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

Abstract

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.

Agasicles hygrophila attack increases nerolidol synthase gene expression in Alternanthera philoxeroides, facilitating host finding

“…Along with the full-length transcriptome sequencing of A. hygrophila 41 , we provided valuable data for the comprehensive study of the molecular mechanisms underlying the specificity between A. philoxeroides and A. hygrophila . Few studies have reported sequencing data for other species in the Alternanthera genus; the genetic and protein data obtained from sequencing other related species in this family are limited to several edible and medicinal crops, such as Amaranthus caudatus L. 42 , Amaranthus hypochondriacus L. 43 – 45 , and Achyranthes bidentata Blume 46 . The transcriptome data of A. philoxeroides has therefore enriched the genetic data available for the Amaranthaceae, especially the Alternanthera genus.…”

Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery

“…In the terminal of lignin biosynthesis, peroxidase (POD) catalyzed individual monolignols to polymerize the complex lignin ( Figure 2 ). The comparison between the CM (consecutive monoculture) and NG (normal growth for 1 year) root transcriptomes of Achyranthes bidentata revealed that genes encoding POD were mostly activated in the CM condition, suggesting the contribution of POD to lignin biosynthesis pathway ( Yang et al., 2018 ). Comparing to the number of research in the area of phenolic acids in medicinal plants, research that focus on exploring lignin synthetic pathway from medicinal plants are limited.…”