Abstract
Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.
Key message
Comparative transcriptome indicated that the flower color of R. palmatum complex was co-regulated by the expression profiles of genes and transcript factors involved in anthocyanin synthesis and natural selection.
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Data availability
All the raw reads generated in this study have been deposited in the NCBI with the BioProject Accession Number of PRJNA735904.
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Acknowledgements
This study was co-supported by the National Natural Science Foundation of China (Nos. 81903739 and 31770364), the Natural Science Foundation of Shaanxi Province (Nos. 2020JQ-024 and 2020JZ-05) and the China Postdoctoral Science Foundation (No. 2018M643680). The Royal Botanic Garden Edinburgh is supported by the Scottish Government’s Rural and Environment Science and Analytical Services Division.
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TZ and XW conceived and designed the experiments. TZ collected samples. TZ, JS, YZ and CG performed the experiments and analyzed the data. TZ, MR and XW wrote the paper. All authors read and approved the final manuscript.
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Supplementary file1 (ZIP 9249 kb)—Figure S1 Top-hit species distribution for non-redundant unigene sequences against the NCBI-nr. database. Figure S2 Gene Ontology (GO) classification of non-redundant unigene sequences from the R. palmatum complex. Figure S3 The top 20 pathway terms enriched in the KEGG database for the DEGs between PL and ZK samples. The q-value indicates the significance of the rich factor ranging from 0 to 1. The circle size represents the number of DEGs. Figure S4 Distribution of transcription factors. Figure S5 Distribution of dN and dS for 6915 pairs of orthologs between ZK and PL samples. Red and green colored dots indicate genes that have undergone positive or negative selection, respectively. Table S1 Annotation information of all non-redundant unigenes in eight databases. Table S2 GO enrichment results of DEGs between PL and ZK samples. Table S3 Annotation results of DEGs between PL and ZK samples in eight databases. Table S4 dN, dS values and dN/dS ratio between orthologs of PL and ZK. Table S5 Annotation information of genes which have undergone positive selection. Table S6 Candidate genes involved in the biosynthesis of anthocyanins which have undergone positive selection.
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Zhou, T., Sun, J., Zhai, Y. et al. Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism. Plant Mol Biol 110, 187–197 (2022). https://doi.org/10.1007/s11103-022-01299-0
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DOI: https://doi.org/10.1007/s11103-022-01299-0