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Transcriptome-sequencing analyses reveal putative genes related to flower color variation in Chinese Rosa rugosa

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Abstract

Rosa rugosa is an excellent landscaping plant famous for its fragrance and primarily red flower. In this study, transcriptome sequencing on R. rugosa ‘Red Zizhi’ and its bud mutations R. rugosa ‘Pink Zizhi’ and R. rugosa ‘White Zizhi’ were conducted using the Illumina HiSeq™ 2000 platform. In total, 103,446 assembled contigs and 51,332 unigenes were obtained with average lengths of 359 and 735 bp, respectively. A total of 40,018 (77.96%) unigenes were functionally annotated; 20,054 (39.07%) of which were annotated in 128 Kyoto Encyclopedia of Genes and Genomes database pathways. Moreover, 316 (1.58%) unigenes were annotated to phenylalanine synthetic pathways related to coloration, 191 (0.95%) to flavonoid synthetic pathways and 15 (0.07%) to anthocyanin synthetic pathways. Analysis of differential gene expression profiles showed that ‘White Zizhi’ and ‘Pink Zizhi’ differed by 431 unigenes, ‘Red Zizhi’, and ‘Pink Zizhi’ by 1319 unigenes, and ‘Red Zizhi’ and ‘White Zizhi’ by 1324 unigenes. Five candidate genes were possibly highly related to the biosynthesis of rose flower pigments; they were selected by applying the differentially expressed gene method. Analyses were conducted to confirm the expression patterns of selected genes and changes and contents of flower pigments in petals of the three rose varieties in different flower development stages. Finally, by analyzing the relationship between gene expression and flower pigment synthesis, we discovered that the 4-coumarate:CoA ligase gene is possibly related to the formation of pink flowers, and low dihydroflavonol 4-reductase gene expression levels may be related to color formation in ‘White Zizhi’.

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Abbreviations

4CL:

4-Coumarate:CoA ligase gene

CHS:

Chalcone synthase

CHI:

Chalcone isomerase

DHK:

Dihydrokaempferol

DHQ:

Dihydroquercetin

DHM:

Dihydromyricetin

DFR:

Dihydroflavonol 4-reductase

UA3′5′GT:

UDP-glucose:anthocyanin 3′,5′-O-glucosyltransferase

DGE:

Digital gene expression

DEGs:

Differentially expressed genes

ESI:

Electrospray ionization

HPLC:

High-performance liquid chromatography

MS:

Mass spectrometry

CDS:

Coding DNA sequence

NR:

Non-redundant protein database

Swiss-Prot:

Swiss-Prot protein database

KEGG:

Kyoto Encyclopedia of Genes and Genomes database

COG:

Cluster of orthologous groups of proteins database

NT:

Non-redundant nucleotide database

GO:

Gene ontology

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Acknowledgements

This research was funded by the National Natural Science Foundation of China (Grant Nos. 31370696 and 31772340), Key Research and Development Program of Jiangsu Province (Modern Agriculture, Grant No. BE2015339), National Natural Science Foundation of Jiangsu Province (Grant No. BK20171284), Postgraduate Training and Innovation Project of Jiangsu Province (Grant No. KYCX17_1887), and Innovation Fund for Science and Technology of Yangzhou University (Grant No. 2016CXJ063).

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Authors and Affiliations

  1. College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China

    Lixia Sheng, Wei Xia, Shu Zang, Yuqian Zeng, Xiaoyu Yuan & Liguo Feng

  2. Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, People’s Republic of China

    Guogui Ning

  3. College of Biological Sciences and Technology, Yangzhou University, Yangzhou, 225009, China

    Shuncang Zhang

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  1. Lixia Sheng
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  2. Wei Xia
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  3. Shu Zang
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  4. Yuqian Zeng
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  5. Xiaoyu Yuan
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  8. Liguo Feng
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Correspondence to Liguo Feng.

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Sheng, L., Xia, W., Zang, S. et al. Transcriptome-sequencing analyses reveal putative genes related to flower color variation in Chinese Rosa rugosa. Acta Physiol Plant 40, 62 (2018). https://doi.org/10.1007/s11738-018-2635-6

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