Journal of Plant Growth Regulation

, Volume 38, Issue 1, pp 273–282 | Cite as

RNA-Sequencing Analysis Reveals Critical Roles of Hormone Metabolism and Signaling Transduction in Seed Germination of Andrographis paniculata

  • Jiayun TongEmail author
  • Rui He
  • Xiaoting Tang
  • Mingzhi Li
  • Tao Yi


Andrographis paniculata is a traditional medicinal plant widely used in South-east Asia. It is cultivated from seed; however, seed germination—even of viable seeds—is unreliable. Understanding the factors controlling germination would enable growers to devise means to improve the efficiency of cultivation. In this study, the transcriptome changes at three time points in A. paniculata seed germination process, namely 0, 28, and 48 h after sowing were analyzed using high-throughput mRNA-sequencing assay (RNA-seq). A total of 198.5 million clean reads were generated and assembled into 84,749 unigenes by merging the de novo and reference assemblies. Transcriptome comparison analysis revealed that the majority of transcriptome changes occurred in the early stage of the germination process. Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway analyses indicated that the differentially expressed genes are mainly involved in butanoate, galactose, glycerophospholipid, and carbon metabolism, and in plant hormone signal transduction. Remarkably, the expression levels of genes involved in gibberellin, abscisic acid and ethylene metabolism, and signal transduction were altered in the germination process. Expression of genes related to gibberellin catabolism was down-regulated, expression of genes related to ethylene signal transduction was activated. Especially, in the initial stage of germination, there was a high expression level of NCED5. This abscisic acid biosynthesis-related gene may play a key role in restraining seed germination. The transcriptional expression levels of related genes were verified by qRT-PCR analysis. That means the critical roles of hormone metabolism and signaling transduction in the germination of A. paniculata seeds were found. On a practical level, the results suggest that gibberellin or/and ethylene treatment in combination with presoaking seeds in warm water may effectively promote germination. This study is the first global overview of gene expression involved in seed germination of A. paniculate and provides transcriptome data for further research on the molecular regulation mechanism of seed germination.


Transcriptome analysis Seed germination Andrographis paniculata 



This work was supported by the National Natural Science Foundation of China (Grant No. 31401277); the Youth Elite Project of Guangzhou University of Chinese Medicine (Grant No. QNYC20140113).

Compliance with Ethical Standards

Conflict of interest

All authors declare no conflict of interest.

Supplementary material

344_2018_9839_MOESM1_ESM.pdf (421 kb)
Supplemental Table S1. Genes and primers for qRT-PCR analysis (PDF 420 KB)
344_2018_9839_MOESM2_ESM.pdf (148 kb)
Supplemental Table S2. A summary of the high-throughput RNA-seq quality (PDF 147 KB)
344_2018_9839_MOESM3_ESM.pdf (59 kb)
Supplemental Table S3. Assemble results of the sequencing data (PDF 58 KB)
344_2018_9839_MOESM4_ESM.pdf (102 kb)
Supplemental Table S4. Statistical summary of functional annotations of the assembled transcripts (PDF 101 KB)
344_2018_9839_MOESM5_ESM.pdf (881 kb)
Supplemental Table S5. Up-regulated genes of 28 HAS versus 0 HAS (PDF 880 KB)
344_2018_9839_MOESM6_ESM.pdf (811 kb)
Supplemental Table S6. Down-regulated genes of 28 HAS versus 0 HAS (PDF 810 KB)
344_2018_9839_MOESM7_ESM.pdf (622 kb)
Supplemental Table S7. Up-regulated genes of 48 HAS versus 28 HAS (PDF 622 KB)
344_2018_9839_MOESM8_ESM.pdf (456 kb)
Supplemental Table S8. Down-regulated genes of 48 HAS versus 28 HAS (PDF 455 KB)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Pharmaceutical SciencesGuangzhou University of Chinese MedicineGuangzhouPeople’s Republic of China
  2. 2.Research Center of Chinese Herbal Resource Science and EngineeringGuangzhou University of Chinese MedicineGuangzhouPeople’s Republic of China
  3. 3.Key Laboratory of Chinese Medicinal Resource from LingnanMinistry of EducationGuangzhouPeople’s Republic of China
  4. 4.Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese MedicinesGuangzhouPeople’s Republic of China
  5. 5.Genepioneer Biotechnologies Co. LtdNanjingPeople’s Republic of China
  6. 6.School of Chinese MedicineHong Kong Baptist UniversityHong KongPeople’s Republic of China

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