
Ancient oak's youthful genome surprises biologists - kafkaesq
https://www.nature.com/news/ancient-oak-s-youthful-genome-surprises-biologists-1.22166
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pvaldes
Not so surprising as we could think.

First of all we have access to less than half of this organism only. What
about root mutations?

And second, we have accces only to the 'bad half' in our search for mutations.
Trees act in some ways as 'colonial organisms'. Each branch competes with
other branches. Some can place itselves in a better place and trive, and other
not. Is a well known fact by gardeners that mutated branches are outcompeted
and die more often. Mutations in cells of flowers, leaves or fruit peduncles
are simply auto-cleaned in winter, and some barks fall also.

Oaks are customed to having several of types of 'cancers' and react actively
against, isolating the tissue or nurturing the tumor for a while before
'autopruning' it.

There is not need here of a genetic mechanism to protect cells from mutations.
Such system may happen, but not necessarily.

~~~
contingo
> First of all we have access to less than half of this organism only. What
> about root mutations?

The study specifically examined the issue of mutations arising in the cell
line from zygote to terminal branches, since that is where reproduction takes
place and we are most interested in mutations that are passed from one
generation to the next. If stem cells at the root tips show more mutations, so
what? The authors established (pending peer-review) a surprisingly low rate
for this particular sequence, that's sufficiently interesting in itself.

> And second, we have accces only to the 'bad half' in our search for
> mutations...

"Sixteen of the 17 SNVs identified in the Napoleon Oak occurred in introns or
non-coding sequences that are probably neutral... These results... demonstrate
[the mutations'] gradual, nested appearance and fixation in developmentally
connected branches during the growth of the oak tree. Thus, while the exact
ontogeny of the Napoleon Oak may be difficult to reconstruct, our SNV analysis
generated nested set of lineages supported by derived mutations"

They sampled across many independent cell lineages and across noncoding
regions, and they are looking specifically at mutation rates in the cell line
that leads to gamete formation. The kind of mutational "auto-cleaning" you
describe is mostly just your unsubstantiated thinking about growth-related
phenomena that are actually explained by a host of non-mutational factors; in
any case undersampling due to rare deleterious mutation self-pruning would not
have a confounding effect on the results here.

>There is not need here of a genetic mechanism to protect cells from
mutations.

Just because trees can tolerate certain kinds of pathogen and insect-induced
tumors doesn't mean they are entirely without need of protecting genome
sequence integrity. Plants like other organisms do have sophisticated
mechanisms to repair and maintain DNA, this becomes especially important in
the stem cell lines leading to reproduction. The study shows these mechanisms
in this oak are particularly efficient.

~~~
pvaldes
> If stem cells at the root tips show more mutations, so what?

So then, we couldn't say that oaks have a surprising absence of mutations. And
we should remember that roots can work as part of the reproductive systems in
this organisms. Could change our interpretation and point of view about
results. The biggest trees in the world (heavier than Sequoias) are root
clonal colonies.

> The kind of mutational "auto-cleaning" you describe is mostly just your
> unsubstantiated thinking about growth-related phenomena that are actually
> explained by a host of non-mutational factors;

I'm not sure that I'm understanding this. Specially the host of factors part.
Could you please rephrase it?

