Amjad Khalaf 🇵🇸

New preprint! We unexpectedly discovered that some Caenorhabditis species delete parts of their somatic genome early in development, which fragments their chromosomes and eliminates key germline genes. Multiple lines of evidence suggest this bizarre process was present in the ancestors of C. elegans

Amjad Khalaf follows the symbiosis genomics session at #biodiversity25 presenting about #microsporidia tetraploid genomes. Most of them are recent autotetraploids. An interesting model of reproduction is proposed with two different paths: sexual and asexual reproduction.

Oh hello! He's only gone and re-written the Microsporidian reproductive tree and published it in @plosbiology.org!

Heroic effort, Amjad. Congrats to all the authors!

You can read about Amjad and his doctoral research in the blog I wrote all about him: sangerinstitute.blog/2025/07/29/s...

Top: Prevalence of Microsporidia in DToL insect genomes. Microsporidian genomes recovered from insect hosts, split by taxonomic order. F: female, M: male, U: unspecified sex. Bottom: Simplified proposed generalized lifecycle for Microsporidia. This proposed model posits that each nucleus is a diploid, and that microsporidian reproduction mirrors reproduction in Fungi with stages similar to karyogamy, plasmogamy, and a stable “heterokaryon” (known as a diplokaryon in Microsporidia). Importantly, both the diplokaryotic and monokaryotic phases are parasitic, and species may spend most of their lifecycle in one or the other phase, giving rise to “diploid” and “tetraploid” lineages.

#Microsporidia are #parasites of growing importance. @amjadkhalaf.bsky.social @mblaxter.bsky.social @marakat.bsky.social &co present 40 new genomes from #DarwinTreeofLife sequencing of their arthropod hosts, revealing insights into #tetraploidy & #reproduction @plosbiology.org 🧪 plos.io/48HsAQJ

Really, really happy that our work on microsporidian genomes is now out in @plosbiology.org! A huge thank you to my coauthors, my supervisors @mblaxter.bsky.social & @marakat.bsky.social, the editors @roliroberts.bsky.social & Joseph Heitman, and the reviewers ❤️ plos.io/48HsAQJ

Retrocopy formation and domestication shape genome evolution in sloths and other xenarthrans Xenarthrans, comprising sloths, anteaters, and armadillos, represent one of the most morphologically and physiologically specialised mammalian clades, yet the genomic basis of their adaptations remain...

Preprint Alert! 🦥
We produced complete genomes for 2 Xenarthra and placed them in a mammalian comparative framework. We found that Xenarthra harbour the largest number of retrocopies in mammals! www.biorxiv.org/content/10.1...

Image shows Amjad Khalaf sitting on a bench outside, working on his laptop.

Meet Amjad Khalaf – who has spent his PhD panning for parasite DNA, allowing him to create a goldmine of information for the research community🔎

Amjad shares what first brought him to the Sanger Institute, his research and what he is dreaming about next:
sangerinstitute.blog/2025/07/29/s...

it's really an honour to be interviewed by the wonderful @carmcdhume.bsky.social -- a huge thank you! ❤️🫂

it was so so lovely to do this together! 🇭🇷❤️🇵🇸

If you’re curious about Microsporidia, polyploidy, or assembling cobionts from non-target organisms — please check out our preprint! A HUGE thank you to my wonderful coauthors, and my supervisors @mblaxter.bsky.social and @marakat.bsky.social

The tetraploid genomes that we see are consistent with autopolyploidy, not allopolyploidy. While we’re unable to place the timing of polyploidisation events in Microsporidia, we propose that tetraploidy is a shared & ancient event in the group, with diploid lineages representing “reduced” forms.

Using the Hi-C data, we find that a tetraploid microsporidian genome is organised into two diploid compartments, likely the two nuclei in a diplokaryon. We also see evidence of recombination both within and between the two compartments - providing evidence for a sexual cycle in Microsporidia.

Forty New Genomes Shed Light on Sexual Reproduction and the Origin of Tetraploidy in Microsporidia Microsporidia are single-celled, obligately intracellular parasites with growing public health, agricultural, and economic importance. Despite this, Microsporidia remain relatively enigmatic, with man...

New preprint! We generate 40 new high-quality microsporidian genomes from infected arthropod hosts that were sequenced to create reference genomes by the Darwin Tree of Life project. 8 of our genomes are chromosome-level, and we’re able to generate Hi-C data for 7! 🧬
www.biorxiv.org/content/10.1...

Struggling to find the tiny microchromosomes in draft bird genome assemblies?

Our new #preprint introducing MicroFinder can help: www.biorxiv.org/content/10.1...

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@sangerinstitute.bsky.social