As for 2, I agree that’s a drawback at the moment - but we are working on a way to do that. Won’t rerun the pipeline (too computationally intensive) but transferring CNS annotations from a close genome.
Good point. We saw that developmental genes and TFs tend to have long and complicated regulatory regions. Enzymes, photosynthesis, structural genes, tend to be shorter and less conserved (general trend - exceptions exist). Our focus on development could bias our experience.
In our hands, this is rarely the case. Easier to get arabidopsis upstream sequences to work in tomato vs the opposite. Case in point- how many tomato developmental reporters are there? I interpret complementation being partial, as proximal promotors promoting some expression, but not the real one.
That is mostly true for Arabidopsis, which has a very compact genome. In other plants, like tomato, for example, we have mostly failures. Also, it is not so easy to determine how precise is the reporter compared to the actual gene expression. Complementation is often only partial.
Phylogeny of the 284 species of plants included in Conservatory data set. Conservatory uncovered ~2.3 million conserved non-coding DNA sequences across 284 plant species from 72 families including eudicots, monocots, gymnosperms, and algae. Illustrations by Professor Madelaine Bartlett.
Hiding in plain sight! 2.3M conserved non-coding sequences traced back 300M years across 284 plant species
Ground-breaking study out in First Release @science.org from labs of @madelaineb.bsky.social, @idane.bsky.social & Zach Lippman
▶️ doi.org/10.1126/scie...
▶️ www.slcu.cam.ac.uk/news/hiding-...
Plato would say that the complex biological systems are also the shadows
An atlas of Brachypodium distachyon lateral root development www.biorxiv.org/content/10.1101/2024.03....
A PhD position is available in my group at SLU. Come join us in Sweden to work on plant regeneration and grafting, supported by Wallenberg Foundation. Details below. Please RT! #plantscijobs #plantscience
A common regulatory switch controls a suite of C4 traits in multiple cell types www.biorxiv.org/content/10.1101/2023.12....
This transient isolation of regenerating cells is mediated by the LATERAL ORGAN BOUNDARY (LBD) transcription factors, which are involved in many plant developmental processes. This is mainly the long and hard work of Itay Cohen with fantastic help from @zivirus.bsky.social and Emmanuelle Bayer.
Plant cells know what type to be based on signals they receive from their neighbors. When you cut the root, existing cells rapidly replace the missing tissues, yet neighbors persist... We show that cells must transiently disconnect in order to regenerate. www.biorxiv.org/content/10.1...
Hi,
I am new here... You may know from X (Twitter) that I organize a free virtual microbiology journal club. Next Tue 16:00 Israel time we have (drum roll...) Prof. Richard Lensky presenting his science. If you want to join please email me alevy@mail.huji.ac.il
Asaf
Thank you! Checking things out…