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Matt Davis

@davismw.bsky.social

27 followers 21 following 8 posts

PhD Candidate at UC Davis Happy to talk about somatic mutation and genetics!

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Reposted by Matt Davis

Proceedings of the National Academy of Sciences @pnas.org · 01/05/2026

One of the most-viewed PNAS articles in the last week is “Genome degradation in plant tissue culture.” Explore the article here: ow.ly/HRLQ50YSz54 For more trending articles, visit ow.ly/tiG850YSz56.

Development and anatomy contribute to differences in mutation burden between clones.

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Matt Davis @davismw.bsky.social · 02/05/2026

Huge thank you to all of the co-authors and collaborators who made this work possible, including but certainly not limited to the @grey-monroe.bsky.social and Brown labs, Luca Comai, @jrossibarra.bsky.social, Julin Maloof, Dan Runcie, & @plantevolution.bsky.social

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Matt Davis @davismw.bsky.social · 02/05/2026

This work began quantifying mutation happening in plant tissue culture, which has been an outstanding question for decades. Somatic mutation can illuminate plant development, but it also highlights that we need to identify and account for these mutations as a part of biotechnology efforts.

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Matt Davis @davismw.bsky.social · 02/05/2026

The somatic mutations expose development. The patterns of somatic mutation reveal they are confined to tissue layers, and there is frequent fixation of clonal cell lineages in somatic embryos.

Development and anatomy contribute to differences in mutation burden between clones. (A) Number of singleton de novo SBS and InDels occurring in a proportion of the cells inferred from allele frequency composing each clone. Plots were generated from minimum quality scores of 5 to 40 and plotted on top of one another with alpha = 0.1. Confidence in the mutation count is therefore depicted by bar darkness, with darker and lighter regions representing higher and lower confidence, respectively. (B) The percentage of de novo SBS within each bin, grouped by the clonal propagation method. Confidence in mutation percentage is depicted by darkness of the bar. (C) Diagram and microscopy depicting somatic embryo growth and development. Somatic embryos at different developmental stages are labeled in the microscope image and a proposed mechanism of somatic mutation fixation in the somatic embryos is presented in the diagram. (D) Schematic portraying a proposed mechanism of mutation fixation within tissue layers in the shoot culture and field-grown tree clones.

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Matt Davis @davismw.bsky.social · 02/05/2026

There is on-going transposable element activation in the somatic embryos. In her Nobel lecture, Barbara McClintock spoke of the "changes induced in genomes ... in tissue culture." Now we get to see it! We found two highly active TEs (though we still don't quite know the identity of one).

TEs are continuously active in the long-read somatic embryo. (A) Frequencies of de novo insertions in the clones sequenced with PacBio HiFi. (B) Morphology of class 900 and 5,500 transposons. (C) Circos plots depicting transposition of 900 and 5,500 class TEs. Lines trace TE movement in the somatic embryo from the putative origin to de novo insertion sites. (D) A comparison of the observed location of TE insertions relative to genomic features. Purple points indicate the observed means of the 900 class TEs and pink points indicate the observed means of the 5,500 class TEs. Gray violins represent the distribution of means of 10,000 random simulations. Brackets are labeled with statistically significant differences (P < 0.05) between observed and simulated means. (E) Class 900 and 5,500 TEs observed in different proportions of cells inferred from allele frequency that compose the somatic embryo, accompanied by a diagram. (F) Tracking a class 5,500 TE through multiple transposition events using mutation accumulation.

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Matt Davis @davismw.bsky.social · 02/05/2026

The somatic embryos were highly unstable. They showed instances of whole chromosome duplications, chromosome loss, large scale deletions, and even somatic recombination!

Genomic instability in the somatic embryo clones. (A) Read depth schematic. (B) Scaled read depth of ancestral heterozygosity in every chromosome of every clone. Red and blue represent high and low sequencing depth, respectively. Bars to the right display the number of telomeric repeats corrected by sequencing depth. (C) Allele frequency of ancestral heterozygosity in chromosomes exhibiting genomic instability. Red and blue represent windows with mean allele frequency significantly greater or less than 0.5, respectively. (D) Normalized expression of entire chromosomes in the somatic embryos. Red indicates higher than average expression. (E) Comparison of individual gene expression across clades of embryos. Red and blue points are comparatively over- and underexpressed genes, respectively.

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Matt Davis @davismw.bsky.social · 02/05/2026

We compared somatic mutation across three clonal propagation methods over five decades. Somatic embryos had a 3500% increase in somatic mutations compared to budwood cuttings, while the plants in shoot culture accumulated new mutations linearly with time.

Somatic embryos exhibit high levels of mutation compared to shoots and trees. (A) Schematic of the relationship among all clones. Icons denote trees, shoot cultures, and somatic embryos. Gray icons represent dead clones. Dashed lines indicate an unknown number of clonal propagations, solid lines indicate a single clonal propagation. (B) Phylogeny of all sequenced clones constructed from de novo somatic single base substitutions (SBS) and InDels. Branch length is proportional to the number of mutations. Bootstrap support less than 1 is displayed. (C) The number of SBS and InDels present in each sample at minimum median quality scores of 20 to 40, in increasing intervals of 1. (D) The mutation spectra of SBS in the clones. Larger squares and darker color indicate higher occurrence of each context.

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Matt Davis @davismw.bsky.social · 02/05/2026

Not all clones are created equal! Our paper quantifying somatic mutation in plant tissue culture is out now in @pnas.org : doi.org/10.1073/pnas... Check out this article for a quick summary, or keep reading: www.plantsciences.ucdavis.edu/news/davis-m...

An image of a developing somatic embryo emerging from a cotyledon. Photo credit: Hannah McCurry

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Matt Davis @davismw.bsky.social · 20/04/2025

I had to wait for hours for this cob to show up

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