Evidence map›Paper›PMID 31730459›Full record

ArticleBMC genomics2019

Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum.

Qi Yang, Shibiao Liu, Xiaoning Han, Jingyi Ma, Wenhong Deng, Xiaodong Wang, Huihong Guo, Xinli Xia

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
2.3field-weighted citation impact, top 10% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed, 12 citations in OpenAlex.

  1. The genetic and developmental enigma of rhizomes: crucial traits with limited understanding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
    Review
  2. Article
  3. Review
  4. Article
  5. MicroRNAs in Medicinal Plants.International journal of molecular sciences · 2022
    Review
  6. Article
  7. Review
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 3 institutions in 1 country.

Qi YangBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China.
Shibiao LiuCollege of Biology and Environmental Sciences, Jishou University, Jishou, 416000, China.
Xiaoning HanBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China.
Jingyi MaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China.
Wenhong DengAnalytical and Testing Center, Beijing Forestry University, Beijing, 100083, China.
Xiaodong WangCentre for Imaging & Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing, China.
Huihong GuoBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China. guohh@bjfu.edu.cn.ORCID http://orcid.org/0000-0001-7344-6837
Xinli XiaBeijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing, 100083, China.
Beijing Forestry University · CNJishou University · CNMinzu University of China · CN

Funding

National Natural Science Foundation of China 31760044, 31870650
6 · The paper itself

Abstract

backgroundGynostemma pentaphyllum is an important perennial medicinal herb belonging to the family Cucurbitaceae. Aerial stem-to-rhizome transition before entering the winter is an adaptive regenerative strategy in G. pentaphyllum that enables it to survive during winter. However, the molecular regulation of aerial stem-to-rhizome transition is unknown in plants. Here, integrated transcriptome and miRNA analysis was conducted to investigate the regulatory network of stem-to-rhizome transition.

resultsNine transcriptome libraries prepared from stem/rhizome samples collected at three stages of developmental stem-to-rhizome transition were sequenced and a total of 5428 differentially expressed genes (DEGs) were identified. DEGs associated with gravitropism, cell wall biosynthesis, photoperiod, hormone signaling, and carbohydrate metabolism were found to regulate stem-to-rhizome transition. Nine small RNA libraries were parallelly sequenced, and seven significantly differentially expressed miRNAs (DEMs) were identified, including four known and three novel miRNAs. The seven DEMs targeted 123 mRNAs, and six pairs of miRNA-target showed significantly opposite expression trends. The GpmiR166b-GpECH2 module involved in stem-to-rhizome transition probably promotes cell expansion by IBA-to-IAA conversion, and the GpmiR166e-GpSGT-like module probably protects IAA from degradation, thereby promoting rhizome formation. GpmiR156a was found to be involved in stem-to-rhizome transition by inhibiting the expression of GpSPL13A/GpSPL6, which are believed to negatively regulate vegetative phase transition. GpmiR156a and a novel miRNA Co.47071 co-repressed the expression of growth inhibitor GpRAV-like during stem-to-rhizome transition. These miRNAs and their targets were first reported to be involved in the formation of rhizomes. In this study, the expression patterns of DEGs, DEMs and their targets were further validated by quantitative real-time PCR, supporting the reliability of sequencing data.

conclusionsOur study revealed a comprehensive molecular network regulating the transition of aerial stem to rhizome in G. pentaphyllum. These results broaden our understanding of developmental phase transitions in plants.

Indexed as

Gene Expression Regulation, PlantTranscriptomeAdaptation, PhysiologicalCarbohydrate MetabolismChinaCold TemperatureGene Expression ProfilingGene LibraryGene OntologyGravitropismGynostemmaMicroRNAsMolecular Sequence AnnotationPlant Components, AerialPlants, MedicinalRhizomeMicroRNAsRNA, PlantAerial stem-to-rhizome transitionGynostemma pentaphyllumIntegrated analysismiRNAsTranscriptome

Identifiers

PMID31730459
PMCPMC6858658
OpenAlexW2983545097

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.