Lightnews — Scholar-powered news

Reposted by Wenfei Xian (冼文飞)

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Aug 2

1/3 New preprint led by Shanshan Wang, in collaboration with the Timmermans lab.

Several groups have presented sc/snRNA-seq analyses of Arabidopsis leaves after bacterial infection before. Is there anything left to discover? Turns out: Yes.

#plantscience
www.biorxiv.org/content/10.1...

2 39 73

Wenfei Xian (冼文飞) @wenfeixian.bsky.social · Aug 7

😃

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Aug 6

1/2 Study led by @wenfeixian.bsky.social revisiting somatic mutations in the Napoleon Oak now out after peer review, using @pacbio.bsky.social data to improve the genome assembly. Wenfei also developed a clever way to map short reads to a highly heterozygous genome.
academic.oup.com/g3journal/ar...

2

Wenfei Xian (冼文飞) @wenfeixian.bsky.social · Aug 6

Super happy to share that I’ve passed my PhD defense! 🍾
It’s been an amazing journey doing my PhD in the Weigel World.
Huge thanks to my supervisor, Detlef @plantevolution.bsky.social , even with your crazy schedule, you always made time to guide me.
Couldn’t have done it without all your support!!!

4 2 26

Reposted by Wenfei Xian (冼文飞)

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Feb 10

In our latest @biorxiv-genomic.bsky.social preprint, we describe our approach to use PacBio HiFi reads to detect somatic TE transposition -- good enough to detect rare events that are present in only single cells. Led by Andrea Movilli.
#plantscience
www.biorxiv.org/content/10.1...

Diagram of somatic TE insertions across the A. thaliana genome

4 38 77

Wenfei Xian (冼文飞) @wenfeixian.bsky.social · Jan 16

Thanks, Eirik 😊

Wenfei Xian (冼文飞) @wenfeixian.bsky.social · Jan 15

Large repeats are common in plant organellar genomes. Half of the A. thaliana mitogenomes we assembled have two large repeat pairs, while others have only one, where we identified two potential HGT events. Large repeats link to geography and cold traits.
Feedback welcome on bioRxiv, Email, etc.!

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Jan 15

New preprint: Chloroplast and mitochondrial #pangenome of #Arabidopsis thaliana! Work led by wenfeixian.bsky.social
#plantscience
www.biorxiv.org/content/10.1...

1 7 15

Reposted by Wenfei Xian (冼文飞)

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Dec 27

Announcing a curated collection of long-read genomes for Arabidopsis thaliana: The 1001 Genomes Plus Project. Currently 453 unique accessions/almost 600 assemblies.
Interested in contributing? Please contact us!
#plantscience
www.biorxiv.org/content/10.1...

2 91 130

Reposted by Wenfei Xian (冼文飞)

Houming Chen @hmchen93.bsky.social · Nov 17

Super excited to announce that our SCRM story is officially published!!! 🎉🎉🎉

Want to discover the exciting new functions of ICE1/SCRM?

Want to dive into the latest model of plant embryo initiation?

Don’t miss out—check it out here:
nph.onlinelibrary.wiley.com/doi/10.1111/...

Phosphorylation‐dependent activation of the bHLH transcription factor ICE1/SCRM promotes polarization of the Arabidopsis zygote

In Arabidopsis thaliana, the asymmetric cell division (ACD) of the zygote gives rise to the embryo proper and an extraembryonic suspensor, respectively. This process is controlled by the ERECTA-YODA...

nph.onlinelibrary.wiley.com

5 6 15

Reposted by Wenfei Xian (冼文飞)

bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · Apr 7

Accessory proteins increase the efficiency of RNA editing by Arabidopsis chloroplast editosomes https://www.biorxiv.org/content/10.1101/2024.04.05.588343v1

RNA editing modifies cytidines to uridines in plant organelle transcripts so that their sequence dif

www.biorxiv.org

1 1

Reposted by Wenfei Xian (冼文飞)

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Apr 7

Effects of spontaneous mutations on survival and reproduction of Drosophila serrata infected with Drosophila C virus https://www.biorxiv.org/content/10.1101/2024.04.04.588202v1

The impact of selection on host immune function genes has been widely documented. However, it remain

www.biorxiv.org

1

Reposted by Wenfei Xian (冼文飞)

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Apr 4

How cool is that -- would not have guessed that the type of genetic incompatibility, hybrid necrosis, that we've studied for many years, is also the cause for graft incompatibility. I wonder whether it's a story of mismatched helper NLRs... @kamounlab.bsky.social

Marc Somssich @somssich.bsky.social · Apr 4

📜 Graft incompatibility between pepper and tomato can be attributed to genetic incompatibility between diverged immune systems

🧑‍🔬 Hannah Rae Thomas, Margaret H. Frank, et al.

📔 @biorxiv-plants.bsky.social

🔗 www.biorxiv.org/content/10.1...

#️⃣ #PlantScience #PlantImmunity #Grafting #PlantDevelopment

Graft incompatibility between pepper and tomato can be attributed to genetic incompatibility between diverged immune systems

bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

www.biorxiv.org

2 5 16

Reposted by Wenfei Xian (冼文飞)

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Mar 30

Transposable elements as evolutionary driving force to ecological speciation in cactophilic Drosophila species https://www.biorxiv.org/content/10.1101/2024.03.27.587021v1

Background The host shift in insects has been considered a key process with potential to collaborate

www.biorxiv.org

2 2

Reposted by Wenfei Xian (冼文飞)

Leo C. Stein @duetosymmetry.com · Mar 27

The Event Horizon Telescope has measured the *polarized* radiation from our friendly neighborhood black hole, Sgr A*! Press release: eventhorizontelescope.org/blog/astrono..., papers in next skeet 🔭🧪

A view of the Milky Way supermassive black hole Sagittarius A* in polarized light.

