Genome-Wide Identification, Characterization and Expression Patterns of the Pectin Methylesterase Inhibitor Genes in Sorghum bicolor
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and PME Activity Analysis
2.2. Identification of SbPMEI Members and Sequence Characterization
2.3. Phylogenetic Analysis, Chromosome Location and Tandem Gene Duplication
2.4. Gene Structure, GO Analysis and Protein–Protein Interaction Analysis
2.5. Cis-Acting Elements Analysis
2.6. Expression Patterns of Sorghum PMEI Genes
2.7. Abiotic Stress Treatments, RNA Isolation and qRT-PCR Analysis
3. Results
3.1. PME Activity Analysis of Six Tissues From Sorghum Bicolor
3.2. Identification, Chromosome Location and Tandem Gene Duplicates of PMEI Genes in Sorghum
3.3. Phylogenetic Analysis and Sequence Characterizations
3.4. Gene Structure Analysis of SbPMEIs
3.5. GO Analysis and Protein–Protein Interaction Prediction
3.6. Cis-Acting Elements Detection in Promoter Regions of SbPMEI Genes
3.7. Expression Patterns of PMEI Genes in Growth Lifecycle
3.8. Expression Patters of SbPMEIs under Exogenous Hormones and Abiotic Stresses
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene Name | Sequence ID | Subfamily | Signal Position | ORF (bp) | Subcellular Localization | Predicted Features | No. of Intron | |||
---|---|---|---|---|---|---|---|---|---|---|
Plant-mPLoc | WOLF PSORT | Length (aa) | NM (kDa) | pI | ||||||
SbPMEI1 | Sobic.001G024300 | II | 1-24 | 564 | C.M | chlo: 9, extr: 4 | 187 | 19.30 | 5.48 | 0 |
SbPMEI2 | Sobic.001G024400 | II | 1-31 | 588 | C.M | chlo: 9, extr: 4 | 195 | 20.85 | 4.68 | 0 |
SbPMEI3 | Sobic.001G024900 | II | 1-34 | 723 | C.M, Nuc | chlo: 14 | 240 | 24.76 | 8.86 | 0 |
SbPMEI4 | Sobic.001G198700 | II | 1-26 | 720 | C.M, Nuc | chlo: 9, vacu: 3, mito: 1 | 239 | 24.29 | 5.09 | 0 |
SbPMEI5 | Sobic.001G198800 | II | 1-24 | 672 | C.M, Nuc | chlo: 12, mito: 1 | 223 | 22.49 | 5.87 | 0 |
SbPMEI6 | Sobic.001G288400 | II | 1-23 | 660 | C.M | chlo: 11, extr: 2 | 219 | 21.93 | 8.83 | 0 |
SbPMEI7 | Sobic.001G323801 | II | 1-20 | 681 | C.M | chlo: 11, nucl: 1, mito: 1 | 227 | 22.88 | 8.72 | 0 |
SbPMEI8 | Sobic.001G328900 | III | 1-19 | 714 | Nuc | extr: 12, vacu: 1 | 231 | 24.31 | 8.18 | 1 |
SbPMEI9 | Sobic.002G091200 | I | 1-25 | 768 | C.M | chlo: 13 | 255 | 25.91 | 4.69 | 0 |
SbPMEI10 | Sobic.002G091300 | I | 1-22 | 948 | Nuc | chlo: 7, extr: 6 | 315 | 30.34 | 4.15 | 0 |
