A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Growth and Tissue Sampling
2.2. RNA Preparation, Libraries, and Sequencing
2.3. Analysis of Gene Expression
- Functional enrichment analysis was performed with the Medicago Classification Superviewer (http://bar.utoronto.ca/ntools/cgi-bin/ntools_classification_superviewer_medicago.cgi accessed multiple times in July 2020) using the default settings and a significance threshold of p < 0.05 [18].
3. Results
3.1. Constitutively Altered Gene Expression in sunn-4 Roots and Shoots
3.2. Response of Genes to Rhizobia in Roots in Wild-Type and sunn-4
3.2.1. Nodulation Pathway Genes
3.2.2. TMLs
3.2.3. Genes Unresponsive to Rhizobia in sunn-4 Mutants
3.2.4. Induction of Small Signaling Peptide Genes in Roots
3.3. Rhizobial Response in Shoots
4. Discussion
4.1. Expression Differences in AON Mutants
4.2. Peptide Responses to Rhizobia
4.3. Rhizobial Response in AON Mutants Includes Induction of TML Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Peptide Family | Induced Genes /Total Genes (v4 Genome) | Increase 12 hpi | Increase 24 hpi | Increase 48–72 hpi | Peptide Family Description |
---|---|---|---|---|---|
BBPI | 1/16 | BBPI16 | Bowman–Birk Peptidase Inhibitor | ||
CAPE | 4/21 | CAPE1 | CAPE2, CAPE16, CAPE18 | CAP-derived Peptide | |
CEP | 1/10 | CEP14 | C-terminally Encoded Peptide | ||
CLE | 10/46 | CLE13, CLE53 | CLE29, CLE35 | CLE12, CLE34, CLE37, CLE41, CLE44, CLE45 | Clavata/Embryo Surrounding Region |
EPFL | 5/21 | EPFL1, EPFL14, EPFL19, EPFL9, | Epidermal Patterning Factor-Like | ||
GASA | 4/28 | GASA25 | GASA17, GASA22, GASA29 | Gibberellic Acid Stimulated in Arabidopsis | |
GLV | 3/15 | GLV9, GLV10 | GLV8 | Golven/Root Growth Factor | |
IDA | 1/38 | IDA15 | Inflorescence Deficient in Abscission | ||
IMA | 14/14 | IMA1, IMA2, IMA3, IMA5, IMA6, IMA7, IMA8, IMA9, IMA10, IMA11, IMA12, IMA13, IMA14, IMA15 | Iron Man | ||
Kunitz | 2/48 | Kunitz13, Kunitz18 | Kunitz-P trypsin inhibitor | ||
LAT52-POE | 3/40 | LAT52/POE1, LAT52/POE12 | LAT52/POE21 | LAT52/Pollen Ole e 1 Allergen | |
LCR | 1/89 | LCR64 | Low-molecular weight Cys-rich | ||
Legin | 8/48 | Legin20 | Legin32, Legin37, Legin38, Legin42, Legin43, Legin44, Legin47 | Leginsulin | |
LP | 4/20 | LP8, LP9, LP14, LP15 | LEED..PEED | ||
N26 | 2/4 | N26-3, N26-4 | Nodulin26 | ||
NCR-A | 13/327 | NCR025, NCR037, NCR267, NCR279, NCR323, NCR376, NCR396, NCR547, NCR639, NCR685/NCR686 | Nodule-Specific Cysteine RichGroup A | ||
NCR-B | 36/365 | NCR150 | NCR031, NCR051, NCR057, NCR117, NCR157, NCR158, NCR209, NCR223, NCR229, NCR235, NCR252, NCR308, NCR386, NCR415, NCR454, NCR455, NCR465, NCR507, NCR527, NCR529, NCR567, NCR568, NCR573, NCR648, NCR657, NCR673, NCR678, NCR708, NCR713, NCR730, NCR736, NCR737, NCR738, NCR757, NCR793 | Nodule-Specific Cysteine RichGroup B | |
NodGRP | 14/54 | NodGRP15, NodGRP45 | NodGRP1B, NodGRP3C, NodGRP4, NodGRP12, NodGRP23, NodGRP30, NodGRP32, NodGRP33, NodGRP34, NodGRP35, NodGRP36 | Nodule-Specific Glycine-rich Protein | |
nsLTP | 18/132 | nsLTP53, nsLTP61, nsLTP62 | nsLTP100 | nsLTP25, nsLTP49, nsLTP50, nsLTP51, nsLTP52, nsLTP54, nsLTP72, nsLTP75, nsLTP76, nsLTP81, nsLTP83, nsLTP84, nsLTP102, nsLTP110 | Non-Specific Lipid Transfer Protein |
PCY | 11/86 | PCY16, PCY27, PCY33 | PCY47, PCY59 | PCY19, PCY35, PCY64, PCY68, PCY72, PCY78 | Plantcyanin/Chemocyanin |
16/16 | PDF5, PDF6, PDF7, PDF10, PDF13, PDF14, PDF39 | PDF2, PDF9, PDF11, PDF27, PDF36, PDF38, PDF44, PDF45, PDF57 | Plant Defensin | ||
PSK | 1/10 | PSK8 | Phytosulfokine | ||
RTFL/DVL | 2/15 | RTFL/DVL1 | RTFL/DVL13 | Rotundifolia/Devil | |
STIG-GRI | 1/18 | STIG/GRI4 | Stigma1/GRI |
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Schnabel, E.L.; Chavan, S.A.; Gao, Y.; Poehlman, W.L.; Feltus, F.A.; Frugoli, J.A. A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Curr. Issues Mol. Biol. 2023, 45, 4612-4631. https://doi.org/10.3390/cimb45060293
Schnabel EL, Chavan SA, Gao Y, Poehlman WL, Feltus FA, Frugoli JA. A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2. Current Issues in Molecular Biology. 2023; 45(6):4612-4631. https://doi.org/10.3390/cimb45060293
Chicago/Turabian StyleSchnabel, Elise L., Suchitra A. Chavan, Yueyao Gao, William L. Poehlman, Frank Alex Feltus, and Julia A. Frugoli. 2023. "A Medicago truncatula Autoregulation of Nodulation Mutant Transcriptome Analysis Reveals Disruption of the SUNN Pathway Causes Constitutive Expression Changes in Some Genes, but Overall Response to Rhizobia Resembles Wild-Type, Including Induction of TML1 and TML2" Current Issues in Molecular Biology 45, no. 6: 4612-4631. https://doi.org/10.3390/cimb45060293