biorxiv.org

Herbaria provide a valuable resource for obtaining informative mRNA

Although DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative to DNA, this has effectively precluded the use of herbaria for transcriptomics. Here, we challenge the assumption that herbaria cannot be used for transcriptomics by assembling transcriptomes from RNA extracted from herbarium specimens. Through systematic comparison of transcriptomes from fresh-collected, silica-dried, and archival specimens, we demonstrate the suitability of herbarium-derived RNA for transcriptomics. We show the practical applicability of archival mRNA by functionally validating a plant immune receptor synthesized from a specimen collected in 1956. These results contradict the community consensus regarding archival RNA and open the door to subsequent transcriptomic explorations of rare and extinct plant species. Our findings highlight the importance of preserving and utilizing the diversity embedded within herbarium collections.

genome.cshlp.org

Leveraging publicly available data to facilitate urban ecology and evolution

doi.org

GitHub - karolisr/treehouse: View and edit gene trees and phylogenies

View and edit gene trees and phylogenies. Contribute to karolisr/treehouse development by creating an account on GitHub.

github.com

Release v0.3.1 · karolisr/treehouse

This is very much a work in progress. Currently: TreeHouse will only open files with .tre and .newick extensions, and will treat them as NEWICK (multi-tree files are supported). NEXUS support comi...

github.com

Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life

Recent studies have demonstrated that it is a misconception that transcriptome sequencing requires tissue preserved at ultracold temperatures. Here, we outline the potential origins of this misconcept...

cell.com

Multiple transitions to high l‐DOPA 4,5‐dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales

Many specialized metabolic pathways have evolved convergently in plants, but distinguishing multiple origins from alternative evolutionary scenarios can be difficult. Here, we explore the evolution .....

nph.onlinelibrary.wiley.com

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae

Background and Aims: The flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite...

biorxiv.org

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae

Background and Aims: The flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite...

doi.org

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants

Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha liverworts and interrogate the mechanisms enabling virulence in non-flowering and flowering plants. Their resu...

cell.com

13 U-M faculty named as 2024 AAAS fellows

Thirteen University of Michigan faculty members earned election to the American Association for the Advancement of Science in 2024.

news.umich.edu

Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data

AbstractMotivation. Genotype datasets typically contain a large number of single nucleotide polymorphisms for a comparatively small number of individuals.

academic.oup.com

Living Herbaria

open.spotify.com

Herbaria provide a valuable resource for obtaining informative mRNA

While DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative ...

doi.org

Semblans: automated assembly and processing of RNA-seq data

AbstractMotivation. Recent advancements in parallel sequencing methods have precipitated a surge in publicly available short-read sequence data. This has e

doi.org

A necrotizing toxin enables Pseudomonas syringae infection across evolutionarily divergent plants

Grenz et al. interrogate the Pseudomonas syringae species complex for its capacity to infect evolutionarily divergent host plants. Their results demonstrate that broad host isolates from phylogroup 2 rely on the lipopeptide toxin syringomycin to promote host necrosis and enhance bacterial growth in plants.

cell.com