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De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing

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Abstract

Rhododendron molle G. Don occupies an important phylogenetic node in the genus rhododendron with unique yellow flower and medicinal functions. However, only limited genetic resources and their genome information are available for the generation of rhododendron flowers. The next generation sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provide a turning point for rhododendron research. Our goal is to use the genetic information to facilitate the relevant research on flowering and flower color formation in R. molle. In total, 66,026 unigenes were identified, among which 31,298 were annotated in the NCBI non-redundant protein database and 22,410 were annotated in the Swiss-Prot database. Of these annotated unigenes, 9490 and 18,680 unigenes were assigned to clusters of orthologous groups and gene ontology categories, respectively. A total of 7177 genes were mapped to 118 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. In addition, 8266 simple sequence repeats (SSRs) were detected, and these SSRs will undoubtedly benefit rhododendron breeding work. Metabolic pathway analysis revealed that 32 unigenes were predicted to be involved in carotenoid biosynthesis. Our transcriptome revealed 32 engines that encode key enzymes in the carotenoid biosynthesis pathway, including PSY, PDS, LCYB, LCYE, etc. The content of β-carotene was much higher than the other carotenoids throughout the flower development. It was consistent with the key genes expression level in the carotenoid biosynthesis pathway by the Illumina expression profile analysis and the qRT-PCR analysis. Our study identified genes associated with carotenoid biosynthesis in R. molle and provides a valuable resource for understanding the flowering and flower color formation mechanisms in R. molle.

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Acknowledgements

This work was supported by the National Science and Technology Program (2013BAD01B070403), National Natural Science Foundation of China (31600570), Jiangsu Natural Science Foundation (BK20150548), Jiangsu Forestry Sciences Innovation Fund (lykj[2017]48), and Jiangsu Agricultural Sciences Innovation Fund (CX(16)1005).

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Authors and Affiliations

  1. Institute of Leisure Agriculture, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China

    Zheng Xiao, Jiale Su, Xiaobo Sun, Chang Li, Lisi He, Shangping Cheng & Xiaoqing Liu

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  1. Zheng Xiao
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  2. Jiale Su
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  3. Xiaobo Sun
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  4. Chang Li
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Correspondence to Xiaoqing Liu.

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Zheng Xiao declares that he does not have conflict of interest. Jiale Su declares that he does not have conflict of interest. Xiaobo Sun declares that she does not have conflict of interest. Chang Li declares that she does not have conflict of interest. Lisi He declares that she does not have conflict of interest. Shangping Cheng declares that he does not have conflict of interest. Xiaoqing Liu declares that she does not have conflict of interest.

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Xiao, Z., Su, J., Sun, X. et al. De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing. Genes Genom 40, 591–601 (2018). https://doi.org/10.1007/s13258-018-0662-8

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