Keywords: paralog processing, comparative transcriptomics, single-cell RNA sequencing

Latest 18 Papers

Network analysis of flowering time genes suggests regulatory changes among SOC1 orthologues in response to cold in Brassica napus

Authors: Sidhu, G. S., Burrows, S., Woolfenden, H., Wells, R., Morris, R. J.

Date: 2026-01-20 · Version: 2

DOI: 10.64898/2025.12.16.694548

Model Organism: Brassica napus

flowering time gene regulatory network comparative transcriptomics Brassica napus subfunctionalisation

Antirrhinum flower shape: unravelling gene expression across developmental axes and boundaries

Authors: Cunha, A. M., Raimundo, J., Verweij, A., Bradley, D., Coen, E., Costa, M. M. R.

Date: 2025-11-11 · Version: 1

DOI: 10.1101/2025.11.10.687484

Model Organism: Antirrhinum majus

Antirrhinum majus dorsoventral axis patterning comparative transcriptomics AmCYC/AmDIV transcription factors NGATHA‑LIKE1‑miR164 regulatory module

Symbiotic diversification relies on an ancestral gene network in plants

Authors: Castanedo, L., Melkonian, K., Vernie, T., Chauderon, L., Pellen, T., Bianconi, M., Lefort, C., Libourel, C., Le Ru, A., Aziz, S., Latorre, C., Thiercelin, O., Rodde, N., Cauet, S., Callot, C., Forrest, L., Nishiyama, T., Wickell, D., Li, F.-W., Keller, J., Delaux, P.-M.

Date: 2025-11-03 · Version: 2

DOI: 10.1101/2025.04.01.646537

Model Organism: Marchantia paleacea

ericoid mycorrhizae intracellular symbiosis ancestral gene module liverwort comparative transcriptomics

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

Usefulness of scRNA-seq data in predicting plant metabolic pathway genes

Authors: Ma, J., Wang, Z., Zou, L., Wang, X., Zuo, X., Wang, F., Wang, Z., Li, Z., Li, L., Wang, P.

Date: 2025-10-02 · Version: 2

DOI: 10.1101/2024.10.07.617125

Model Organism: Arabidopsis thaliana

metabolic pathway genes single-cell RNA sequencing machine learning co-expression networks prediction accuracy

Cell-type specific gating of gene regulatory modules as a hallmark of early immune responses in Arabidopsis leaves

Authors: Wang, S., Bezrukov, I., Wu, P.-J., Gauss, H., Timmermans, M., Weigel, D.

Date: 2025-08-01 · Version: 1

DOI: 10.1101/2025.08.01.668105

Model Organism: Arabidopsis thaliana

single-cell RNA sequencing Arabidopsis thaliana plant immunity PTI and ETI WRKY transcription factors

Single-cell metabolome and RNA-seq multiplexing on single plant cells

Authors: Kang, M., Vu, A. H., Casper, A. L., Kim, R., Wurlitzer, J., Heinicke, S., Yeroslaviz, A., Caputi, L., O'Connor, S. E.

Date: 2025-05-23 · Version: 1

DOI: 10.1101/2025.05.20.655036

Model Organism: General

single-cell RNA sequencing single-cell mass spectrometry metabolomics gene‑to‑metabolite correlation plant biosynthetic pathways multimodal single‑cell analysis

Conserved spatial patterning of gene expression in independent lineages of C4 plants

Authors: Sun, T., Bonthala, V. S., Stich, B., Luginbuehl, L. H., Hibberd, J. M.

Date: 2025-05-15 · Version: 1

DOI: 10.1101/2025.05.14.654047

Model Organism: Gynandropsis gynandra, Flaveria bidentis

C4 photosynthesis single-cell RNA sequencing single-nucleus RNA sequencing bundle sheath cells transcription factors

Imputation integrates single-cell and spatial gene expression data to resolve transcriptional networks in barley shoot meristem development

Authors: Demesa-Arevalo, E., Dorpholz, H., Vardanega, I., Maika, J. E., Pineda-Valentino, I., Eggels, S., Lautwein, T., Kohrer, K., Schnurbusch, T., von Korff, M., Usadel, B., Simon, R.

Date: 2025-05-11 · Version: 1

DOI: 10.1101/2025.05.09.653223

Model Organism: Hordeum vulgare

Barley (Hordeum vulgare)inflorescence meristems single-cell RNA sequencing spatial transcriptomics developmental gene regulation

Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation

Authors: Xu, X., Passalacqua, M., Rice, B., Demesa-Arevalo, E., Kojima, M., Takebayashi, Y., Harris, B., Sakakibara, H., Gallavotti, A., Gillis, J., Jackson, D.

Date: 2025-04-17 · Version: 2

DOI: 10.1101/2024.03.04.583414

Model Organism: Multi-species

single-cell RNA sequencing shoot stem cells Arabidopsis thaliana Zea mays stem cell regulators

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