Physiological and transcriptomic analyses to reveal underlying phenolic acid action in consecutive monoculture problem of <i>Polygonatum odoratum</i>

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Abstract

Background

The root rot of fragrant solomonseal ( Polygonatum odoratum) has occurred frequently in the traditional P. odoratum cultivating areas in recent years, causing a heavy loss in yield and quality. The phenolic acids in soil, which are the exudates from the P. odoratum root, act as allelochemicals that contribute to the consecutive monoculture problem (CMP) of the medicinal plant. The aim of this study was to get a better understanding of P. odoratum CMP.

Results

The phenolic acid contents, the nutrient chemical contents, and the enzyme activities related to the soil nutrient metabolism in the first cropping (FC) soil and continuous cropping (CC) soil were determined, and the differentially expressed genes (DEGs) related to the regulation of the phenolic acids in roots were analyzed. The results showed that five low-molecule-weight phenolic acids were detected both in the CC soil and FC soil, but the phenolic acid contents in the CC soil were significantly higher than those in the FC soil except vanillic acid. The contents of the available nitrogen, available phosphorus, and available potassium in the CC soil were significantly decreased, and the activities of urease and sucrase in the CC soil were significantly decreased. The genomic analysis showed that the phenolic acid anabolism in P. odoratum in the CC soil was promoted. These results indicated that the phenolic acids were accumulated in the CC soil, the nutrient condition in the CC soil deteriorated, and the nitrogen metabolism and sugar catabolism of the CC soil were lowered. Meantime, the anabolism of phenolic acids was increased in the CC plant.

Conclusions

The CC system promoted the phenolic acid anabolism in P. odoratum and made phenolic acids accumulate in the soil.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12870-021-03135-x.

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Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

Manfred Grabherr, Brian Haas, Moran Yassour … (2011)

Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from recently duplicated genes. In all cases, Trinity performs better than other available de novo transcriptome assembly programs, and its sensitivity is comparable to methods relying on genome alignments. Our approach provides a unified and general solution for transcriptome reconstruction in any sample, especially in the complete absence of a reference genome.

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Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber (2010)

High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.

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Plant phenolics: recent advances on their biosynthesis, genetics, and ecophysiology.

Veronique Cheynier, Gilles Comte, Kevin Davies … (2013)

Land-adapted plants appeared between about 480 and 360 million years ago in the mid-Palaeozoic era, originating from charophycean green algae. The successful adaptation to land of these prototypes of amphibious plants - when they emerged from an aquatic environment onto the land - was achieved largely by massive formation of "phenolic UV light screens". In the course of evolution, plants have developed the ability to produce an enormous number of phenolic secondary metabolites, which are not required in the primary processes of growth and development but are of vital importance for their interaction with the environment, for their reproductive strategy and for their defense mechanisms. From a biosynthetic point of view, beside methylation catalyzed by O-methyltransferases, acylation and glycosylation of secondary metabolites, including phenylpropanoids and various derived phenolic compounds, are fundamental chemical modifications. Such modified metabolites have altered polarity, volatility, chemical stability in cells but also in solution, ability for interaction with other compounds (co-pigmentation) and biological activity. The control of the production of plant phenolics involves a matrix of potentially overlapping regulatory signals. These include developmental signals, such as during lignification of new growth or the production of anthocyanins during fruit and flower development, and environmental signals for protection against abiotic and biotic stresses. For some of the key compounds, such as the flavonoids, there is now an excellent understanding of the nature of those signals and how the signal transduction pathway connects through to the activation of the phenolic biosynthetic genes. Within the plant environment, different microorganisms can coexist that can establish various interactions with the host plant and that are often the basis for the synthesis of specific phenolic metabolites in response to these interactions. In the rhizosphere, increasing evidence suggests that root specific chemicals (exudates) might initiate and manipulate biological and physical interactions between roots and soil organisms. These interactions include signal traffic between roots of competing plants, roots and soil microbes, and one-way signals that relate the nature of chemical and physical soil properties to the roots. Plant phenolics can also modulate essential physiological processes such as transcriptional regulation and signal transduction. Some interesting effects of plant phenolics are also the ones associated with the growth hormone auxin. An additional role for flavonoids in functional pollen development has been observed. Finally, anthocyanins represent a class of flavonoids that provide the orange, red and blue/purple colors to many plant tissues. According to the coevolution theory, red is a signal of the status of the tree to insects that migrate to (or move among) the trees in autumn. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

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Author and article information

Contributors

Yong Chen: henon@163.com

Yihong Hu: huyhongwangyi@163.com

Journal

Journal ID (nlm-ta): BMC Plant Biol

Journal ID (iso-abbrev): BMC Plant Biol

Title: BMC Plant Biology

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2229

Publication date (Electronic): 7 August 2021

Publication date PMC-release: 7 August 2021

Publication date Collection: 2021

Volume: 21

Electronic Location Identifier: 362

Affiliations

[1 ]GRID grid.440781.e, Collaborative Innovation Center for Field Weeds Control of Hunan Province, , Hunan University of Humanities, Science and Technology, ; Loudi, 417000 China

[2 ]GRID grid.257160.7, ISNI 0000 0004 1761 0331, College of Agronomy, , Hunan Agricultural University, ; Changsha, 410128 China

Article

Publisher ID: 3135

DOI: 10.1186/s12870-021-03135-x

PMC ID: 8349006

PubMed ID: 34364388

SO-VID: baf750e1-ef47-4c65-accc-00358c929abc

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 23 March 2021

Date accepted : 25 July 2021

Custom metadata

ScienceOpen disciplines: Plant science & Botany

Keywords: fragrant solomonseal,root rot,continuous cropping soil,first cropping soil,low-molecule-weight phenolic acids,genomic analysis

Data availability:

ScienceOpen disciplines: Plant science & Botany

Keywords: fragrant solomonseal, root rot, continuous cropping soil, first cropping soil, low-molecule-weight phenolic acids, genomic analysis

Physiological and transcriptomic analyses to reveal underlying phenolic acid action in consecutive monoculture problem of Polygonatum odoratum

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Abstract

Background

Results

Conclusions

Supplementary Information

Related collections

Plant MYBs

Most cited references 50

Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data

Differential expression analysis for sequence count data

Plant phenolics: recent advances on their biosynthesis, genetics, and ecophysiology.

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