Avril Harder

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome Summary · Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biod...

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

Another hit from @alabamarivers.bsky.social and Southern Exposure

A two-panel Scooby-Doo meme. In the top panel, Fred pulls the mask off a villain labeled “Presence-absence-variation in plant genomes.” In the bottom panel, the unmasked villain is revealed to be “Annotation artifacts.”

🌿Plant pangenomes🌿 have a LOT of genomic presence-absence-variation.

Or do they???

A new @jgi.doe.gov preprint by @tomasbruna.bsky.social @jotlovell.bsky.social @avril-m-harder.bsky.social Avinash Sreedasyam takes a closer look

www.biorxiv.org/content/10.1...

'Hoods are out!!! Big thank you to @plantevolution.bsky.social for the support throughout. Luisa, @kdm9.bsky.social , @aconga.bsky.social , @hajkdrost.bsky.social it was intellectually stimulating ride with you, so congratulations!!!! #diversity #NLR #immune #pan-genome #graphs #networktheory

my new idea is to look at runs of homozygosity (ROH) only for mutations that are restricted to heterozygous state in other pops, suggesting they are low freq. and enriched for deleterious stuff. a good measure of inbreeding. I call my new statistic

This began as a @jgi.doe.gov Community Science Program (CSP) project in 2017 with the goal of uniting the diverse sorghum breeding and mapping populations in the framework of a 'pangenome'.

Thanks to a huge efforts across many stakeholders, the article was preprinted today. A 🧵 w/ what we found:

🚨 We're looking for a #postdoc to join our team at the Center for Bioenergy Innovation at Oak Ridge National Labs, TN 🚨

Project: Advance poplar bioenergy by understanding adaptive trait/genomic variation — breeding/pop gen/bioinformatics

Apply by 18-Aug

Apply here: jobs.ornl.gov/job/Oak-Ridg...

Fig. 3 | DEEPSPACE synteny map highlighting positions of centromeric repeats. Collinear blocks between the same chromosomes are shown as transparent ‘braids’ and chromosome segments are visualized as color-gradient rectangles along an x-axis that scales each genome by its physical size. Regions that do not map between chromosomes are visualized as black ‘wedges’ in the map. These can be due to ineffective unique mapping in highly repetitive centromeres (e.g. Chr 9 IM62-IM767), expansion of centromeric arrays (e.g. Chr 11 IM62-IM767) or sequence presence/absence. The orange-blue color gradient indicates regions that are gene-rich (blue) or centromeres (orange); fully saturated colors indicate that all sequence in those intervals is masked by that annotation type. White regions have neither genes nor Cent728 repeats, and are likely repeat-rich pericentromeres.

Fig. 4 | Exploration of the pan-genome graph. A 2.34-2.37Mb on chromosome 1 is a complex region in the genome that illustrates how the pan-genome graph handles large scale presence594 absence variation. Here, any variants smaller than 52bp are excluded so that the large insertion deletions in this region are apparent. Haplotypes containing similar sequences are binned in the transparent rounded rectangles (“nodes”), divergent but syntenic/orthologous sequences have stacked nodes, and deleted sequences show the path outside of a node. B The first exon and the first 28bp of the first intron of a gene with family members across all four genomes is shown as an example of how SNPs and INDELs appear at the base pair level in a sequence graph. C The positions of aligned sequence retained in the graph (colored following the tubes in panels A-B) and that which is un-alignable and clipped (black) are presented in a pan-genome anchored by IM62.

Ok, fine I'm willing to admit it now: Mimulus is interesting www.authorea.com/doi/full/10....

That time in 2013 when this crabeater seal decided to see what this noisy orange menace was doing in its territory....In 2013 near Peter I Island in #Antarctica on our research cruise (LMG 13-12). Bonus (the 'wait for it' at the end): amazing sunset/sunrise around 1am that night :) 🧪🌎🦑🐧🇦🇶

I remember this like it was yesterday 😄

Such a cool talk on a sweet system! Looking forward to seeing what else you find 🦎

Wow, the cover looks great!
Nice work Patrice and @roederlab.bsky.social

The GENESPACE plot uses our new @jgi.doe.gov Pennycress and Brassica rapa genomes built in collaboration with @spicybotrytis.bsky.social & Katie Greenham, hosted on phytozome

PG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers Motivation Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graph quality rely primarily on technical parameters (...

