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Genome-wide dissection of the chalcone synthase gene family in Oryza sativa

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Abstract

Enzymes of the chalcone synthase (CHS) family catalyze the generation of multiple secondary metabolites in fungi, plants, and bacteria. These metabolites have played key roles in antimicrobial activity, UV protection, flower pigmentation, and pollen fertility during the evolutionary process of land plants. We performed a genome-wide investigation about CHS genes in rice (Oryza sativa). The phylogenetic relationships, gene structures, chromosomal locations, and functional predictions of the family members were examined. Twenty-seven CHS family genes (OsCHS01–27) were identified in the rice genome and were found to cluster into six classes according to their phylogenetic relationships. The 27 OsCHS genes were unevenly distributed on six chromosomes, and 17 genes were found in the genome duplication zones with two segmental duplication and five tandem duplication events that may have played key roles in the expansion of the rice CHS gene family. In addition, the OsCHS genes exhibited diverse expression patterns under salicylic acid treatment. Our results revealed that the OsCHS genes exhibit both diversity and conservation in many aspects, which will contribute to further studies of the function of the rice CHS gene family and provide a reference for investigating this family in other plants.

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Acknowledgements

We thank the members of the Key Laboratory of Crop Biology of Anhui Province for their assistance in this study. This work was supported by the Natural Science Foundation of China (31371980, 31301324). We extend our thanks to the reviewers for their careful reading and helpful comments on this manuscript.

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Authors and Affiliations

  1. State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China

    Yahui Han

  2. College of Life Science, Anhui Agricultural University, Hefei, 230036, China

    Yunpeng Cao, Haiyang Jiang & Ting Ding

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  1. Yahui Han
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  2. Yunpeng Cao
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Contributions

Y. H. conceived of the study and designed the experiments, analyzed the data, and wrote the paper. Y. C. performed the experiments and analyzed the data. H. J. analyzed the data. T. D. conceived of the study and designed the experiments.

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Correspondence to Ting Ding.

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Electronic supplementary material

Table S1

Primers used in quantitative real-time PCR (qRT-PCR) (DOC 54 kb).

Table S2

Relevant information for the chalcone synthase superfamily genes of Oryza sativa (DOCX 19 kb).

Table S3

Relevant information for the chalcone synthase superfamily genes of maize, sorghum and Arabidopsis (DOC 62 kb).

Table S4

Blast2GO annotation details of 34 OsCHS protein sequences. (DOCX 29 kb).

Table S5

Major MEME motif sequences in OsCHS proteins. (DOCX 17 kb).

Table S6

Ka/Ks analysis of duplicated OsCHS paralogs. (DOCX 16 kb).

Table S7

Ka/Ks analysis of duplicated OsCHS-SbCHS and OsCHS-ZmCHS orthologs. (DOCX 16 kb).

Table S8

Values of CT for the 22 OsCHSs by quantitative real time PCR (qRT-PCR) (DOCX 27 kb).

Fig. S1

Phylogenetic tree and gene structures of the 34 predicted rice CHS proteins. The left side is the NJ tree. The right side shows the exon–intron structures. Exons, introns and untranslated regions (UTRs) are indicated by green rectangles, thin lines and blue rectangles, respectively. (GIF 72 kb)

High resolution image (TIFF 1311 kb).

Fig. S2

Phylogenetic tree of the 27 predicted OsCHS proteins with the CHSs in rice. (GIF 44 kb).

High resolution image (TIFF 247 kb).

Fig. S3

Gene Ontology analysis of the OsCHS proteins. The Blast2GO program was used to define the gene ontology. (A) Biological processes, (B) molecular functions and (C) cellular components. (GIF 95 kb).

High resolution image (TIFF 11675 kb).

Fig. S4

Motif distribution in the OsCHS proteins. The protein names and P values are annotated on the left side. The sizes and orders of motifs do not represent their size or order in the proteins. (GIF 165 kb).

High resolution image (TIFF 2010 kb).

Fig. S5

Location and duplication of CHS genes in the rice genome. The scale along each chromosome is in megabases. Duplicated genes are joined by lines. Some lines may be on top of each other. (GIF 294 kb).

High resolution image (TIFF 3708 kb).

Fig. S6

Extensive microsynteny of CHS genes across O. sativa, S. bicolor and Z. mays. The chromosomes of O. sativa, Z. mays and S. bicolor are indicated in different colors and labeled Os, Zm and Sb respectively. The scale along each chromosome is in megabases (Mb). The syntenic relationships of the CHS regions between O. sativa and Z. mays are represented by red lines, and those between O. sativa and S. bicolor are represented by blue lines. (GIF 200 kb).

High resolution image (TIFF 2095 kb).

Fig. S7

Sliding-window analysis of duplicated OsCHS genes. The gray blocks, from dark to light, represent the Chal_sti_synt_N and Chal_sti_synt_C domains. The window size is 150 bp, and the step size is 9 bp. (GIF 139 kb).

High resolution image (TIFF 2009 kb).

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Han, Y., Cao, Y., Jiang, H. et al. Genome-wide dissection of the chalcone synthase gene family in Oryza sativa . Mol Breeding 37, 119 (2017). https://doi.org/10.1007/s11032-017-0721-x

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