Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species
Climate change is expected to intensify the occurrence of abiotic stress in plants, such as hypoxia and salt stresses, leading to the production of reactive oxygen species (ROS), which need to be effectively managed by various oxido-reductases encoded by the so-called ROS gene network. Here, we stud...
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| Format: | Article |
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MDPI AG
2024-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/3/1938 |
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| author | Thomas Horst Berthelier Sébastien Christophe Cabanac Caroline Callot Arnaud Bellec Catherine Mathé Elisabeth Jamet Christophe Dunand |
| author_facet | Thomas Horst Berthelier Sébastien Christophe Cabanac Caroline Callot Arnaud Bellec Catherine Mathé Elisabeth Jamet Christophe Dunand |
| author_sort | Thomas Horst Berthelier |
| collection | DOAJ |
| description | Climate change is expected to intensify the occurrence of abiotic stress in plants, such as hypoxia and salt stresses, leading to the production of reactive oxygen species (ROS), which need to be effectively managed by various oxido-reductases encoded by the so-called ROS gene network. Here, we studied six oxido-reductases families in three <i>Brassicaceae</i> species, <i>Arabidopsis thaliana</i> as well as <i>Nasturtium officinale</i> and <i>Eutrema salsugineum</i>, which are adapted to hypoxia and salt stress, respectively. Using available and new genomic data, we performed a phylogenomic analysis and compared RNA-seq data to study genomic and transcriptomic adaptations. This comprehensive approach allowed for the gaining of insights into the impact of the adaptation to saline or hypoxia conditions on genome organization (gene gains and losses) and transcriptional regulation. Notably, the comparison of the <i>N. officinale</i> and <i>E. salsugineum</i> genomes to that of <i>A. thaliana</i> highlighted changes in the distribution of ohnologs and homologs, particularly affecting class III peroxidase genes (<i>CIII Prxs</i>). These changes were specific to each gene, to gene families subjected to duplication events and to each species, suggesting distinct evolutionary responses. The analysis of transcriptomic data has allowed for the identification of genes related to stress responses in <i>A. thaliana</i>, and, conversely, to adaptation in <i>N. officinale</i> and <i>E. salsugineum</i>. |
| first_indexed | 2024-03-08T03:54:51Z |
| format | Article |
| id | doaj.art-98eb1b119e9f4edb9ca9bc704d9192ee |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T03:54:51Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-98eb1b119e9f4edb9ca9bc704d9192ee2024-02-09T15:15:18ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-02-01253193810.3390/ijms25031938Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> SpeciesThomas Horst Berthelier0Sébastien Christophe Cabanac1Caroline Callot2Arnaud Bellec3Catherine Mathé4Elisabeth Jamet5Christophe Dunand6Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, FranceLaboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, FranceCentre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, FranceCentre National de Ressources Génomiques Végétales, INRAE, 31320 Auzeville-Tolosane, FranceLaboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, FranceLaboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, FranceLaboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, FranceClimate change is expected to intensify the occurrence of abiotic stress in plants, such as hypoxia and salt stresses, leading to the production of reactive oxygen species (ROS), which need to be effectively managed by various oxido-reductases encoded by the so-called ROS gene network. Here, we studied six oxido-reductases families in three <i>Brassicaceae</i> species, <i>Arabidopsis thaliana</i> as well as <i>Nasturtium officinale</i> and <i>Eutrema salsugineum</i>, which are adapted to hypoxia and salt stress, respectively. Using available and new genomic data, we performed a phylogenomic analysis and compared RNA-seq data to study genomic and transcriptomic adaptations. This comprehensive approach allowed for the gaining of insights into the impact of the adaptation to saline or hypoxia conditions on genome organization (gene gains and losses) and transcriptional regulation. Notably, the comparison of the <i>N. officinale</i> and <i>E. salsugineum</i> genomes to that of <i>A. thaliana</i> highlighted changes in the distribution of ohnologs and homologs, particularly affecting class III peroxidase genes (<i>CIII Prxs</i>). These changes were specific to each gene, to gene families subjected to duplication events and to each species, suggesting distinct evolutionary responses. The analysis of transcriptomic data has allowed for the identification of genes related to stress responses in <i>A. thaliana</i>, and, conversely, to adaptation in <i>N. officinale</i> and <i>E. salsugineum</i>.https://www.mdpi.com/1422-0067/25/3/1938adaptationα-dioxygenaseascorbate peroxidaseBrassicaceaecatalaseclass III peroxidase |
| spellingShingle | Thomas Horst Berthelier Sébastien Christophe Cabanac Caroline Callot Arnaud Bellec Catherine Mathé Elisabeth Jamet Christophe Dunand Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species International Journal of Molecular Sciences adaptation α-dioxygenase ascorbate peroxidase Brassicaceae catalase class III peroxidase |
| title | Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species |
| title_full | Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species |
| title_fullStr | Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species |
| title_full_unstemmed | Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species |
| title_short | Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three <i>Brassicaceae</i> Species |
| title_sort | evolutionary analysis of six gene families part of the reactive oxygen species ros gene network in three i brassicaceae i species |
| topic | adaptation α-dioxygenase ascorbate peroxidase Brassicaceae catalase class III peroxidase |
| url | https://www.mdpi.com/1422-0067/25/3/1938 |
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