5 47 100

Reposted by Wenfei Xian (冼文飞)

Mario Coiro @lepidodendron.bsky.social · Mar 22

last week my latest paper on #cycads came out.
The article deals with the idea of cycads as "living #fossils", but what does this mean exactly, and what did we actually test? A thread for #FossilFriday!
www.nature.com/articles/s42...

Disparity of cycad leaves dispels the living fossil metaphor - Communications Biology

An analysis of leaf disparity through time in cycads shows that this group has a dynamic and expanding morphological diversity until the present, and thus does not fit the ‘living fossil’ hypothesis o...

www.nature.com

1 24 31

Reposted by Wenfei Xian (冼文飞)

Space Telescope Science Institute @stsci.edu · Mar 22

Asymmetry has never been so pleasing! Hubble’s near-infrared and visible-light view shows jostled dark brown dust lanes and a core knocked off center. Why? Galaxy M96 is part of a group of galaxies in a gravitational “tug of war.”

Credit: ESA/Hubble, NASA, and the LEGUS Team. 🔭 🧪

A spiral galaxy takes up almost the entire frame, from bottom left to top right. The circular-shaped galaxy is not seen perfectly face-on, but is slightly tilted. The galaxy has a bright light yellow central core that is surrounded by tightly wound spiral arms that are oriented counter clockwise. Beginning at the core and going to the right and then to the top are prominent, dark brown dust lanes. The other region forms an arc toward the bottom left, starting near the core at around 9 o’clock. The outer edges of the galaxy are where there are brighter blue areas filled with clusters of stars. Pink star clusters are found throughout, are most obvious toward the edges, and appear more clustered toward the middle-right edge and toward the bottom left corner. The background of space is black.

1 13 39

Reposted by Wenfei Xian (冼文飞)

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Mar 20

Permutation analysis prior to variable selection greatly enhances robustness of OPLS analysis in small cohorts https://www.biorxiv.org/content/10.1101/2024.03.18.585475v1

The R-workflow roplspvs (R orthogonal projections of latent structures with permutation over variabl

www.biorxiv.org

1

Reposted by Wenfei Xian (冼文飞)

George Matsumoto @georgeimatsumoto.bsky.social · Mar 16

reposting to 🧪 cause it's a very cool paper

Matt Bracken @brackenlab.bsky.social · Mar 16

Super-cool new paper by Varney et al. (2024 *Science*) about evolution of vision in chitons! @ostratodd.bsky.social 🦑 #MarineScience #Invertebrate www.sciencealert.com/researchers-...

Researchers Solve Mystery of The Sea Creature That Evolved Eyes All Over Its Shell

Not once, but four times.

www.sciencealert.com

1 5 26

Reposted by Wenfei Xian (冼文飞)

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Mar 19

IDRWalker: A Random Walk based Modeling Tool for Disordered Regions in Proteins https://www.biorxiv.org/content/10.1101/2024.03.17.585378v1

Motivation: With the advancement of structural biology techniques, the elucidation of increasingly l

www.biorxiv.org

1

Reposted by Wenfei Xian (冼文飞)

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Mar 18

Estimation of spatial demographic maps from polymorphism data using a neural network https://www.biorxiv.org/content/10.1101/2024.03.15.585300v1

A fundamental goal in population genetics is to understand how variation is arrayed over natural lan

www.biorxiv.org

4 2

Reposted by Wenfei Xian (冼文飞)

Zhigui Bao 鲍志贵 @zbao.bsky.social · Mar 17

T2T with ONT-only 🏃🏻🍅🌽

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Mar 17

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing https://www.biorxiv.org/content/10.1101/2024.03.15.585294v1

The combination of ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi

www.biorxiv.org

1 1

Reposted by Wenfei Xian (冼文飞)

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Mar 17

Characterising tandem repeat complexities across long-read sequencing platforms with TREAT https://www.biorxiv.org/content/10.1101/2024.03.15.585288v1

Tandem repeats (TR) play important roles in genomic variation and disease risk in humans. Long-read

www.biorxiv.org

1

Reposted by Wenfei Xian (冼文飞)

PlantEvolution 🌱🌾 @plantevolution.bsky.social · Mar 16

German-Spanish-Argentinean collaboration on haplotype-resolved Malbec 🍇🍷genome. Trio-binning used short reads from the parental varietals Prunelard and Magdeleine Noire des Charentes, which are both almost extinct

academic.oup.com/hr/advance-a...

3 7

Reposted by Wenfei Xian (冼文飞)

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Mar 16

Global climate change effect on Asian Mus musculus; Implication from last glacial maximum to the end of the 21st century https://www.biorxiv.org/content/10.1101/2024.03.14.584992v1

Global climate change poses unprecedented challenges to biodiversity, prompting urgent investigation

www.biorxiv.org

2

Reposted by Wenfei Xian (冼文飞)

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Mar 16

FST and genetic diversity in an island model with background selection https://www.biorxiv.org/content/10.1101/2024.03.15.585154v1

Background selection, by which selection on deleterious alleles reduces diversity at linked neutral

www.biorxiv.org

2 2

Reposted by Wenfei Xian (冼文飞)

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Mar 15

Genome streamlining: effect of mutation rate and population size on genome size reduction https://www.biorxiv.org/content/10.1101/2024.03.14.584996v1

Genome streamlining, i.e. genome size reduction, is observed in bacteria with very different life tr

www.biorxiv.org

3 2