Custom methods to identify conserved genetic modules applied to novel transcriptomic data from Amborella trichopoda
© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissionsoup.com.
| Publié dans: | Journal of experimental botany. - 1985. - 73(2022), 8 vom: 18. Apr., Seite 2487-2498 |
|---|---|
| Auteur principal: | |
| Autres auteurs: | , , , , , , |
| Format: | Article en ligne |
| Langue: | English |
| Publié: |
2022
|
| Accès à la collection: | Journal of experimental botany |
| Sujets: | Journal Article Research Support, Non-U.S. Gov't Amborella trichopoda Arabidopsis thaliana angiosperm carpel evo-devo flower laser-assisted microdissection ovule plus... |
| Résumé: | © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissionsoup.com. We have devised a procedure for the inter-species comparison of transcriptomic data and used this procedure to reconstruct the expression dynamics of major genetic modules that were present at least 149 million years ago in the most recent common ancestor of living angiosperms. We began by using laser-assisted microdissection to generate novel transcriptomic data from female flower tissues of Amborella trichopoda, the likely sister to all other living angiosperms. We then employed a gene-expression clustering method, followed by a custom procedure to compare genetic modules on the basis of gene orthology between Amborella and the molecular-genetic model angiosperm Arabidopsis thaliana. Using this protocol, we succeeded in identifying nine major genetic modules that appear to have conserved their expression dynamics from an early stage in angiosperm evolution. The genes of these modules, representing over 5000 orthogroups, include around one third of those known to control female reproductive development in Arabidopsis. Our study constitutes a proof of concept for the comparison of transcriptomic data between widely diverged plant species and represents a first step in the large-scale analysis of gene expression dynamics in a macro-evolutionary context |
|---|---|
| Description: | Date Completed 20.04.2022 Date Revised 23.05.2022 published: Print Citation Status MEDLINE |
| ISSN: | 1460-2431 |
| DOI: | 10.1093/jxb/erac044 |