Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species
Abstract
:1. Introduction
2. Results and Discussion
2.1. A New Genome of N. officinale
2.2. Gene Duplications, Gains and Losses
2.3. Differentially Expressed OR Genes upon Salt Stress
2.4. Differentially Expressed OR Genes upon Hypoxia
3. Materials and Methods
3.1. Growth of N. officinale
3.2. HMW DNA Extraction
3.3. N. officinale Genome Sequencing: HiFi PacBio Library Preparation
3.4. Genome Annotation
3.5. Phylogeny
3.6. RNA-Seq Data
3.7. Pipeline for the OR Families Expression Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Family | E. salsugineum | A. thaliana | N. officinale | |
---|---|---|---|---|
APx | Total gene number | 10 | 8 + 1 Ψ | 12 + 2 Ψ |
% Ψ | 0 | 11.1 | 14.3 | |
Gene gain | 2 | 0 | 0 | |
Gene loss | 0 | 0 | 2 | |
% gene lost + Ψ | 0 | nd | 25.0 | |
Kat | Total gene number | 3 | 3 | 5 |
% Ψ | 0 | 0 | 0 | |
Gene gain | 0 | 0 | 0 | |
Gene loss | 0 | 0 | 1 | |
% gene lost + Ψ | 0 | nd | 16.6 | |
CIII Prx | Total gene number | 66 + 8 Ψ | 73 + 2 Ψ | 111 + 17 Ψ |
% Ψ | 10.8 | 2.7 | 14.1 | |
Gene gain | 8 | 5 | 5 | |
Gene loss | 3 | 0 | 16 | |
% gene lost + Ψ | 15.9 | nd | 24.5 | |
DiOx | Total gene number | 2 | 2 | 3 |
% Ψ | 0 | 0 | 0 | |
Gene gain | 0 | 0 | 0 | |
Gene loss | 0 | 0 | 1 | |
% gene lost + Ψ | 0 | nd | 25.0 | |
RBOH | Total gene number | 11 | 10 | 15 + 4 Ψ |
% Ψ | 0 | 0 | 21.0 | |
Gene gain | 1 | 0 | 0 | |
Gene loss | 0 | 0 | 1 | |
% gene lost + Ψ | 0 | nd | 25.0 | |
SOD | Total gene number | 9 | 9 | 17 + 1 Ψ |
% Ψ | 0 | 0 | 5.5 | |
Gene gain | 0 | 0 | 0 | |
Gene loss | 0 | 0 | 0 | |
% gene lost + Ψ | 0 | nd | 5.5 |
E. salsugineum Redoxibase ID | E. salsugineum log2(FC) | A. thaliana log2(FC) | A. thaliana Redoxibase ID |
---|---|---|---|
TsPrx10/Thhalv10011619 | −3.01 | 15.87 | AtPrx10/At1g49570 |
TsAPx01/Thhalv10008402m | 0.67 | −1.41 | AtAPx01/At1g07890 |
E. salsugineum Redoxibase ID | E. salsugineum log2(FC) | A. thaliana log2(FC) | A. thaliana Redoxibase ID |
---|---|---|---|
TsPrx02/Thhalv10008157 | −2.88 | FDR > 0.05 | AtPrx02/At1g05250 |
TsPrx03/Thhalv10008189 | −0.69 | FDR > 0.05 | AtPrx03/At1g05260 |
TsPrx11/Thhalv10018830 | 0.97 | FDR > 0.05 | AtPrx11/At1g68850 |
TsPrx12/Thhalv10018753 | −2.07 | FDR > 0.05 | AtPrx12/At1g71695 |
TsPrx25/Thhalv10016924 | −0.89 | FDR > 0.05 | AtPrx25/At2g41480 |
TsPrx27/Thhalv10021152 | −1.96 | FDR > 0.05 | AtPrx27/At3g01190 |
TsPrx28/Thhalv10021155 | −2.02 | no FDR | AtPrx28/At3g03670 |
TsPrx30/Thhalv10021123 | −0.85 (+) | FDR > 0.05 | AtPrx30/At3g21770 |
TsPrx39/Thhalv10028797 | −2.80 | FDR > 0.05 | AtPrx39/At4g11290 |
TsPrx45/Thhalv10025699 | −1.65 | FDR > 0.05 | AtPrx45/At4g30170 |
TsPrx56/Thhalv10014085 | −1.44 | FDR > 0.05 | AtPrx56/At5g15180 |
TsPrx58-1/Thhalv10014083 | −2.15 (−) | FDR > 0.05 | AtPrx58/At5g19880 |
TsPrx59/Thhalv10014080 | −2.84 | FDR > 0.05 | AtPrx59/At5g19890 |
TsPrx66/Thhalv10014117 | 2.43 | FDR > 0.05 | AtPrx66/At5g51890 |
