Transcriptomic analysis of Lycium ruthenicum Murr. during fruit ripening provides insight into structural and regulatory genes in the anthocyanin biosynthetic pathway

PLoS One. 2018 Dec 7;13(12):e0208627. doi: 10.1371/journal.pone.0208627. eCollection 2018.

Abstract

Fruit development in Lycium ruthenicum Murr. involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptomic responses during fruit ripening in L. ruthenicum, most have been limited in scope, and thus systematic data representing the structural genes and transcription factors involved in anthocyanin biosynthesis are lacking. In this study, the transcriptomes of three ripening stages associated with anthocyanin accumulation, including S1 (green ripeness stage), S2 (skin color change) and S3 (complete ripeness stage) in L. ruthenicum were investigated using Illumina sequencing. Of a total of 43,573 assembled unigenes, 12,734 were differentially expressed during fruit ripening in L. ruthenicum. Twenty-five significantly differentially expressed structural genes (including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, F3'5'H, DFR, ANS and UFGT) were identified that might be associated with anthocyanin biosynthesis. Additionally, several transcription factors, including MYB, bHLH, WD40, NAC, WRKY, bZIP and MADS, were correlated with the structural genes, implying their important interaction with anthocyanin biosynthesis-related genes. Our findings provide insight into anthocyanin biosynthesis and regulation patterns in L. ruthenicum and offer a systematic basis for elucidating the molecular mechanisms governing anthocyanin biosynthesis in L. ruthenicum.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anthocyanins / biosynthesis*
  • Fruit / growth & development*
  • Gene Expression Profiling*
  • Lycium / genetics*
  • Lycium / growth & development*
  • Lycium / metabolism
  • Molecular Sequence Annotation
  • Transcription Factors / metabolism

Substances

  • Anthocyanins
  • Transcription Factors

Grants and funding

This work was supported by the National Natural Science Foundation of China (grant No. 31560215, 31760244 and 31700338) (http://www.nsfc.gov.cn/), the Key Science and Technology Foundation of Gansu Province (GS-GEF/OP12-02) (http://www.gsly.gov.cn/) and the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2014-LIHPS-08) (http://www.caas.net.cn/). YM had roles in the study conceptualization and design, also the plant material preparation. HD had roles in the RNA-seq data analysis and the manuscript writing. RM had a role in the manuscript revision.