Evidence map›Paper›PMID 32240514›Full record

ArticleGenes & genomics2020

Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation.

Sujung Kim, Hualin Nie, Byungki Jun, Jiseong Kim, Jeongeun Lee, Seungill Kim, Ekyune Kim, Sunhyung Kim

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Article in Genes & genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
1.9field-weighted citation impact, top 14% 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

2 citing papers in PubMed, 8 citations in OpenAlex.

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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 2 countries.

Sujung KimDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
Hualin NieDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
Byungki JunDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
Jiseong KimDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
Jeongeun LeeDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
Seungill KimDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea.
Ekyune KimCollege of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongbuk, 38430, Korea.
Sunhyung KimDepartment of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea. pgel2006@gmail.com.
University of Seoul · KRCatholic University of Daegu · KRUniversity of Agribusiness and Rural Development · BG

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear.

objectiveTo understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato.

methodsRNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression.

results42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation.

conclusionsThe detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.

Indexed as

TranscriptomeGene Expression Regulation, DevelopmentalGene Expression Regulation, PlantGibberellinsIndoleacetic AcidsIpomoea batatasOxidative StressPlant ProteinsPlant RootsTranscription FactorsGibberellinsIndoleacetic AcidsPlant ProteinsTranscription FactorsDifferentially expressed genesQuantitative real-time RT-PCRRoot formationStem cuttingsSweet potatoTranscriptome

Identifiers

PMID32240514
OpenAlexW3014172864

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Registered trials

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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.