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Genome-Wide Identification and Characterization of DIR Genes in Medicago truncatula

  • Min SongEmail author
  • Xiangyong Peng
Original Article

Abstract

Dirigent proteins (DIRs) are critically involved in the formation of lignans, a diverse and widely distributed class of secondary plant metabolites exhibiting interesting pharmacological activities and implicated in natural plant defense. However, no detailed information is available about DIR gene family in Medicago truncatula. In this study, a total of 45 DIR genes were identified in M. truncatula. DIR proteins have variability in sequence. Most MtDIR genes have no intron. All MtDIR proteins contain single dirigent domain. A large number of MtDIR genes were expanded via gene duplication, and 37 MtDIR genes were duplicated in tandem. Digital expression data showed that 40% MtDIR genes had a higher expression level in the root. Analysis of RNA-seq and microarray data indicated that more than 30% MtDIR genes were responsive to biotic and/or abiotic treatments. This study will facilitate further studies on DIR family and provide useful clues for functional validation of DIR genes in higher plants.

Keywords

Medicago truncatula Dirigent domain Gene family Expression pattern 

Notes

Author Contributions

MS designed the experiments and wrote the paper. XYP analyzed the data. All authors read and approved the final manuscript.

Funding

This work was supported by the Science and Technology project of Shandong Education Department to Min Song (Grant No. J15LE02), and China Postdoctoral Science Foundation funded project to Min Song (Grant No. 2018M632646).

Compliance with Ethical Standards

Conflict of interest

Min Song declares that she does not have conflict of interest. Xiangyong Peng declares that he does not have conflict of interest.

Ethical Approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Informed Consent

This article does not contain any studies with human participants.

Supplementary material

10528_2019_9903_MOESM1_ESM.docx (28 kb)
Supplementary file1 (DOCX 28 kb) Text S1. Sequences of MtDIR CDSs and proteins.
10528_2019_9903_MOESM2_ESM.docx (305 kb)
Supplementary file2 (DOCX 305 kb) Figure S1. Phylogenetic tree (Left) and gene structure (Right) of MtDIRs. Orange boxes represent exons, blue lines represent UTRs, and black lines show introns. The lengths of the exons, introns and UTRs were drawn to scale. Figure S2. Hierarchial clustering display of DIR genes of M. truncatula seedlings exposed to salinity. Two week-old seedlings were grown in hydroponics media with 180mM NaCl for 0, 6, 24 and 48h (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc¬GSE13921). The logFC values were shown in heatmap drown by ClustVis tool. Rows were centered, no scaling was applied to rows. Rows were clustered using Euclidean distance and average linkage.
10528_2019_9903_MOESM3_ESM.docx (16 kb)
Supplementary file3 (DOCX 16 kb) Table S1. Subcellular localization, N-Glyc (Asn) position andsignal peptide of DIR genes in M. truncatula.
10528_2019_9903_MOESM4_ESM.docx (16 kb)
Supplementary file4 (DOCX 16 kb) Table S2. Motif sequences identified by the MEME Suite.
10528_2019_9903_MOESM5_ESM.xlsx (21 kb)
Supplementary file5 (XLSX 21 kb) Table S3. Cis-elements in the promoter region of 45 MtDIR genes.
10528_2019_9903_MOESM6_ESM.docx (21 kb)
Supplementary file6 (DOCX 20 kb) Table S4. Expression levels of MtDIR genes measured by transcriptome analysis.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.College of Life ScienceQufu Normal UniversityQufuPeople’s Republic of China

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