Keywords: paralog processing, CRISPR/Cas9, transcriptomic analysis, RNA-seq

Latest 31 Papers

Engineering compact Physalis peruviana (goldenberry) to promote its potential as a global crop

Authors: Santo Domingo, M., Fitzgerald, B., Robitaille, G. M., Ramakrishnan, S., Swartwood, K., Karavolias, N., Schatz, M., Van Eck, J., Lippman, Z.

Date: 2025-10-24 · Version: 2

DOI: 10.1101/2025.08.15.670557

Model Organism: Physalis peruviana

Physalis peruviana Goldenberry CRISPR/Cas9 plant architecture compact ideotype

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)

Authors: Moore-Pollard, E. R., Ellestad, P., Mandel, J.

Date: 2025-10-13 · Version: 2

DOI: 10.1101/2025.09.14.676143

Model Organism: Multi-species

phylogenomic discordance polyploidy paralog processing Packera historical biogeography

Antifungal activity and mechanism of limonene against Fusarium oxysporum, a pathogen of potato dry rot

Authors: Xia, Q., Dong, P.

Date: 2025-10-06 · Version: 1

DOI: 10.1101/2025.10.06.675995

Model Organism: Fusarium oxysporum

limonene Fusarium oxysporum potato dry rot bio‑based fungicide transcriptomic analysis

Wounding activates the HSFA1 transcription factors to promote cellular reprogramming in Arabidopsis

Authors: Coleman, D., Iwase, A., Kawamura, A., Takebayashi, A., Jaeger, K. E., Peng, M., Kodama, Y., Favero, D. S., Takahashi, T., Ikeuchi, M., Suzuki, T., Ohama, N., Yamaguchi-Shinozaki, K., Wigge, P. A., De Veylder, L., Sugimoto, K.

Date: 2025-09-30 · Version: 1

DOI: 10.1101/2025.09.29.679115

Model Organism: Arabidopsis thaliana

HSFA1 transcription factors wound-induced regeneration callus formation RNA-seq SUMOylation

Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering

Authors: Zhou, H.-R., Doan, D. T. H., Hartwig, T., Turck, F.

Date: 2025-09-25 · Version: 1

DOI: 10.1101/2025.09.23.678055

Model Organism: Arabidopsis thaliana

FLOWERING LOCUS T enhancer architecture cis‑regulatory logic CRISPR/Cas9 chromatin accessibility

Choosing the Best Route: Comparative Optimization of Wheat Transformation Methods for Improving Yield by Targeting TaARE1-D with CRISPR/Cas9

Authors: Tek, M. I., Budak Tek, K., Sarikaya, P., Ahmed, A. R., Fidan, H.

Date: 2025-09-12 · Version: 1

DOI: 10.1101/2025.09.11.675438

Model Organism: Triticum aestivum

Triticum aestivum CRISPR/Cas9 Agrobacterium-mediated transformation TaARE1-D yield improvement

Time-series transcriptomics of grapevine deacclimation reveals chilling-dependent genetic responses to temperature increase during dormancy

Authors: Wang, H., Londo, J. P.

Date: 2025-08-09 · Version: 1

DOI: 10.1101/2025.08.08.669328

Model Organism: Vitis vinifera

Dormancy Chilling accumulation Temperature response RNA-seq Weighted gene co-expression network analysis

tRNA-Based Polycistronic CRISPR/Cas9 System Boosts Efficiency of Multi-Gene Deletion in the Moss Physcomitrella.

Authors: Kozgunova, E.

Date: 2025-08-01 · Version: 1

DOI: 10.1101/2025.07.29.667574

Model Organism: Physcomitrium patens

CRISPR/Cas9 polycistronic tRNA‑gRNA array large gene deletion multiplex editing Physcomitrium patens

Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens

Authors: Belloeil, C., Garcia de la Torre, V. S., Contreras Aguilera, R., Kupper, H., Lopez-Roques, C., Iampetro, C., Vandecasteele, C., Klopp, C., Launay-Avon, A., Leemhuis, W., Yamjabok, J., van den Heuvel, J., Aarts, M. G. M., Quintela Sabaris, C., Thomine, S., MERLOT, S.

Date: 2025-07-25 · Version: 1

DOI: 10.1101/2025.07.22.664359

Model Organism: Noccaea caerulescens

nickel hyperaccumulation Noccaea caerulescens genome assembly transcriptomic analysis metal transporters

Integrative transcriptomic and phosphoproteomic analysis reveals key components of SnRK1 signaling network in rice

Authors: Faria-Bates, M. C., Maurya, C., Jamsheer K, M., Srivastava, V.

Date: 2025-07-23 · Version: 1

DOI: 10.1101/2025.07.22.666209

Model Organism: Oryza sativa

SnRK1 rice CRISPR/Cas9 phosphoproteomics stress response

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