Functional & Integrative Genomics

, Volume 18, Issue 6, pp 659–671 | Cite as

Comparative genomics analysis reveals gene family expansion and changes of expression patterns associated with natural adaptations of flowering time and secondary metabolism in yellow Camellia

  • Xinlei Li
  • Zhengqi Fan
  • Haobo Guo
  • Ning Ye
  • Tao Lyu
  • Wen Yang
  • Jie Wang
  • Jia-Tong Wang
  • Bin Wu
  • Jiyuan Li
  • Hengfu YinEmail author
Original Article


Yellow-flowering species are unique in the genus Camellia not only for their bright yellow pigments but also the health-improving substances in petals. However, little is known regarding the biosynthesis pathways of pigments and secondary metabolites. Here, we performed comparative genomics studies in two yellow-flowered species of the genus Camellia with distinctive flowering periods. We obtained 112,190 and 89,609 unigenes from Camellia nitidissima and Camellia chuongtsoensis, respectively, and identified 9547 gene family clusters shared with various plant species and 3414 single-copy gene families. Global gene expression analysis revealed six comparisons of differentially expressed gene sets in different developmental stages of floral bud. Through the identification of orthologous pairs, conserved and specific differentially expressed genes (DEGs) between species were compared. Functional enrichment analysis suggested that the gibberellin (GA) biosynthesis pathway might be related to the alteration of flowering responses. Furthermore, the expression patterns of secondary metabolism pathway genes were analyzed between yellow- and red-flowered Camellias. We showed that the key enzymes involved in glycosylation of flavonoids displayed differential expression patterns, indicating that the direct glycosylation of flavonols rather than anthocyanins was pivotal to coloration and health-improving metabolites in the yellow Camellia petals. Finally, the gene family analysis of UDP-glycosyltransferases revealed an expansion of group C members in C. nitidissima. Through comparative genomics analysis, we demonstrate that changes of gene expression and gene family members are critical to the variation of natural traits. This work provides valuable insights into the molecular regulation of trait adaptations of floral pigmentation and flowering timing.


Comparative genomics Gene expression Gene family Camellia Trait adaptation Floral pigmentation 



We are grateful to the anonymous reviewer for critical comments and suggestions on the earlier version of manuscript.

Authors’ contributions

XL, WY, TL, JW, and JTW prepared samples and RNA sequencing. HG, LX, NY, and HY carried out data processing, assembly, and gene family analysis. JW, ZF, and BW performed gene expression analysis. XL, JL, and HY interpreted the data and supervised the project. HY and XL drafted the manuscript and all authors participated in revision. All authors read and approved the final manuscript.


This work was supported by Nonprofit Research Projects (CAFYBB2017ZX001-7, CAFYBB2016SZ001) of Chinese Academy of Forestry, and National Science Foundation of China (NSFC) Grant 31470697. We also acknowledge the supports from the Zhejiang province science and technology plan (2013C32075) and International Sci. & Tech. Cooperation Program of China (2016YFE0126100). We thank Prof. Tongming Yin from Nanjing Forestry University (Nanjing, China) for the help of YellowCamelliaDB web portal.

Compliance with ethical standards

Competing interests

The authors declare that they have no competing interests.

Supplementary material

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ESM 1 (PDF 429 kb)
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Supplementary table 1 (DOCX 17 kb)
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Supplementary table 2 (DOCX 20 kb)
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Supplementary table 3 (DOCX 22 kb)
10142_2018_617_MOESM5_ESM.docx (19 kb)
Supplementary table 4 (DOCX 18 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical ForestryChinese Academy of ForestryZhejiangChina
  2. 2.Key Laboratory of Forest Genetics and BreedingChinese Academy of ForestryZhejiangChina
  3. 3.Colleges of Engineering and Computer Science, SimCenterUniversity of Tennessee ChattanoogaChattanoogaUSA
  4. 4.The Southern Modern Forestry Collaborative Innovation CenterNanjing Forestry UniversityNanjingChina
  5. 5.College of Marine SciencesNingbo UniversityNingboChina

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