Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Retrieval and Identification of Putative MAP Kinase Cascade Genes
2.2. Phylogenetic Tree Construction and Homology Assessment
2.3. Chromosomal Locations and Gene Structure
2.4. Nomenclature of MPKs and MKKs
2.5. Expression Analysis and miRNA Prediction of Sunflower MPKs and MKKs
2.6. Tajima’s Relative Rate and Neutrality Test
3. Results
3.1. The Diversity of MPK and MKK Genes in Sunflower Relative to Other Species
3.2. Gene Location, Subcellular Localization and Structural Variation of MPKs and MKKs in H. annuus
3.3. Phylogenetic Analyses
3.3.1. MPKs
3.3.2. MKKs
3.4. Expression Analysis and miRNA Prediction of Sunflower MPKs and MKKs
3.5. Tajima’s Relative Rate and Neutrality Tests on MPKs and MKKs
4. Discussion
4.1. Nomenclature of MPKs and MKKs
4.2. Diversity and the Phylogenetic Relationship of MPKs
4.3. Diversity and Phylogenetic Relationship of MKKs
4.4. Expression Analysis and miRNA Prediction
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Plant Species | Ploidy | Size of Genome (Mbs) γ | No. of loci γ | MPK | MKK |
---|---|---|---|---|---|
Amborella trichopoda ‡ | Diploid | 706 | 26846 | 8 | 7 |
Aquilegia coerulea ‡ | Diploid | 302 | 24823 | 11 | 5 |
Arabidopsis thaliana | Diploid | 135 | 27416 | 20 a | 10 a |
Chlamydomonas reinhardtii ‡ | Haploid | 111.1 | 17741 | 6 | 1 |
Daucus carota ‡ | Diploid | 421 | 32,113 | 17 | 5 |
Glycine max | Tetraploid | 975 | 56044 | 38 b | 11 b |
Helianthus annuus ‡ | Diploid | 3600 | 52243 | 28 | 8 |
Oryza sativa | Diploid | 372 | 39049 | 16 c | 8 c |
Solanum lycopersicum ‡ | Diploid | 900 | 34727 | 15 | 5 |
Sphagnum fallax ‡ | Haploid/Diploid | 395 | 26939 | 11 | 6 |
Vitis vinifera | Diploid | 487 | 26346 | 14 d | 5 d |
Name | Gene ID | Chr | Str | Start | End | PL | Exo | Int | Sl | pI | Mw |
---|---|---|---|---|---|---|---|---|---|---|---|
MPK | |||||||||||
HaMPK6-1 | HanXRQChr01g0023391 | Ha1 | - | 130301686 | 130292965 | 359 | 6 | 5 | - | 5.85 | 41581.61 |
HaMPK16-1 | HanXRQChr03g0071491 | Ha3 | - | 77378137 | 77372246 | 564 | 10 | 9 | - | 9.17 | 64059.43 |
HaMPK7 | HanXRQChr03g0074811 | Ha3 | + | 102410161 | 102406169 | 353 | 3 | 2 | - | 7.62 | 40274.83 |
HaMPK23-1 | HanXRQChr03g0081221 | Ha3 | + | 129978443 | 129973452 | 453 | 15 | 14 | - | 9.65 | 50392.28 |
HaMPK23-3 | HanXRQChr03g0081391 | Ha3 | + | 130506162 | 130500013 | 423 | 16 | 15 | - | 8.91 | 47648.79 |
HaMPK22 | HanXRQChr04g0108301 | Ha4 | - | 77321727 | 77315970 | 432 | 18 | 17 | - | 5.46 | 49633.87 |
HaMPK11-1 | HanXRQChr04g0121371 | Ha4 | + | 158781451 | 158778221 | 358 | 6 | 5 | M | 6.42 | 41228.21 |
HaMPK3-1 | HanXRQChr05g0133161 | Ha5 | + | 21064225 | 21061089 | 358 | 6 | 5 | - | 5.68 | 41323.35 |
HaMPK8 | HanXRQChr05g0143371 | Ha5 | - | 116774638 | 116767923 | 505 | 11 | 10 | - | 6.8 | 57051.89 |
HaMPK2 | HanXRQChr05g0151241 | Ha5 | - | 169574750 | 169571609 | 349 | 3 | 2 | - | 6.54 | 40295.67 |
HaMPK11-2 | HanXRQChr06g0167011 | Ha6 | - | 7104659 | 7099870 | 359 | 6 | 5 | M | 6.25 | 41336.17 |
HaMPK4 | HanXRQChr06g0170261 | Ha6 | + | 16894292 | 16893100 | 157 | 2 | 1 | M | 8.36 | 17702.54 |
HaMPK13-1 | HanXRQChr06g0175501 | Ha6 | - | 34635251 | 34631528 | 363 | 7 | 6 | - | 5.22 | 41353.31 |
HaMPK9-1 | HanXRQChr06g0183531 | Ha6 | + | 90706107 | 90699312 | 478 | 11 | 10 | - | 6.53 | 54442.91 |
