Albrecht, S., Andreani, T., Andrade-Navarro, M.A., and Fontaine, J.F. (2022). Single-cell specific and interpretable machine learning models for sparse scChIP-seq data imputation. Plos One 17, e270043.
Alvarez, J.P., Furumizu, C., Efroni, I., Eshed, Y., and Bowman, J.L. (2016). Active suppression of a leaf meristem orchestrates determinate leaf growth. Elife 5:e15023.
Anderson, C.T., and Kieber, J.J. (2020). Dynamic Construction, Perception, and Remodeling of Plant Cell Walls. Annual Review of Plant Biology 71:39-69.
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., and Eppig, J.T., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25, 25-29.
Bai, D., Peng, J., and Yi, C. (2021). Advances in single-cell multi-omics profiling. RSC Chemical Biology 2, 441-449.
Becht, E., McInnes, L., Healy, J., Dutertre, C.A., Kwok, I., Ng, L.G., Ginhoux, F., and Newell, E.W. (2019). Dimensionality reduction for visualizing single-cell data using UMAP. Nature Biotechnology 37: 4314 38-44.
Bergen, V., Soldatov, R.A., Kharchenko, P.V., and Theis, F.J. (2021). RNA velocity-current challenges and future perspectives. Molecular System Biology 17, e10282.
Bertioli, D.J., Cannon, S.B., Froenicke, L., Huang, G., Farmer, A.D., Cannon, E.K., Liu, X., Gao, D., Clevenger, J., and Dash, S., et al. (2016). The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nature Genetics 48, 438-446.
Bertioli, D.J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S., Ren, L., Farmer, A.D., and Pandey, M.K., et al. (2019). The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics 51, 877-884.
Butler, A., Hoffman, P., Smibert, P., Papalexi, E., and Satija, R. (2018). Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology 36, 411-420.
Castro-Mondragon, J.A., Riudavets-Puig, R., Rauluseviciute, I., Lemma, R.B., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., and Manosalva, P.N., et al. (2022). JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. Nucleic Acids Research 50, D165-D173.
Chen, H., Yin, X., Guo, L., Yao, J., Ding, Y., Xu, X., Liu, L., Zhu, Q.H., Chu, Q., and Fan, L. (2021). PlantscRNAdb: A database for plant single-cell RNA analysis. Molecular Plant 14, 855-857.
Chen, X., Li, H., Pandey, M.K., Yang, Q., Wang, X., Garg, V., Li, H., Chi, X., Doddamani, D., and Hong, Y., et al. (2016). Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens. Proceeding of the National Academy of Sciences of the United State of America 113, 6785-6790.
Chen, X., Lu, Q., Liu, H., Zhang, J., Hong, Y., Lan, H., Li, H., Wang, J., Liu, H., and Li, S., et al. (2019). Sequencing of cultivated peanut, Arachis hypogaea, yields insights into genome evolution and oil improvement. Molecular Plant 12(7):920-934.
Conde, D., Triozzi, P.M., Balmant, K.M., Doty, A.L., Miranda, M., Boullosa, A., Schmidt, H.W., Pereira, W.J., Dervinis, C., and Kirst, M. (2021). A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus. Plos One 16, e251149.
Dorrity, M.W., Alexandre, C.M., Hamm, M.O., Vigil, A.L., Fields, S., Queitsch, C., and Cuperus, J.T. (2021). The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution. Nature Communications 12, 3334.
Evans, J.R. (2020). Mesophyll conductance: walls, membranes and spatial complexity. New Phytologist 229(4):1864-1876.
Farmer, A., Thibivilliers, S., Ryu, K.H., Schiefelbein, J., and Libault, M. (2021). Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. Molecular Plant 14, 372-383.
Guo, K., Huang, C., Miao, Y., Cosgrove, D.J., Hsia, K.J. (2022) Leaf morphogenesis: The multifaceted roles of mechanics. Molecular Plant 15: 1098-1119.
Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W.R., Zheng, S., Butler, A., Lee, M.J., Wilk, A.J., Darby, C., and Zager, M., et al. (2021). Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587.
Inagaki, S., and Umeda, M. (2011). Cell-cycle control and plant development. Int Rev Cell Molecular Biology 291, 227-261.
Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28, 27-30.
Kierzkowski, D., Runions, A., Vuolo, F., Strauss, S., Lymbouridou, R., Routier-Kierzkowska, A.L., Wilson-Sanchez, D., Jenke, H., Galinha, C., and Mosca, G., et al. (2019). A Growth-Based Framework for Leaf Shape Development and Diversity. Cell 177, 1405-1418.
Kim, J.Y., Symeonidi, E., Pang, T.Y., Denyer, T., Weidauer, D., Bezrutczyk, M., Miras, M., Zollner, N., Hartwig, T., and Wudick, M.M., et al. (2021). Distinct identities of leaf phloem cells revealed by single cell transcriptomics. Plant Cell 33, 511-530.
Kobak, D., and Berens, P. (2019). The art of using t-SNE for single-cell transcriptomics. Nature Communications 10, 5416.
Korsunsky, I., Millard, N., Fan, J., Slowikowski, K., Zhang, F., Wei, K., Baglaenko, Y., Brenner, M., Loh, P.R., and Raychaudhuri, S. (2019). Fast, sensitive and accurate integration of single-cell data with Harmony. Nature Methods 16, 1289-1296.
La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M.E., Lonnerberg, P., and Furlan, A., et al. (2018). RNA velocity of single cells. Nature 560, 494-498.
Li, N., Jin, K., Bai, Y., Fu, H., Liu, L., and Liu, B. (2020). Tn5 Transposase Applied in Genomics Research. International Journal of Molecular Sciences 21(21):8329.
Liu, H., Dong, S., Li, M., Gu, F., Yang, G., Guo, T., Chen, Z., and Wang, J. (2020). The Class III Peroxidase gene OsPrx30, Transcriptionally Modulated by the AT-hook Protein OsATH1, Mediates Rice Bacterial Blight-induced ROS Accumulation. Journal of Integrated Plant Biology 63(2):393-408.
Liu, H., Hu, D., Du P, Wang, L., Liang, X., Li, H., Lu, Q., Li, S., Liu, H., and Chen, X., et al. (2021). Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.). Plant Biotechnology Journal 19, 2261-2276.
Long, Y., Liu, Z., Jia, J., Mo, W., Fang, L., Lu, D., Liu, B., Zhang, H., Chen, W., and Zhai, J. (2021). FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants. Genome Biology 22, 66.
Ma, S., Zhang, B., LaFave, L.M., Earl, A.S., Chiang, Z., Hu, Y., Ding, J., Brack, A., Kartha, V.K., and Tay, T., et al. (2020). Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin. Cell 183, 1103-1116.
Marand, A.P., Chen, Z., Gallavotti, A., and Schmitz, R.J. (2021). A cis-regulatory atlas in maize at single-cell resolution. Cell 184, 3041-3055.
Moncada, R., Barkley, D., Wagner, F., Chiodin, M., Devlin, J.C., Baron M, Hajdu, C.H., Simeone, D.M., and Yanai, I. (2020). Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nature Biotechnology 38, 333-342.
Ouyang, W., Luan, S., Xiang, X., Guo, M., Zhang, Y., Li, G., and Li, X. (2022). Profiling plant histone modification at single-cell resolution using snCUT&Tag. Plant Biotechnology Journal 20, 420-422.
Pireyre, M., and Burow, M. (2015). Regulation of MYB and bHLH transcription factors: a glance at the protein level. Molecular Plant 8, 378-388.
Reynoso, M.A., Borowsky, A.T., Pauluzzi, G.C., Yeung, E., Zhang, J., Formentin, E., Velasco, J., Cabanlit, S., Duvenjian, C., and Prior, M.J., et al. (2022). Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Development Cell57, 1177-1192.
Rhee, S.Y., Birnbaum, K.D., and Ehrhardt, D.W. (2019). Towards Building a Plant Cell Atlas. Trends in Plant Science 24, 303-310.
Ryu, K.H., Huang, L., Kang, H.M., and Schiefelbein, J. (2019a). Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells. Plant Physiology 179, 1444-1456.