TsPrx69/Thhalv10004557 | −0.62 | FDR > 0.05 | AtPrx69/At5g64100 |
TsAPx-R/Thhalv10025686m | 0.96 | FDR > 0.05 | AtAPx-R/At4g32320 |
TsAPx02/Thhalv10021381m | 1.87 (+) | FDR > 0.05 | AtAPx02/At3g09640 |
TsDiOx01/Thhalv10020279 | −3.33 | FDR > 0.05 | AtDiOx01/At3g01420 |
TsDiOx02/Thhalv10018266 | 0.97 | FDR > 0.05 | AtDiOx02/At1g73680 |
TsFSD01-1A/Thhalv10026218 | 1.11 | FDR > 0.05 | AtFSD01/At4g25100 |
TsMSD01-1A/Thhalv10021449 | 0.61 | FDR > 0.05 (+) | AtMSD01/At3g10920 |
no sequence | −4.04 | AtPrx08/At1g34510 | |
TsPrx21/Thhalv10016921 | FDR > 0.05 (−) | −1.74 | AtPrx21/At2g37130 |
TsPrx34/Thhalv10010494 | FDR > 0.05 | −1.69 (+) | AtPrx34/At3g49120 |
TsPrx35/Thhalv10010538 | FDR > 0.05 | −3.61 | AtPrx35/At3g49960 |
TsPrx42/Thhalv10025680 | FDR > 0.05 | −1.29 | AtPrx42/At4g21960 |
TsPrx50/Thhalv10025717 | no transcript | 1.61 | AtPrx50/At4g37520 |
TsPrx54/Thhalv10013916 | no transcript | −1.97 | AtPrx54/At5g06730 |
TsPrx60/Thhalv10015253 | no transcript | −5.01 | AtPrx60/At5g22410 |
TsRboh03/Thhalv10012613 | FDR > 0.05 | −1.46 | AtRboh03/At5g51060 |
TsRboh04/Thhalv10003619 | FDR > 0.05 | −1.40 | AtRboh04/At5g47910 |
TsKat02/Thhalv10025015 | no transcript (+) | 1.32 | AtKat02/At4g35090 |
TsCSD01/Thhalv10008927 | FDR > 0.05 (+) | 1.80 | AtCSD01/At1g08830 |
TsCSD02/Thhalv10017094 | FDR > 0.05 | 1.77 | AtCSD02/At2g28190 |
TsCCS01/Thhalv10008232 | FDR > 0.05 | 1.92 | AtCCS01/At1g12520 |
N. officinale Redoxibase ID | N. officinale log2(FC) | A. thaliana HN-score | A. thaliana Redoxibase ID |
---|---|---|---|
NoffPrx09-1B | 5.56 | −3 | AtPrx09/At1g44970 |
NoffPrx16-1A | 3.18 | −5 | AtPrx16/At2g18980 |
NoffPrx22-1A | 6.16 | −1 | AtPrx22/At2g38380 |
NoffPrx23-1A | 6.36 | −2 | AtPrx23/At2g38390 |
NoffPrx27-1A | 3.83 | −2 | AtPrx27/At3g01190 |
NoffPrx45-1A | 2.87 | −4 | AtPrx45/At4g30170 |
NoffPrx56-1A | 4.27 | −2 | AtPrx56/At5g15180 |
NoffPrx64-1A | 1.92 | −2 | AtPrx64/At5g42180 |
NoffPrx67-1A | 4.59 | −2 | AtPrx67/At5g58390 |
NoffAPx02-1A | −3.56 | 1 | AtAPx02/At3g09640 |
NoffRboh04-1A | −0.40 | 26 | AtRboh04/At5g47910 |
NoffCCS01-1A | 1.97 | −3 | AtCCS01/At1g12520 |
NoffCSD03-1A | 0.74 | −1 | AtCSD03/At5g18100 |
NoffFSD01-1A | −5.38 | 3 | AtFSD01/At4g25100 |
N. officinale Redoxibase ID | N. officinale log2(FC) | A. thaliana HN-score | A. thaliana Redoxibase ID |
---|---|---|---|
NoffPrx38-1A | 2.42 | 0 | AtPrx38/At4g08780 |
NoffRboh05 | 1.38 | 0 | AtRboh05/At1g19230 |
NoffPrx02-1A | no transcript | −4 | AtPrx02/At1g05250 |
NoffPrx04-1B | FDR > 0.05 | 15 | AtPrx04/At1g14540 |
NoffPrx05-1A | no transcript | 6 | AtPrx05/At1g14550 |
NoffPrx07-1A | no transcript | −4 | AtPrx07/At1g30870 |
no sequence | −13 | AtPrx08/At1g34510 | |
NoffPrx11-1A | no transcript | −2 | AtPrx11/At1g68850 |
NoffPrx12-1A | FDR > 0.05 | −9 | AtPrx12/At1g71695 |
NoffPrx15-1A | no transcript | −3 | AtPrx15/At2g18150 |
NoffPrx17-1A | FDR > 0.05 | −1 | AtPrx17/At2g22420 |
NoffPrx21-1A | FDR > 0.05 | 2 | AtPrx21/At2g37130 |
