Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis.
Photoperiod is an annual cue measured by biological systems to align growth and reproduction with the seasons. In plants, photoperiodic flowering has been intensively studied for over 100 years, but we lack a complete picture of the transcriptional networks and cellular processes that are photoperio...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2023-09-01
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| Series: | PLoS Biology |
| Online Access: | https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3002283&type=printable |
| _version_ | 1797266432393740288 |
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| author | Chun Chung Leung Daniel A Tarté Lilijana S Oliver Qingqing Wang Joshua M Gendron |
| author_facet | Chun Chung Leung Daniel A Tarté Lilijana S Oliver Qingqing Wang Joshua M Gendron |
| author_sort | Chun Chung Leung |
| collection | DOAJ |
| description | Photoperiod is an annual cue measured by biological systems to align growth and reproduction with the seasons. In plants, photoperiodic flowering has been intensively studied for over 100 years, but we lack a complete picture of the transcriptional networks and cellular processes that are photoperiodic. We performed a transcriptomics experiment on Arabidopsis plants grown in 3 different photoperiods and found that thousands of genes show photoperiodic alteration in gene expression. Gene clustering, daily expression integral calculations, and cis-element analysis then separate photoperiodic genes into co-expression subgroups that display 19 diverse seasonal expression patterns, opening the possibility that many photoperiod measurement systems work in parallel in Arabidopsis. Then, functional enrichment analysis predicts co-expression of important cellular pathways. To test these predictions, we generated a comprehensive catalog of genes in the phenylpropanoid biosynthesis pathway, overlaid gene expression data, and demonstrated that photoperiod intersects with 2 major phenylpropanoid pathways differentially, controlling flavonoids but not lignin. Finally, we describe the development of a new app that visualizes photoperiod transcriptomic data for the wider community. |
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| format | Article |
| id | doaj.art-7fdf412996ff49c7a9e2e80514d6069b |
| institution | Directory Open Access Journal |
| issn | 1544-9173 1545-7885 |
| language | English |
| last_indexed | 2024-04-25T01:00:36Z |
| publishDate | 2023-09-01 |
| publisher | Public Library of Science (PLoS) |
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| series | PLoS Biology |
| spelling | doaj.art-7fdf412996ff49c7a9e2e80514d6069b2024-03-11T05:30:57ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852023-09-01219e300228310.1371/journal.pbio.3002283Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis.Chun Chung LeungDaniel A TartéLilijana S OliverQingqing WangJoshua M GendronPhotoperiod is an annual cue measured by biological systems to align growth and reproduction with the seasons. In plants, photoperiodic flowering has been intensively studied for over 100 years, but we lack a complete picture of the transcriptional networks and cellular processes that are photoperiodic. We performed a transcriptomics experiment on Arabidopsis plants grown in 3 different photoperiods and found that thousands of genes show photoperiodic alteration in gene expression. Gene clustering, daily expression integral calculations, and cis-element analysis then separate photoperiodic genes into co-expression subgroups that display 19 diverse seasonal expression patterns, opening the possibility that many photoperiod measurement systems work in parallel in Arabidopsis. Then, functional enrichment analysis predicts co-expression of important cellular pathways. To test these predictions, we generated a comprehensive catalog of genes in the phenylpropanoid biosynthesis pathway, overlaid gene expression data, and demonstrated that photoperiod intersects with 2 major phenylpropanoid pathways differentially, controlling flavonoids but not lignin. Finally, we describe the development of a new app that visualizes photoperiod transcriptomic data for the wider community.https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3002283&type=printable |
| spellingShingle | Chun Chung Leung Daniel A Tarté Lilijana S Oliver Qingqing Wang Joshua M Gendron Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. PLoS Biology |
| title | Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. |
| title_full | Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. |
| title_fullStr | Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. |
| title_full_unstemmed | Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. |
| title_short | Systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in Arabidopsis. |
| title_sort | systematic characterization of photoperiodic gene expression patterns reveals diverse seasonal transcriptional systems in arabidopsis |
| url | https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.3002283&type=printable |
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