Ryu, K.H., Huang, L., Kang, H.M., and Schiefelbein, J. (2019b). Single-Cell RNA Sequencing Resolves Molecular Relationships Among Individual Plant Cells. Plant Physiology 179, 1444-1456.
Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 13, 2498-2504.
Song, Y.H., Shim, J.S., Kinmonth-Schultz, H.A., and Imaizumi, T. (2015). Photoperiodic flowering: time measurement mechanisms in leaves. Annual Review of Plant Biology 66, 441-464.
Sunaga-Franze, D.Y., Muino, J.M., Braeuning, C., Xu, X., Zong, M., Smaczniak, C., Yan, W., Fischer, C., Vidal, R., and Kliem, M., et al. (2021). Single-nucleus RNA sequencing of plant tissues using a nanowell-based system. The Plant Journal 108, 859-869.
Szklarczyk, D., Gable, A.L., Nastou, K.C., Lyon, D., Kirsch, R., Pyysalo, S., Doncheva, N.T., Legeay, M., Fang, T., and Bork, P., et al. (2021). The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Research 49, D605-D612.
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N.J., Livak, K.J., Mikkelsen, T.S., and Rinn, J.L. (2014). The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nature Biotechnology 32, 381-386.
Wang, Y., Yuan, P., Yan, Z., Yang, M., Huo, Y., Nie, Y., Zhu, X., Qiao, J., and Yan, L. (2021). Single-cell multiomics sequencing reveals the functional regulatory landscape of early embryos. Nature Communications 12, 1247.
Wendrich, J.R., Yang, B., Vandamme, N., Verstaen, K., Smet, W., Van de Velde, C., Minne, M., Wybouw, B., Mor, E., and Arents, H.E., et al. (2020). Vascular transcription factors guide plant epidermal responses to limiting phosphate conditions. Science 370(6518):eaay4970.
Wolf, F.A., Hamey, F.K., Plass, M., Solana, J., Dahlin, J.S., Gottgens, B., Rajewsky, N., Simon, L., and Theis, F.J. (2019). PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biology 20, 59.
Xia, K., Sun, H.X., Li, J., Li, J., Zhao, Y., Chen, L., Qin, C., Chen, R., Chen, Z., and Liu, G., et al. (2022). The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves. Development Cell 57, 1299-1310.
Xu, M., Du Q, Tian, C., Wang, Y., and Jiao, Y. (2021). Stochastic gene expression drives mesophyll protoplast regeneration. Science Advances 7(33):eabg8466.
Xu, W., Wen, Y., Liang, Y., Xu, Q., Wang, X., Jin, W., and Chen, X. (2021). A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility. Nature Protocol 16, 4084-4107.
Xu, Z., Wang, Q., Zhu, X., Wang, G., Qin, Y., Ding, F., Tu, L., Daniell, H., Zhang, X., and Jin, S. (2022). Plant Single Cell Transcriptome Hub (PsctH): an integrated online tool to explore the plant single-cell transcriptome landscape. Plant Biotechnology Journal 20, 10-12.
Yin, D., Ji, C., Song, Q., Zhang, W., Zhang, X., Zhao, K., Chen, C.Y., Wang, C., He, G., and Liang, Z., et al. (2020). Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut. Advanced Science (Weinh) 7, 1901672.
Zhai, N., and Xu, L. (2021). Pluripotency acquisition in the middle cell layer of callus is required for organ regeneration. Nature Plants 7, 1453-1460.
Zhang, T.Q., Chen, Y., and Wang, J.W. (2021). A single-cell analysis of the Arabidopsis vegetative shoot apex. Development Cell 56, 1056-1074.
Zhang, T.Q., Xu, Z.G., Shang, G.D., and Wang, J.W. (2019). A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root. Molecular Plant 12, 648-660.
Zhixin, L., Yaping, Z., Jinggong, G., Jiaoai, L., Zixia, T., Zhinan, Z., Jiajing, W., Rui, W., Bo, Z., and Yongjian, H., et al. (2020). Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing. Molecular Plant 13(8):1178-1193.
Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M.K., Zhang, C., Chang, W.C., Zhang, L., Zhang, X., and Tang, R., et al. (2019). The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics 51, 865-876.