Clever new BUSCO-like method to evaluate the quality of pangenome graphs www.biorxiv.org/content/10.1...

Diversification of large-effect loci in a duplicated genomic region leads to complex phenotypes Whole genome duplication provides evolutionary opportunities to increase biological complexity and phenotypic diversity by selective retention of duplicated genes. We identify a small genomic region a...

Quick break from the doom and gloom for science! We're really proud of this one. We found that two major effect loci on duplicated versions of the same ancestral chromosome play a major role in run timing diversity across four species of salmon (pink, chum, sockeye, coho) shorturl.at/GISX2

GitHub - yangao07/longcallD: A local-haplotagging-based small and structural variant caller A local-haplotagging-based small and structural variant caller - yangao07/longcallD

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/lon...

Post a warning.

"Our results reveal substantial differences between pipelines, with many inversions either misrepresented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches."

Our paper on the past, present, and genomics-enabled future of American chestnut (Castanea dentata) tree breeding for resistance to invasive pathogens is on BioRxiv.

🧵with some background and a few things we found 👇 bsky.app/profile/bior...

VG logo

A new version of our variation graphs (vg) tool, "Boccaleone," is now available! Updates include:
🔵 HiFi and Oxford Nanopore read support to the Giraffe read mapper
🔵 Faster read sorting
🔵 New Unix manual page
Link: github.com/vgteam/vg/re...

Welcome to Day 2 of #PAG32 | #PAG2025. Today's cant miss session is Comparative Genomics hosted by Vijay Tiwari and John Lovell. It is 10:30 - 12:40 in Pacific A. pag.confex.com/pag/32/meeti...

Are you headed to #PAG32 and interested in plant reproduction? 🌼 Come check out my talk in the “Sex Chromosomes and Sex Determination” session on Saturday!

I’ll be talking about ancient ZW sex chromosomes, the impact of polyploidy on sexual system evolution, “leaky” dioecy, and much more.

A) Summary of Camelina sativa progenitors and allopolyploid formation. B) Synteny between Arabidopsis thaliana and the three Camelina sativa subgenomes

What's better than one polyploid genome? Twelve polyploid genomes! We report a pangenome of the hexaploid oilseed crop Camelina sativa and investigate pangenomic variation and genome evolution in a complex allopolyploid genome. www.biorxiv.org/content/10.1...

Comparative genomics plot of sugarcane

Our groups' goal is to produce genomes that are useful; this does not always mean 'telomere-to-telomere' assemblies. The hybrid sugarcane genome is a nice example of this. The article is out this week in Nature: www.nature.com/articles/s41...

GenotypeGVCFs and the death of the dot If you have been keeping up with our GATK release notes, then you know that we have been rolling out a number of backend changes, tools, and features to GATK that we are hoping will improve the eff...

@ksamuk.bsky.social pointed this out on the other site, but I don't see much discussion here.

GATK will now encode missing genotypes as "0/0", or homozygous ref, instead of "./." in VCF files. To identify sites with missing data, you'll have to check the DP field.

HudsonAlpha - Staff Scientist - Genome Sequencing Center - Huntsville, AL Position: STAFF-SCIENTIST: Evolutionary gen

🚨We're hiring🚨

We are looking for a scientist to bridge the gap between genomics and breeding, focusing on traditionally under-invested crops and regions. It's physically located at Colorado State University in beautiful Ft. Collins, CO.

Pls share!
hudsonalpha.applicantpro.com/jobs/3211389

A new study shows that flowers have evolved over the past three decades to have less sex—potentially in response to the disappearance of bees. It could be a death spiral for some species. Here’s my story. 🧪 Gift link: www.nytimes.com/2024/01/04/s...