HaMPK23-4 | HanXRQChr08g0226701 | Ha8 | + | 84318787 | 84308381 | 442 | 18 | 17 | - | 9.52 | 49480.06 |
HaMPK15 | HanXRQChr08g0227231 | Ha8 | + | 87599490 | 87591577 | 501 | 11 | 10 | - | 8.53 | 57073.07 |
HaMPK3-2 | HanXRQChr08g0229941 | Ha8 | - | 101013127 | 101009864 | 358 | 6 | 5 | - | 5.58 | 41298.31 |
HaMPK13-2 | HanXRQChr08g0230171 | Ha8 | - | 102808229 | 102804252 | 362 | 6 | 5 | - | 5.85 | 41552.83 |
HaMPK14 | HanXRQChr09g0243011 | Ha9 | + | 34673154 | 34669292 | 362 | 3 | 2 | - | 5.57 | 41423.42 |
HaMPK16-2 | HanXRQChr09g0248301 | Ha9 | + | 76212398 | 76202758 | 559 | 10 | 9 | - | 9.07 | 63370.4 |
HaMPK1 | HanXRQChr09g0269211 | Ha9 | - | 185086347 | 185083825 | 361 | 3 | 2 | - | 6.64 | 41831.44 |
HaMPK19-2 | HanXRQChr11g0330461 | Ha11 | + | 43791321 | 43784989 | 574 | 9 | 8 | - | 9.33 | 65344.85 |
HaMPK6-2 | HanXRQChr11g0343001 | Ha11 | - | 125967866 | 125963374 | 359 | 6 | 5 | - | 5.8 | 41553.72 |
HaMPK19-1 | HanXRQChr13g0389781 | Ha13 | - | 19048315 | 19044532 | 588 | 10 | 9 | - | 9.06 | 66613.36 |
HaMPK23-2 | HanXRQChr13g0411961 | Ha13 | - | 142634442 | 142625511 | 459 | 18 | 17 | - | 9.63 | 50984.95 |
HaMPK9-2 | HanXRQChr14g0432771 | Ha14 | - | 49683290 | 49679650 | 484 | 10 | 9 | - | 6.57 | 55530.13 |
HaMPK17 | HanXRQChr15g0484561 | Ha15 | - | 84424855 | 84420653 | 429 | 11 | 10 | - | 6.24 | 49909.6 |
HaMPK18 | HanXRQChr15g0495321 | Ha15 | - | 160155012 | 160149273 | 563 | 9 | 8 | - | 9.47 | 64374.62 |
MKK | |||||||||||
HaMKK9 | HanXRQChr03g0087071 | Ha3 | - | 148424902 | 148425825 | 308 | 1 | 0 | M | 6.75 | 34332.34 |
HaMKK4 | HanXRQChr04g0094171 | Ha4 | + | 471743 | 472816 | 351 | 1 | 0 | C | 9.04 | 38917.18 |
HaMKK6-1 | HanXRQChr09g0238861 | Ha9 | + | 9311933 | 9322916 | 357 | 8 | 7 | - | 6.76 | 39934.36 |
HaMKK5 | HanXRQChr10g0311571 | Ha10 | + | 219604899 | 219606004 | 355 | 1 | 0 | C | 9.25 | 39840.46 |
HaMKK6-2 | HanXRQChr10g0318871 | Ha10 | + | 244056044 | 244064185 | 355 | 8 | 7 | - | 7.13 | 39751.09 |
HaMKK2 | HanXRQChr10g0319531 | Ha10 | - | 245318274 | 245324118 | 371 | 9 | 8 | - | 5.43 | 40967.01 |
HaMKK1 | HanXRQChr12g0354521 | Ha12 | - | 1236278 | 1243005 | 358 | 10 | 9 | - | 5.77 | 39199.81 |
HaMKK3 | HanXRQChr14g0450561 | Ha14 | - | 141579116 | 141587170 | 520 | 12 | 11 | M | 5.79 | 68568.6 |
Clades | Consensus Common Docking Sites |
---|---|
Clade A | K-M-L-V-F-D-P-N-K-R-I-V-E-E-A-L |
Clade B | K-M-L-V-F-D-P-S-K-R-I-S-V-T-E-A-L |
Clade C | S-L-C-S-W-D-P-C-K-R-P-T-A-E-E-A-L |
Clade D | R-L-L-A-F-D-P-K-D-R-P-T-A-E-E-A-L |
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Neupane, S.; Schweitzer, S.E.; Neupane, A.; Andersen, E.J.; Fennell, A.; Zhou, R.; Nepal, M.P. Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). Plants 2019, 8, 28. https://doi.org/10.3390/plants8020028
Neupane S, Schweitzer SE, Neupane A, Andersen EJ, Fennell A, Zhou R, Nepal MP. Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.). Plants. 2019; 8(2):28. https://doi.org/10.3390/plants8020028
Chicago/Turabian StyleNeupane, Surendra, Sarah E. Schweitzer, Achal Neupane, Ethan J. Andersen, Anne Fennell, Ruanbao Zhou, and Madhav P. Nepal. 2019. "Identification and Characterization of Mitogen-Activated Protein Kinase (MAPK) Genes in Sunflower (Helianthus annuus L.)" Plants 8, no. 2: 28. https://doi.org/10.3390/plants8020028