Diversity of organ-specific plant transcriptomes

Abstract

Plant transcriptomes comprise nuclear and organellar (mitochondrial and plastid) transcripts expressed by nuclear and organellar genomes, respectively. They are spatiotemporally shaped during development. The aim of this review was to summarize the most relevant transcriptomic responses in various plant organs and tissues in the developmental context. The dynamicity of organ- or tissue-specific transcriptomic responses was discussed based on the complexity and diversity of the recently characterized plant genomes and transcriptomes. Data were taken from high-throughput studies on numerous species, including model, crop and medicinal plant species. Vascular element transcriptomes as well as the root, leaf, flower and seed transcriptomes were exhaustively characterized. Transcriptomic alterations within various tissue and organ-specific transcriptomes employed various gene classes depending on the species, a given organ/tissue and the developmental stage. The specificity of organ-specific transcriptomes related to the over-representation of certain gene families and a plethora of transcription factors was focused. In addition, transcriptomes of medicinal plant species were characterized. The perspectives of medicinal plant species to synthesize valuable secondary metabolites (including quinones, carotenoids, phytoestrogens, terpenoids, steroids, flavonoids, phenolic derivatives, polysaccharides, glycosides, anthocyanins and macrocyclic peptides) were described based on organ transcriptomic patterns. Future research should be broadened by investigation of transcriptomes from field grown plants. Also, the potential of biomedical plants should be better revealed by genetic engineering and genome editing in further biotechnological applications.

Keywords: RNA-seq; medicinal plant species; plant organs; plant transcriptome; secondary metabolites.

FIGURE 1

The summary of gene functions (GO: terms) for the most relevant, upregulated gene families in diverse plant organs. The most common and specific organo-specific transcriptomic replies from cited literature are shown. The data specific for distinct organs were presented in diverse colors on Venn diagram. Venn diagrams for five datasets (representing roots, vascular elements, leaves, flowers and seeds) were drawn using tool from https://www.biotools.fr/misc/venny.

FIGURE 2

The summary of the most important TFs in diverse plant organs. The most common and specific organo-specific TFs from cited literature are shown. The data specific for distinct organs were presented in diverse colors on Venn diagram. Venn diagrams for five datasets (representing roots, vascular elements, leaves, flowers and seeds) were drawn using tool from https://www.biotools.fr/misc/venny.

FIGURE 3

Tissue- and developmentally specific expression patterns in roots and leaves. The functional GO: terms for the most relevant, upregulated gene families and the most important TFs in various tissues of roots and leaves and across the diverse developmental stages were shown in separate boxes.

FIGURE 4

Tissue- and developmentally specific expression patterns in seeds. Venn diagrams showing (A) most abundant TFs active during various seed developmental stages (cotyledon, germination, globular, mature green, postmature green); (B) mostly enriched protein families coded by DEGs in coleorhiza, embryo, scutellum, endosperm as well as aleurone layer. Venn diagrams for five datasets at each time were drawn using tool from https://www.biotools.fr/misc/venny.

FIGURE 5

The pharmaceutical potential of selected medicinal plant species. Valuable compounds (formulas added) as secondary metabolism products of medicinal plant species were shown together with small species images.

FIGURE 6

The detailed number of publications per year related to RNA-seq and investigated plant organs, medicinal plant species and single cell studies (values indicated above each bar; data for subterms indicated by the various colors and checking patterns). Keywords used in the NCBI PubMed search (https://pubmed.ncbi.nlm.nih.gov/) included: “plant,” “RNA-seq,” and the given subterm (indicated in the legend below the histogram). Data for roots, leaves, flowers, seeds, medicinal plant species and scRNA-seq were presented from 2010 onward. The analysis was performed in June 2025.