared between them. Elements are coloured according to the coleopteran ALGs and the original descriptions of the lepidopteran Merian elements and dipteran ALGs. Sex-linked ancestral elements are indicated as CX, D6, and MZ. Elements are ordered from top to bottom as C1–C7 and CX for Coleoptera, D1–D6 for Diptera, and MZ followed by M1–M31 for Lepidoptera. (B) Temporal dynamics of chromosomal evolution (fusion and fission) in beetles, flies, and butterflies. For each species, cumulative trajectories are shown separately for fissions above zero and fusions below zero, from the origin of each order to the present. Rearrangement events occurring along branches between parent and descendant nodes were accumulated at the descendant nodes, and node ages were calibrated using published divergence-time estimates for major taxonomic groups. Ang. R, Angiosperm radiation; dotted lines, K-Pg boundary. (C) Characteristics of chromosomal rearrangements across the three insect orders. For each species, the total number of interchromosomal rearrangements, defined as the sum of fusion and fission events since the origin of each order to the present, is plotted against the intrachromosomal rearrangement index. Points are coloured according to the difference between the numbers of fissions and fusions, with positive values indicating a fission excess and negative values indicating a fusion excess. Marginal histograms show the distributions of interchromosomal and intrachromosomal rearrangements within each order.

KamilSJaron.bsky.social@kamilsjaron· 20d

Although the ancestral sex chromosome is very intact, it fairly frequently fuses to other chromosomes. We identified 50 CX-autosome fusions, meaning that beetles have even more frequent neo-X chromosome formation than flies. There is only a single case of true sex chromosome turnover.

Sex chromosome evolution in beetles. Phylogeny of beetles showing the occurrence of sex chromosome changes. The inner layers, including the tip extension lines, indicate taxonomic assignments across taxonomic ranks, from family, as shown by alternating shades of blue of the phylogeny tip extension lines, to superfamily, infraorder, and order in the outermost layer. The circular layers above it show (a) the type of sex chromosome changes if sex chromosomes are characterised, or “implied” if sex chromosomes are unknown, but the canonical beetle sex chromosome CX rearranged (b) X chromosome size, and (c) painting of the X (if known) or CX-associated (if implied) chromosomes using ALGs. The painting is at single-gene resolution, with each gene represented by an individual stacked line. For species with more than one X or CX-associated chromosome, the X chromosomes are separated by white space. Numbered black circles on the tree indicate sex chromosome transitions shared among multiple species of the same subgenus (3. Pterostichus), genus (1. Carabus; 2. Nebria; 4. Dorcus; 5. Euwallacea; 7. Cryptocephalus; 8. Longitarsus), two genera (9. Diorhabda + Galeruca), or a subfamily (6. Ceutorhynchinae). The beetles shown in the plot are representative examples of species with sex chromosome changes. Photo credits: Udo Schmidt, Lech Borowiec, Yves Bousquet, David Ignace, Guillaume Jacquemin, Ilya Zabaluev, Sang Woo Jung, David Crossley (UK Crown), and Damian F. Gomez.

KamilSJaron.bsky.social@kamilsjaron· 20d

We did tons of exploration of what drives the patterns of rearrangements. Identifying chromosome undergoing fusion to be more typically acrocentric, while fusion typically leading to metacentric... And of course, the ancestral X chromosome CX was a remarkable intact ancestral linkage group.

