Plant Cell Reports

, Volume 37, Issue 4, pp 611–625 | Cite as

The root transcriptome of Achyranthes bidentata and the identification of the genes involved in the replanting benefit

  • Yan Hui Yang
  • Ming Jie Li
  • Yan Jie Yi
  • Rui Fang Li
  • Cheng Dong
  • Zhong Yi Zhang
Original Article


Key message

The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis.


The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called “replanting benefit” is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.


A. bidentata Consecutive monoculture RNA-seq Technology, transcript profiles Differentially transcribed genes Function analysis 



This work was supported by Grants from the National Natural Science Foundation of China (nos. 81403037, 81503193 and 31601366) and the Science Foundation of Henan University of Technology (no. 2017RCJH05).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

299_2018_2255_MOESM1_ESM.doc (709 kb)
Supplementary material 1 (DOC 709 KB)
299_2018_2255_MOESM2_ESM.doc (1.8 mb)
Supplementary material 2 (DOC 1806 KB)


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

Authors and Affiliations

  1. 1.College of BioengineeringHenan University of TechnologyZhengzhouChina
  2. 2.College of Crop SciencesFujian Agriculture and Forestry UniversityFuzhouChina

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