no sequence | −5 | AtPrx24/At2g39040 | |
NoffPrx25-1A | no transcript | −11 | AtPrx25/At2g41480 |
NoffPrx28-1A | no transcript | 5 | AtPrx28/At3g03670 |
NoffPrx30-1A | FDR > 0.05 | −3 | AtPrx30/At3g21770 |
NoffPrx32-1A | FDR > 0.05 | −2 | AtPrx32/At3g32980 |
NoffPrx33-1A | FDR > 0.05 | −1 | AtPrx33/At3g49110 |
NoffPrx[P]34-1A | [P] | 5 | AtPrx34/At3g49120 |
NoffPrx35-1B | no transcript | −6 | AtPrx35/At3g49960 |
NoffPrx39-1A | FDR > 0.05 | −2 | AtPrx39/At4g11290 |
NoffPrx40-1A | FDR > 0.05 | −1 | AtPrx40/At4g16270 |
NoffPrx44-1A | no transcript | −3 | AtPrx44/At4g26010 |
NoffPrx46-1B | FDR > 0.05 | 10 | AtPrx46/At4g31760 |
NoffPrx53-1A | no transcript | −3 | AtPrx53/At5g06720 |
NoffPrx57-1A | no transcript | −2 | AtPrx57/At5g17820 |
NoffPrx58-1A | FDR > 0.05 | 2 | AtPrx58/At5g19880 |
NoffPrx59-1A | no transcript | 6 | AtPrx59/At5g19890 |
NoffPrx60-1A | no transcript | −10 | AtPrx60/At5g22410 |
NoffPrx61-1A | no transcript | 6 | AtPrx61/At5g24070 |
no sequence | −11 | AtPrx63/At5g40150 | |
NoffPrx65-1A | no transcript | −1 | AtPrx65/At5g47000 |
NoffPrx72-1A | FDR > 0.05 | −2 | AtPrx72/At5g66390 |
NoffPrx73-1A | FDR > 0.05 | −4 | AtPrx73/At5g67400 |
NoffAPx-R01-1A | FDR > 0.05 | −2 | AtAPx-R/At4g32320 |
NoffAPx03-1A | FDR > 0.05 | −1 | AtAPx03/At4g35000 |
NoffAPx06-1A | FDR > 0.05 | −5 | AtAPx06/At1g77490 |
NoffDiOx01-1A | FDR > 0.05 | −1 | AtDiOx01/At3g01420 |
NoffRboh03-1A | no transcript | 3 | AtRboh03/At5g51060 |
NoffRboh06-1A | FDR > 0.05 | 1 | AtRboh06/At1g64060 |
NoffRboh07-1B | FDR > 0.05 | −1 | AtRboh07/At4g25090 |
NoffRboh09-1B | no transcript | 3 | AtRboh09/At4g11230 |
NoffKat01-1B | FDR > 0.05 | −2 | AtKat01/At1g20630 |
NoffKat02-1A | FDR > 0.05 | −4 | AtKat02/At4g35090 |
NoffCSD02-1A | FDR > 0.05 | −1 | AtCSD02/At2g28190 |
NoffFSD02-1A | FDR > 0.05 | −2 | AtFSD02/At5g51100 |
NoffFSD03-1A | FDR > 0.05 | −4 | AtFSD03/At5g23310 |
NoffMSD01-1A | FDR > 0.05 | −1 | AtMSD01/At3g10920 |
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© 2024 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
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Berthelier, T.H.; Cabanac, S.C.; Callot, C.; Bellec, A.; Mathé, C.; Jamet, E.; Dunand, C. Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species. Int. J. Mol. Sci. 2024, 25, 1938. https://doi.org/10.3390/ijms25031938
Berthelier TH, Cabanac SC, Callot C, Bellec A, Mathé C, Jamet E, Dunand C. Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species. International Journal of Molecular Sciences. 2024; 25(3):1938. https://doi.org/10.3390/ijms25031938
Chicago/Turabian StyleBerthelier, Thomas Horst, Sébastien Christophe Cabanac, Caroline Callot, Arnaud Bellec, Catherine Mathé, Elisabeth Jamet, and Christophe Dunand. 2024. "Evolutionary Analysis of Six Gene Families Part of the Reactive Oxygen Species (ROS) Gene Network in Three Brassicaceae Species" International Journal of Molecular Sciences 25, no. 3: 1938. https://doi.org/10.3390/ijms25031938