$Pattern of chromosomal rearrangements in beetles. (A) Predicted numbers of fission and fusion events per chromosome as a function of chromosome size. (B) Sizes of chromosomes involved in rearrangements compared with those of non-rearranged chromosomes. The number of BUSCO genes was used as a proxy to chromosome size. (C) Distribution of centromere positions among chromosomes that have recently undergone fission (dark blue) and all chromosomes (light blue). The x-axis indicates the relative position of the centromere along a chromosome, with 0.5 indicating a metacentric position. Recent fissions tend to produce acrocentric chromosomes. (D) Distribution of rearranged chromosome fragments according to the proportion of the parental chromosome retained in each fragment, decomposed by rearrangement history. The proportion of parental chromosomes retained was calculated as the number of BUSCO genes in each fragment divided by the number of BUSCO genes in its parental chromosome before rearrangement. Values close to 1 indicate that nearly the entire parental chromosome was retained, whereas lower values indicate that only a fraction of the parental chromosome was retained. Blue represents fragments generated by fission that were not subsequently involved in fusion, whereas salmon represents parental chromosome fragments involved in fusion. (E) Relationship between centromere positions among recently fused chromosomes and the ancestry division score (ADS). ADS is a measure of ALG separation by centromeres. A score of 0 indicates that distinct ALGs are completely separated by the centromere. This measure is plotted against the relative centromere position, showing that chromosomes in which different ancestries are almost perfectly separated following fusion are nearly always metacentric.$

KamilSJaron.bsky.social@kamilsjaron· 20d

We reconstructed ancestral linkage groups that were fairly consistent with previously defined Stevens elements, except we found 8, not 9, which seems to be due to rearrangement specific to Polyphaga. This rearrangement was not the only old rearrangement, beetles rearranged A LOT.

Ancestral linkage groups (ALGs) and chromosomal evolution in beetles. Linkage groups at internal nodes are simplified and visualised as coloured rectangles, with the colours showing the proportion of genes assigned to each ALG. Open circles indicate internal nodes at which a karyotype of 10 haploid chromosomes evolved independently from the nine polyphagan ALGs. On the right side: genome sizes (Gs), haploid chromosome numbers (Cn), gene order fragmentation index (FI) and intrachromosomal rearrangements (IaR) for each species. (B) ALGs. (C) Sankey plot of Adephaga and Polyphaga ALGs. Each ribbon is proportional to the number of genes shared among the chromosomes in the two ALG being compared, providing visual support for the inferred eight beetle ALGs (Fig. S12). Beetle images: 1, Dytiscidae; 2, Carabidae; 3, Scirtidae; 4, Dascillidae; 5, Buprestidae; 6, Elmidae; 7, Eucnemidae; 8, Lampyridae; 9–10 Elateridae; 11, Cantharidae; 12, Histeridae; 13, Hydrophilidae; 14, Lucanidae; 15, Geotrupidae; 16, Scarabaeidae; 17, Leiodidae; 18–20, Staphylinidae; 21, Dermestidae; 22, Bostrichidae; 23, Ptinidae; 24, Biphyllidae; 25, Cleridae; 26, Melyridae; 27, Bothrideridae; 28, Latridiidae; 29, Endomychidae; 30–31, Coccinellidae; 32, Ripiphoridae; 33, Scraptiidae; 34, Salpingidae; 35, Oedemeridae; 36, Pyrochroidae; 37, Anthicidae; 38, Meloidae; 39, Zopheridae; 40, Melandyridae; 41, Ciidae; 42, Tetratomidae; 43, Mycetophagidae; 44, Tenebrionidae; 45, Silvanidae; 46, Cucujidae; 47, Cryptophagidae; 48, Monotomidae; 49, Kateretidae; 50, Nitidulidae; 51, Anthribidae; 52, Attelabidae; 53, Apionidae; 54, Erirhinidae; 55–57, Curculionidae; 58, Cerambycidae; 59–62, Chrysomelidae: sagrine, eumolpine, Chrysomelinae, Galerucinae, respectively. Photo credits: Udo Schmidt and John Hallmén.

KamilSJaron.bsky.social@kamilsjaron· 20d

New preprint: 338 coleopteran genomes reveal exceptional rearrangement variation compared to other insect orders. Big congrats to @arf-mln.bsky.social, for getting this giant piece together. Big collaboration of @joanameier.bsky.social's and my groups. 🧵👇 doi.org/10.64898/202...

