Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars
Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Cambridge University Press
2021-01-01
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| Series: | Quantitative Plant Biology |
| Subjects: | |
| Online Access: | https://www.cambridge.org/core/product/identifier/S2632882821000060/type/journal_article |
| _version_ | 1811155771955609600 |
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| author | Alexander Calderwood Jo Hepworth Shannon Woodhouse Lorelei Bilham D. Marc Jones Eleri Tudor Mubarak Ali Caroline Dean Rachel Wells Judith A. Irwin Richard J. Morris |
| author_facet | Alexander Calderwood Jo Hepworth Shannon Woodhouse Lorelei Bilham D. Marc Jones Eleri Tudor Mubarak Ali Caroline Dean Rachel Wells Judith A. Irwin Richard J. Morris |
| author_sort | Alexander Calderwood |
| collection | DOAJ |
| description | Comparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. We find that different curve registration functions are required for different genes, indicating that there is no single common ‘developmental time’ between Arabidopsis and B. rapa. A detailed comparison between Arabidopsis and B. rapa and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa and highlights the importance of registration methods for the comparison of developmental gene expression data. |
| first_indexed | 2024-04-10T04:39:09Z |
| format | Article |
| id | doaj.art-f1956aace8794a2c90a90a63c1912eb4 |
| institution | Directory Open Access Journal |
| issn | 2632-8828 |
| language | English |
| last_indexed | 2024-04-10T04:39:09Z |
| publishDate | 2021-01-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | Quantitative Plant Biology |
| spelling | doaj.art-f1956aace8794a2c90a90a63c1912eb42023-03-09T12:43:33ZengCambridge University PressQuantitative Plant Biology2632-88282021-01-01210.1017/qpb.2021.6Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivarsAlexander Calderwood0Jo Hepworth1https://orcid.org/0000-0002-4621-8414Shannon Woodhouse2https://orcid.org/0000-0001-8048-9536Lorelei Bilham3D. Marc Jones4https://orcid.org/0000-0003-3167-2590Eleri Tudor5Mubarak Ali6Caroline Dean7https://orcid.org/0000-0002-6555-3525Rachel Wells8https://orcid.org/0000-0002-1280-7472Judith A. Irwin9Richard J. Morris10https://orcid.org/0000-0003-3080-2613Department of Computational and Systems Biology, John Innes Centre, Norwich, United KingdomDepartment of Crop Genetics, John Innes Centre, Norwich, United KingdomDepartment of Computational and Systems Biology, John Innes Centre, Norwich, United KingdomDepartment of Crop Genetics, John Innes Centre, Norwich, United KingdomDepartment of Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom VIB-UGent Centre for Plant Systems Biology, Gent, BelgiumDepartment of Crop Genetics, John Innes Centre, Norwich, United KingdomBangladesh Agricultural Research Institute, Gazipur, BangladeshDepartment of Cell and Developmental Biology, John Innes Centre, Norwich, United KingdomDepartment of Crop Genetics, John Innes Centre, Norwich, United KingdomDepartment of Crop Genetics, John Innes Centre, Norwich, United KingdomDepartment of Computational and Systems Biology, John Innes Centre, Norwich, United KingdomComparative transcriptomics can be used to translate an understanding of gene regulatory networks from model systems to less studied species. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. We find that different curve registration functions are required for different genes, indicating that there is no single common ‘developmental time’ between Arabidopsis and B. rapa. A detailed comparison between Arabidopsis and B. rapa and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa and highlights the importance of registration methods for the comparison of developmental gene expression data.https://www.cambridge.org/core/product/identifier/S2632882821000060/type/journal_articleArabidopsisBrassica rapacomparative transcriptomicsfloweringFTSOC1 |
| spellingShingle | Alexander Calderwood Jo Hepworth Shannon Woodhouse Lorelei Bilham D. Marc Jones Eleri Tudor Mubarak Ali Caroline Dean Rachel Wells Judith A. Irwin Richard J. Morris Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars Quantitative Plant Biology Arabidopsis Brassica rapa comparative transcriptomics flowering FT SOC1 |
| title | Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars |
| title_full | Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars |
| title_fullStr | Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars |
| title_full_unstemmed | Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars |
| title_short | Comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between Arabidopsis and Brassica rapa cultivars |
| title_sort | comparative transcriptomics reveals desynchronisation of gene expression during the floral transition between arabidopsis and brassica rapa cultivars |
| topic | Arabidopsis Brassica rapa comparative transcriptomics flowering FT SOC1 |
| url | https://www.cambridge.org/core/product/identifier/S2632882821000060/type/journal_article |
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