Dataset for "Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana"

Zenker S, Wulf D, Meierhenrich A, et al. Dataset for "Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana". Bielefeld University; 2023.Supplemental dataset for the publication "Transcription factors operate on a limited vocabulary of binding motifs in *Arabidopsis thaliana*". Contains binding data from the publication "Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape" (O'Malley et al. 2016, 10.1016/j.cell.2016.04.038) mapped onto promoters of all nuclear encoded genes in *A. thaliana*. Visualizations available as interactive htmls

Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana

Zenker S, Wulf D, Meierhenrich A, et al. Transcription factors operate on a limited vocabulary of binding motifs in Arabidopsis thaliana. bioRxiv. 2023.Predicting gene expression from promoter sequence requires understanding of the different signal integration points within a promoter. Sequence-specific transcription factors (TFs) binding to their cognate TF binding motifs control gene expression in eukaryotes by activating and repressing transcription. Their interplay generates complex expression patterns in reaction to environmental conditions and developmental cues. We hypothesized that signals are not only integrated by different TFs binding various positions in a promoter, but also by single TF binding motifs onto which multiple TFs can bind. Analyzing 2,190 binding motifs, we identified only 76 core TF binding motifs in plants. Twenty-one TF protein families act highly specific and bind a single conserved motif. Four TF families are classified as semi-conserved as they bind up to four motifs within a family, with divisions along phylogenetic groups. Five TF families bind diverse motifs. Expression analyses revealed high competition within TF families for the same binding motif. The results show that singular binding motifs act as signal integrators in plants where a combination of binding affinity and TF abundance likely determine the output

Whole-genome sequence of Paenibacillus marchantiae isolated from the liverwort Marchantia polymorpha subsp. ruderalis Ecotype BoGa

The bacterium Paenibacillus marchantiae was isolated from male plants of the liverwort Marchantia polymorpha subsp. ruderalis ecotype BoGa. Here, we report on the complete genome sequence generated from long Nanopore reads. The genome sequence comprises 6,983,959 bp with a GC content of 46.02% and 6,195 predicted protein-coding genes

Whole-Genome Sequence of Paenibacillus marchantiae Isolated from the Liverwort Marchantia polymorpha subsp. Ecotype BoGa

Meierhenrich A, Frommer B, Halpape W, et al. Whole-Genome Sequence of Paenibacillus marchantiae Isolated from the Liverwort Marchantia polymorpha subsp. Ecotype BoGa. Microbiology Resource Announcements. 2023;12(7):3 Seiten.The bacterium Paenibacillus marchantiae was isolated from male plants of the liverwort Marchantia polymorpha subsp. ruderalis ecotype BoGa. Here, we report on the complete genome sequence generated from long Nanopore reads. The genome sequence comprises 6,983,959 bp with a GC content of 46.02% and 6,195 predicted protein-coding genes

The Marchantia pangenome reveals ancient mechanisms of plant adaptation to the environment

Beaulieu C, Libourel C, Mbadinga Zamar DL, et al. The Marchantia pangenome reveals ancient mechanisms of plant adaptation to the environment. bioRxiv. 2023.**Abstract** Plant adaptation to a terrestrial life 450 million years ago played a major role in the evolution of life on Earth. This shift from an aquatic environment has been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the non-vascular plantsMarchantia polymorphaand studied its intraspecific diversity using selection signature analyses, genome-environment association study and a gene-centered pangenome. We identified adaptive features shared with flowering plants, such as peroxidases or nucleotide-binding and leucine-rich repeat (NLR), which likely played a role in the adaptation of the first land plants to the terrestrial habitat. TheM. polymorphapangenome also harbored lineage-specific accessory genes absent from seed plants. We conclude that different land plants lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage specific polymorphisms and gene family evolutions