Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation
In response to colonization by rhizobia bacteria, legumes are able to form nitrogen-fixing nodules in their roots, allowing the plants to grow efficiently in nitrogen-depleted environments. Legumes utilize a complex, long-distance signaling pathway to regulate nodulation that involves signals in bot...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.861639/full |
| _version_ | 1819047456594198528 |
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| author | Yueyao Gao Bradley Selee Elise L. Schnabel William L. Poehlman William L. Poehlman Suchitra A. Chavan Julia A. Frugoli Frank Alex Feltus Frank Alex Feltus Frank Alex Feltus |
| author_facet | Yueyao Gao Bradley Selee Elise L. Schnabel William L. Poehlman William L. Poehlman Suchitra A. Chavan Julia A. Frugoli Frank Alex Feltus Frank Alex Feltus Frank Alex Feltus |
| author_sort | Yueyao Gao |
| collection | DOAJ |
| description | In response to colonization by rhizobia bacteria, legumes are able to form nitrogen-fixing nodules in their roots, allowing the plants to grow efficiently in nitrogen-depleted environments. Legumes utilize a complex, long-distance signaling pathway to regulate nodulation that involves signals in both roots and shoots. We measured the transcriptional response to treatment with rhizobia in both the shoots and roots of Medicago truncatula over a 72-h time course. To detect temporal shifts in gene expression, we developed GeneShift, a novel computational statistics and machine learning workflow that addresses the time series replicate the averaging issue for detecting gene expression pattern shifts under different conditions. We identified both known and novel genes that are regulated dynamically in both tissues during early nodulation including leginsulin, defensins, root transporters, nodulin-related, and circadian clock genes. We validated over 70% of the expression patterns that GeneShift discovered using an independent M. truncatula RNA-Seq study. GeneShift facilitated the discovery of condition-specific temporally differentially expressed genes in the symbiotic nodulation biological system. In principle, GeneShift should work for time-series gene expression profiling studies from other systems. |
| first_indexed | 2024-12-21T11:00:39Z |
| format | Article |
| id | doaj.art-f96658a436a14660b997a46b5da4a237 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-21T11:00:39Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-f96658a436a14660b997a46b5da4a2372022-12-21T19:06:22ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-04-011310.3389/fpls.2022.861639861639Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early NodulationYueyao Gao0Bradley Selee1Elise L. Schnabel2William L. Poehlman3William L. Poehlman4Suchitra A. Chavan5Julia A. Frugoli6Frank Alex Feltus7Frank Alex Feltus8Frank Alex Feltus9Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United StatesDepartment of Electrical and Computer Engineering, Clemson University, Clemson, SC, United StatesDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, United StatesDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, United StatesSage Bionetworks, Seattle, WA, United StatesDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, United StatesDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, United StatesDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, United StatesBiomedical Data Science and Informatics Program, Clemson University, Clemson, SC, United StatesClemson Center for Human Genetics, Greenwood, SC, United StatesIn response to colonization by rhizobia bacteria, legumes are able to form nitrogen-fixing nodules in their roots, allowing the plants to grow efficiently in nitrogen-depleted environments. Legumes utilize a complex, long-distance signaling pathway to regulate nodulation that involves signals in both roots and shoots. We measured the transcriptional response to treatment with rhizobia in both the shoots and roots of Medicago truncatula over a 72-h time course. To detect temporal shifts in gene expression, we developed GeneShift, a novel computational statistics and machine learning workflow that addresses the time series replicate the averaging issue for detecting gene expression pattern shifts under different conditions. We identified both known and novel genes that are regulated dynamically in both tissues during early nodulation including leginsulin, defensins, root transporters, nodulin-related, and circadian clock genes. We validated over 70% of the expression patterns that GeneShift discovered using an independent M. truncatula RNA-Seq study. GeneShift facilitated the discovery of condition-specific temporally differentially expressed genes in the symbiotic nodulation biological system. In principle, GeneShift should work for time-series gene expression profiling studies from other systems.https://www.frontiersin.org/articles/10.3389/fpls.2022.861639/fulldifferential gene expressionnodulationrhizobiaMedicago truncatulatranscriptional dynamictime series |
| spellingShingle | Yueyao Gao Bradley Selee Elise L. Schnabel William L. Poehlman William L. Poehlman Suchitra A. Chavan Julia A. Frugoli Frank Alex Feltus Frank Alex Feltus Frank Alex Feltus Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation Frontiers in Plant Science differential gene expression nodulation rhizobia Medicago truncatula transcriptional dynamic time series |
| title | Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation |
| title_full | Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation |
| title_fullStr | Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation |
| title_full_unstemmed | Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation |
| title_short | Time Series Transcriptome Analysis in Medicago truncatula Shoot and Root Tissue During Early Nodulation |
| title_sort | time series transcriptome analysis in medicago truncatula shoot and root tissue during early nodulation |
| topic | differential gene expression nodulation rhizobia Medicago truncatula transcriptional dynamic time series |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.861639/full |
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