Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors in Rosa roxburghii During Fruit
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ORIGINAL PAPER
Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors in Rosa roxburghii During Fruit Ripening Min Lu 1 & Wen-Tao Ma 1 & Yu-Qian Liu 1 & Hua-Ming An 1,2 & Richard A. Ludlow 3
# Springer Science+Business Media, LLC, part of Springer Nature 2020
Abstract The high lignin content of Rosa roxburghii fruits imparts a strong rough taste, which has restricted its use in industry. Little is known about the molecular mechanisms underlying lignin biosynthesis in R. roxburghii fruits. Illumina and single-molecule real-time (SMRT) sequencing platforms were combined to analyze the transcriptomic changes during the ripening of R. roxburghii fruits. After assembly, 67,739 transcripts with an average length of 1866 bp were obtained, of which 17,470 transcripts were differentially expressed during fruit ripening. Biological pathway analysis putatively identified 25 differentially expressed genes were involved in lignin biosynthesis. Furthermore, 43 putative transcription factors were identified, including bHLH, bZip, Dof, MYB, NAC, WRKY, and zf-HD, which were previously reported to control lignin biosynthesis. Among which, 28 were positive transcription factors and 15 were negative. Quantitative RT-PCR analysis of candidate genes and transcription factors correlated with the transcriptome data. The transcriptomic data generated in this study provide a basis for further studies of fruit ripening in R. roxburghii. Keywords Next-generation sequencing . Rosa roxburghii Tratt. . Lignin biosynthesis . Transcription factor . Fruit ripening
Introduction Rosa roxburghii Tratt. is a perennial shrub rose that is endemic to China, especially common in the Guizhou Province. It is a medicinal plant with several nutritional and functional Key Message 1. The transcriptome of Rosa roxburghii fruits at several stages of ripening was studied to identify genes related to lignin biosynthesis. 2. Data from short-read (Illumina) and long-read (PacBio) NGS sequencing platforms was used to assemble the transcriptome. 3. From differentially expressed transcripts between three ripening states, 25 were putatively identified as lignin associated. 4. Putatively lignin-related transcription factors (43) were identified. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11105-020-01193-3) contains supplementary material, which is available to authorized users. * Hua-Ming An [email protected] 1
Agricultural College, Guizhou University, Guiyang, Guizhou, China
2
Guizhou Engineering Research Center for Fruit Crops, Guiyang, Guizhou, China
3
School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, UK
components that have been shown effective in the treatment of various diseases, including some cancers (van Rensburg et al. 2005; Liu et al. 2012). To date, there was only one cultivar “Guinong 5” (Fan et al. 2011) and some elite lines have been identified, the economic cultivation area of this only one cultivar in China covers m
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