Phylogeny of 338 species with tips painted by the chromosomal ancestry of their contemporary genomes (well separated colours indicate only few changes, while blending indicates rearrangements). Colouring of the branches is by the number of rearrangements. The ring between paints and phylogeny indicates wether the chromosomal rearrangement was fusion dominated (brown) or fission dominated (teal) process.
Photo credits: Udo Schmidt, Lech Borowiec, JL Tachet, David Navrátil, Fred Chevaillot, Siga, Cosmin Manci, John Hallmén, Igor Souza-Gonçalves, Alex Hyde, H. Coiffait, David Ignace, Yves Bousquet.

KamilSJaron.bsky.social@kamilsjaron· Jun 19

Last chance to register for a Scalable genomics course this autumn! It will be a banger. With @katiejenike.bsky.social @richard-durbin.bsky.social @npmalfoy.bsky.social and @vikramshivakumar.bsky.social! coursesandconferences.wellcomeconnectingscience.org/event/scalab...

KamilSJaron.bsky.social@kamilsjaron· Jun 5

Ah, transparent background betrayed me.

KamilSJaron.bsky.social@kamilsjaron· Jun 5

One of my favourite small things that came out vary late during manuscript preparation is the sex chromosome evolution in Culicomorpha. It turns out there is an extreme diversity associated with (possibly recurnent) loss of ALG 6. Sex chromosomes are in boxes, chromosomes coloured by ancestry.

KamilSJaron.bsky.social@kamilsjaron· Jun 5

This ALG 6 turns out to be the ancestral sex chromosome. However, chromosomes corresponding to this linkage group are typically much much bigger than what remained on the Drosophila dot. Turns out that the◼️➡️▪️is specific for drosophilids!

KamilSJaron.bsky.social@kamilsjaron· Jun 5

One of the linkage group (ALG 6, in blue), is really tiny and gene poor compared to other chromosomes (in yellow).

KamilSJaron.bsky.social@kamilsjaron· Jun 5

So, this karyotype γ is corresponding quite well to Muller Elements. Except Muller elements are chromosomal arms, while karyotype γ is a set of metacetric chromosomes with well retained identities of the two chromosomal halves.

KamilSJaron.bsky.social@kamilsjaron· Jun 5

We found 6 ancestral LGs. Some dipteran lineages keep remarkably syntenic karyotype, such as St. Marks fly, Bibio marci, but there were several old rearrangements shared by many. Most notably, in the common ancestor of Brachycera ancestral linkages started to split in two (karyotype β)!

KamilSJaron.bsky.social@kamilsjaron· Jun 5

A big preprint from my group! Muller Elements are considered to be conserved in flies. We tested it by reconstructing the ancestral dipteran karyotype using 340 chromosomal genomes and suprise suprise, they're not... Led by @juliagries.bsky.social and Sam Ebdon. www.biorxiv.org/content/10.6... 🧵👇

Schema of three major chromosomal rearrangements leading to Muller Elements of Drosophila melanogaster since the common ancestor of Diptera.

KamilSJaron.bsky.social@kamilsjaron· Apr 24

We have a few spots left on our amazing #ScalableGenomics course. Perfect for anyone doing #genomics of many or difficult genomes, ideal for #PhD students, #postdocs or anyone else who would like to get hands-on experience. Register in the link below! tinyurl.com/scalableGeno... RT appreciated!

Invitation for our scalable genomics course 11 - 16 of October 2026

KamilSJaron.bsky.social@kamilsjaron· Mar 31

Do you plan to analyse lots of genomes? Or few that are large? One or multiple species? Join us for the course on analysing data at scale! (and yes, it will involve a lot of k-mers!). With @katiejenike.bsky.social and others... @sangerinstitute.bsky.social @connectingscience.bsky.social

https://coursesandconferences.wellcomeconnectingscience.org/event/scalable-genomics-and-pangenomics-20261011/

KamilSJaron.bsky.social@kamilsjaron· Jan 22

Last two weeks to apply for a senior faculty position at the Tree of Life. Great environment, amazing colleagues and the world's biggest genome engine... Come to join us at the Tree of Life @sangerinstitute.bsky.social sanger.wd103.myworkdayjobs.com/en-US/Wellco...

