PCMDB: a curated and comprehensive resource of plant cell markers

Abstract

The advent of single-cell sequencing opened a new era in transcriptomic and genomic research. To understand cell composition using single-cell studies, a variety of cell markers have been widely used to label individual cell types. However, the specific database of cell markers for use by the plant research community remains very limited. To overcome this problem, we developed the Plant Cell Marker DataBase (PCMDB, http://www.tobaccodb.org/pcmdb/), which is based on a uniform annotation pipeline. By manually curating over 130 000 research publications, we collected a total of 81 117 cell marker genes of 263 cell types in 22 tissues across six plant species. Tissue- and cell-specific expression patterns can be visualized using multiple tools: eFP Browser, Bar, and UMAP/TSNE graph. The PCMDB also supports several analysis tools, including SCSA and SingleR, which allows for user annotation of cell types. To provide information about plant species currently unsupported in PCMDB, potential marker genes for other plant species can be searched based on homology with the supported species. PCMDB is a user-friendly hierarchical platform that contains five built-in search engines. We believe PCMDB will constitute a useful resource for researchers working on cell type annotation and the prediction of the biological function of individual cells.

Single‐cell transcriptome atlas reveals developmental trajectories and a novel metabolic pathway of catechin esters in tea leaves

“…To identify the cell type, we first performed orthologous gene alignments of the reported marker genes in Arabidopsis (Jin et al, 2021). The marker gene list was downloaded from the Plant Cell Marker DataBase (PCMDB, http://www.tobaccodb.…”

“…The marker gene list was downloaded from the Plant Cell Marker DataBase (PCMDB, http://www.tobaccodb. org/pcmdb/) (Jin et al, 2021), and the protein sequences of tea plant and Arabidopsis were download from the TAIR and TPIA (Garcia-Hernandez et al, 2002;Xia et al, 2019). Using the Arabidopsis marker genes as the query sequences, the homologous genes of the tea plant were searched by TBtools (BLASTP: e-value: 1-e 5 ) (Chen et al, 2020a).…”

“…Currently, scRNA‐seq of several plant species, such as Arabidopsis, strawberry, rice and maize, peanuts, and one woody plant populus were reported (Bai et al ., 2022 ; Chen et al ., 2021 ; Kim et al ., 2021 ; Li et al ., 2021 ; Liu et al ., 2020 , 2021 ; Marand et al ., 2021 ; Xie et al ., 2021 ; Zhang et al ., 2021a , b ). Through these studies, a database of cell‐specific markers and a single‐cell atlas of various tissues and organs from different species has been established, providing new insights into organ development, cell differentiation and cell division (Jin et al ., 2021 ). However, gene function identification of non‐model species often fails to reach the level of cell specificity, because of the lack of reliable specific marker genes for cell type identification.…”

“…Moreover, the relatively long growth cycles and lack of effective transgenic technologies to validate the spatial and temporal expression profiles of genes have resulted in few cell type‐specific marker genes being detected in the non‐model woody plants. This exacerbates the difficulty of cell type identification and largely explains why most scRNA‐seq analyses were done in model plants (Jin et al ., 2021 ; Liu et al ., 2021 ; Seyfferth et al ., 2021 ; Zhang et al ., 2021a ). Leaf is one of the principal vegetative organs of vascular plants for photosynthesis and transpiration.…”

First Plant Cell Atlas symposium report

“…To streamline the transfer of information between experimental systems, cell‐type marker homologs across species should be investigated. While the Plant Cell Marker DataBase already incorporates some of these functionalities (Jin et al, 2022 ), a platform enabling open‐access gene function curation would also benefit the plant biology community.…”