Cargando…
Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade
Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen‐fixing bacteria in the root nodule. This root–nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggest...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9302667/ https://www.ncbi.nlm.nih.gov/pubmed/35092309 http://dx.doi.org/10.1111/nph.18006 |
_version_ | 1784751683383853056 |
---|---|
author | Pereira, Wendell J. Knaack, Sara Chakraborty, Sanhita Conde, Daniel Folk, Ryan A. Triozzi, Paolo M. Balmant, Kelly M. Dervinis, Christopher Schmidt, Henry W. Ané, Jean‐Michel Roy, Sushmita Kirst, Matias |
author_facet | Pereira, Wendell J. Knaack, Sara Chakraborty, Sanhita Conde, Daniel Folk, Ryan A. Triozzi, Paolo M. Balmant, Kelly M. Dervinis, Christopher Schmidt, Henry W. Ané, Jean‐Michel Roy, Sushmita Kirst, Matias |
author_sort | Pereira, Wendell J. |
collection | PubMed |
description | Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen‐fixing bacteria in the root nodule. This root–nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen‐fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula. |
format | Online Article Text |
id | pubmed-9302667 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-93026672022-07-22 Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade Pereira, Wendell J. Knaack, Sara Chakraborty, Sanhita Conde, Daniel Folk, Ryan A. Triozzi, Paolo M. Balmant, Kelly M. Dervinis, Christopher Schmidt, Henry W. Ané, Jean‐Michel Roy, Sushmita Kirst, Matias New Phytol Research Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen‐fixing bacteria in the root nodule. This root–nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen‐fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula. John Wiley and Sons Inc. 2022-02-21 2022-04 /pmc/articles/PMC9302667/ /pubmed/35092309 http://dx.doi.org/10.1111/nph.18006 Text en © 2022 The Authors New Phytologist © 2022 New Phytologist Foundation https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. |
spellingShingle | Research Pereira, Wendell J. Knaack, Sara Chakraborty, Sanhita Conde, Daniel Folk, Ryan A. Triozzi, Paolo M. Balmant, Kelly M. Dervinis, Christopher Schmidt, Henry W. Ané, Jean‐Michel Roy, Sushmita Kirst, Matias Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
title | Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
title_full | Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
title_fullStr | Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
title_full_unstemmed | Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
title_short | Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
title_sort | functional and comparative genomics reveals conserved noncoding sequences in the nitrogen‐fixing clade |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9302667/ https://www.ncbi.nlm.nih.gov/pubmed/35092309 http://dx.doi.org/10.1111/nph.18006 |
work_keys_str_mv | AT pereirawendellj functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT knaacksara functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT chakrabortysanhita functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT condedaniel functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT folkryana functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT triozzipaolom functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT balmantkellym functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT dervinischristopher functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT schmidthenryw functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT anejeanmichel functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT roysushmita functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade AT kirstmatias functionalandcomparativegenomicsrevealsconservednoncodingsequencesinthenitrogenfixingclade |