Keywords: decoding modules, codon usage, transcriptome reprogramming, structural variants, yield, autophagy

Latest 25 Papers

Unveiling the molecular identity of plant autophagic compartments: A proteo-lipidomic study in Arabidopsis thaliana

Authors: Lupette, J., Chambaud, C., Buridan, M., Castets, J., Wattelet-Boyer, V., Toboso Moreno, I., Kosuth, T., Yatim, C., Dittrich-Domergue, F., Gros, V., Jouhet, J., Claverol, S., Herice, C., Melser, S., Genva, M., Fouillen, L., Bessoule, J.-J., Domergue, F., Bernard, A.

Date: 2025-08-28 · Version: 1

DOI: 10.1101/2025.08.25.671700

Model Organism: Arabidopsis thaliana

autophagy phagophore membrane proteomics lipidomics membrane remodeling

A dual component system instructs membrane hydrolysis during the final stages of plant autophagy

Authors: Castets, J., Buridan, M., Toboso Moreno, I., Sanchez de Medina Hernandez, V., Gomez, R. E., Dittrich-Domergue, F., Lupette, J., Chambaud, C., Pascal, S., Ibrahim, T., Bozkurt, T. O., Dagdas, Y., Domergue, F., Joubes, J., Minina, A. E. A., Bernard, A.

Date: 2025-08-02 · Version: 1

DOI: 10.1101/2025.08.01.668046

Model Organism: Arabidopsis thaliana

autophagy phospholipase Arabidopsis thaliana vacuolar lumen LCAT3/LCAT4

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Authors: Sun, H., Zhang, J., Liao, S., Guo, S., Zhou, Z., Zhao, X., Wu, S., Zhao, J., Gong, G., Wang, J., Li, M., Yu, Y., Ren, Y., Tian, S., Li, S., Zhang, H., Hammar, S. A., McGregor, C., Jarret, R., Wechter, P., Branham, S. E., Kousik, C., Levi, A., Grumet, R., Xu, Y., Fei, Z.

Date: 2025-07-27 · Version: 1

DOI: 10.1101/2025.07.25.666869

Model Organism: Citrullus lanatus (watermelon)

watermelon super-pangenome structural variants genome-wide association study copy number variation genomic prediction

Graph pangenome reveals structural variation dynamics during cucumber breeding

Authors: Zhao, X., Yu, J., Zhang, J., Sun, H., Wu, S., Zhao, J., Zhou, Y., Hammar, S., Lin, Y.-C., Zhang, Z., Huang, S., Dymerski, R., Chen, F., Weng, Y., Grumet, R., Xu, Y., Fei, Z.

Date: 2025-07-21 · Version: 1

DOI: 10.1101/2025.07.17.665377

Model Organism: Cucumis sativus

structural variants graph pangenome cucumber domestication genomic prediction purifying selection

ATG8i Autophagy activation is mediated by cytosolic Ca2+ under osmotic stress in Arabidopsis thaliana

Authors: Castillo-Olamendi, L., Gutierrez-Martinez, J., Jimenez-Nopala, G., Galindo, A., Barrera-Ortiz, S., Rosas-Santiago, P., Cordoba, E., Leon, P., Porta, H.

Date: 2025-07-02 · Version: 1

DOI: 10.1101/2025.07.02.662772

Model Organism: General

autophagy osmotic stress Ca²⁺ signaling ATG8i ER‑phagy

SnRK1.1 Coordinates Organ-Specific Growth-Defense Programs via Transcriptomic Rewiring in Arabidopsis thaliana

Authors: Kalachova, T., Muller, K., Lacek, J., Pree, S., Antonova, A., Bondarenko, O., Burketova, L., Retzer, K., Weckwerth, W.

Date: 2025-04-29 · Version: 1

DOI: 10.1101/2025.04.25.650715

Model Organism: Arabidopsis thaliana

SnRK1 KIN10 transcriptome reprogramming plant immunity tissue-specific signaling

The autophagy-related genes AtATG5 and AtATG7 influence reserve mobilisation and responses to ABA during seed germination in Arabidopsis thaliana

Authors: Contreras, E., Sanchez-Vicente, I., Pastor-Mora, E., Aylon-Rodriguez, M., Gonzalez-Ceballos, M., Delgado-Gutierrez, M. A., Lorenzo, O., Vicente-Carbajosa, J., Iglesias-Fernandez, R.

Date: 2025-04-21 · Version: 2

DOI: 10.1101/2024.05.15.593177

Model Organism: Arabidopsis thaliana

autophagy Arabidopsis thaliana ABA signaling ATG5/ATG7 ABI5

Structural variations contribute to subspeciation and heterosis in rice

Authors: Dan, Z., Chen, Y., Huang, W.

Date: 2025-04-14 · Version: 2

DOI: 10.1101/2024.11.03.621459

Model Organism: Oryza sativa

heterosis structural variants rice subspeciation indica japonica genome assembly

Revisiting the Central Dogma: the distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana

Authors: Zhong, Z., Bailey, M., Kim, Y.-I., Pesaran-Afsharyan, N., Parker, B., Arathoon, L., Li, X., Rundle, C. A., Behrens, A., Nedialkova, D. D., Slavov, G., Hassani-Pak, K., Lilley, K. S., Theodoulou, F. L., Mott, R.

Date: 2025-03-31 · Version: 2

DOI: 10.1101/2025.01.08.631880

Model Organism: Arabidopsis thaliana

Arabidopsis thaliana codon usage gene expression DNA methylation ribosome profiling

Root hair lifespan is antagonistically controlled by autophagy and programmed cell death

Authors: Feng, Q., Zhu, S., Wang, X., Liu, Y., Zhao, J., Dagdas, Y., Nowack, M. K.

Date: 2025-03-19 · Version: 1

DOI: 10.1101/2025.03.18.643910

Model Organism: Arabidopsis thaliana

root hair longevity autophagy ATG2 ATG5 ATG7 NAC transcription factors programmed cell death

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