KamilSJaron.bsky.social@kamilsjaron· Nov 25

Forgot to add a showcase of the new version... Look at this beautiful polished visuals

Smudgeplot of tetraploid Saccharomyces data

KamilSJaron.bsky.social@kamilsjaron· Nov 18

Does anyone have a photo of Charles W. Metz by any chance? He originally isolated the Holo2 line of Bradysia coprophila we still use after more than 100 years after their original capture.

Photo of Bradysia coprophila by Sam Ebdon

KamilSJaron.bsky.social@kamilsjaron· Aug 24

Great, I like how ToS members took on our branding (look at the shirt and laptop stickers)

KamilSJaron.bsky.social@kamilsjaron· Aug 18

“More we study (germ line restricted chromosomes), less we know” — @fjruizruano.bsky.social quotes from #ESEB2025

KamilSJaron.bsky.social@kamilsjaron· Aug 18

Found it :)

KamilSJaron.bsky.social@kamilsjaron· Aug 16

We are excited to attending #ESB2025 find … @arf-mln.bsky.social to chat about beetle genomics @jamesimcc.bsky.social about sedges or springtails evolution Sam Ebdon about distr. of dominance Myself about diptera comparative genomics And all of us to chat about any whacky reproduction #obscuromics

A slightly outdated group photo of the obacuromics group, at the tree of life programme, Wellcome Sanger Institute - so you know spot us at ESEB

KamilSJaron.bsky.social@kamilsjaron· Jun 6

The k-mer workshop is over. In the Friday 3 hour hackathon, people really showed that you CAN learn k-mers in a week! It's been great. Thanks to all the co-teachers, @connectingscience.bsky.social organising team and all the participants!

KamilSJaron.bsky.social@kamilsjaron· Mar 6

5 days left to register for the #k-mer workshop! 🧬 I would strongly recommend for anyone doing large scale biodiversity genomics. tinyurl.com/register-for...

KamilSJaron.bsky.social@kamilsjaron· Feb 28

Last two weeks to register for the workshop on #k-mer s in biodiversity genomics 🧬💻! With @connectingscience.bsky.social @katiejenike.bsky.social @rayanchikhi.bsky.social and Gene Myers. coursesandconferences.wellcomeconnectingscience.org/event/k-mer-...

KamilSJaron.bsky.social@kamilsjaron· Feb 14

With @katiejenike.bsky.social and a bunch more of our fellow k-mer enthusiasts, we put together a manuscript on k-mers in biodiversity genomics. A guide if you will, that covers k-mers from basics to some really funky stuff... genome.cshlp.org/content/35/2...

KamilSJaron.bsky.social@kamilsjaron· Feb 1

We also did plenty of RNA-seq and found a very promising candidate (histone acetyltransferase Rtt109/CBP) that could be the key for understanding how these chromosomes cheat in male meiosis!

KamilSJaron.bsky.social@kamilsjaron· Feb 1

We sequenced single B individual with PacBio, no B and 3 B individuals with illumina - using some fun bioinformatics we got reliable set of scaffolds that were core / B / or to our suprise... shared.

Showing three different assignment critera of B-linked scaffolds. Based on B-specific k-mers, based on draft assemblies of individual datasets and based on expected coverage ratio, which is further shown on the last panel comparing single B line vs 3 Bs line.

KamilSJaron.bsky.social@kamilsjaron· Jan 31

🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!

https://coursesandconferences.wellcomeconnectingscience.org/event/k-mer-workshop-for-biodiversity-genomics-20250601/

KamilSJaron.bsky.social@kamilsjaron· Jan 13

Got it!