SbPMEI11 | Sobic.002G102800 | III | 1-23 | 555 | C.M | extr: 5, vacu: 5, chlo: 1, cyto: 1, plas: 1 | 184 | 18.64 | 6.24 | 0 |
SbPMEI12 | Sobic.002G103000 | III | 1-38 | 579 | C.M | extr: 5, chlo: 4, mito: 2, E.R._plas: 2, plas: 1.5 | 198 | 20.15 | 4.86 | 0 |
SbPMEI13 | Sobic.003G099500 | I | 1-32 | 639 | Nuc | chlo: 9, mito: 2, vacu: 2 | 212 | 23.01 | 10.39 | 0 |
SbPMEI14 | Sobic.003G099600 | I | 1-23 | 477 | C.M | chlo: 9, mito: 2, extr: 2 | 158 | 17.11 | 5.72 | 0 |
SbPMEI15 | Sobic.003G100100 | I | 1-30 | 603 | C.M, Nuc | chlo: 11, vacu: 2 | 200 | 21.41 | 9.32 | 0 |
SbPMEI16 | Sobic.003G114800 | I | 1-25 | 552 | C.M | extr: 5, chlo: 3, cyto: 3, vacu: 2 | 183 | 19.92 | 9.10 | 0 |
SbPMEI17 | Sobic.003G114900 | I | 1-22 | 507 | C.M | extr: 9, vacu: 3, chlo: 1 | 168 | 18.06 | 4.75 | 0 |
SbPMEI18 | Sobic.003G147700 | II | 1-42 | 594 | C.M | E.R.: 2.5, E.R._plas: 2.5, chlo: 2, mito: 2, extr: 2, vacu: 2, plas: 1.5, nucl: 1 | 213 | 22.19 | 4.57 | 1 |
SbPMEI19 | Sobic.003G203900 | III | 1-27 | 570 | C.M | chlo: 4, extr: 4, vacu: 4, mito: 1 | 189 | 19.61 | 9.50 | 0 |
SbPMEI20 | Sobic.003G270700 | I | 1-25 | 657 | C.M | chlo: 9, extr: 4 | 218 | 22.85 | 4.62 | 1 |
SbPMEI21 | Sobic.004G002700 | I | 1-37 | 642 | C.M | extr: 8, plas: 2, golg: 2, chlo: 1 | 213 | 23.48 | 9.00 | 0 |
SbPMEI22 | Sobic.004G002800 | II | 1-40 | 720 | C.M | chlo: 3, mito: 2, vacu: 2, E.R.: 2, nucl: 1, cyto: 1, plas: 1, extr: 1 | 239 | 25.16 | 4.79 | 0 |
SbPMEI23 | Sobic.004G147700 | III | 1-25 | 558 | C.M | vacu: 7, E.R.: 3, plas: 2, extr: 2 | 185 | 19.22 | 5.09 | 0 |
SbPMEI24 | Sobic.004G167700 | III | 1-27 | 570 | C.M | extr: 9, chlo: 2, vacu: 2 | 189 | 19.62 | 5.07 | 0 |
SbPMEI25 | Sobic.004G167800 | III | 1-35 | 600 | C.M | chlo: 13 | 199 | 20.66 | 5.89 | 0 |
SbPMEI26 | Sobic.004G167900 | III | 1-22 | 543 | C.M | extr: 13 | 180 | 18.85 | 5.43 | 0 |
SbPMEI27 | Sobic.004G168000 | III | 1-25 | 513 | C.M | extr: 10, chlo: 1, mito: 1, vacu: 1 | 170 | 18.17 | 5.90 | 1 |
SbPMEI28 | Sobic.004G277100 | I | 1-19 | 543 | C.M | extr: 6, chlo: 3, vacu: 3, nucl: 1 | 180 | 18.79 | 4.46 | 0 |
SbPMEI29 | Sobic.004G277600 | I | 1-27 | 537 | C.M | chlo: 8, extr: 5 | 178 | 18.87 | 4.98 | 0 |
SbPMEI30 | Sobic.004G277700 | I | 1-26 | 546 | Nuc | extr: 12, chlo: 1 | 183 | 18.91 | 5.45 | 0 |
SbPMEI31 | Sobic.005G022600 | III | 1-23 | 588 | C.M | extr: 11, chlo: 1, cyto: 1 | 193 | 19.47 | 6.09 | 0 |
SbPMEI32 | Sobic.005G160700 | II | 1-30 | 696 | C.M | chlo: 13 | 231 | 23.52 | 8.42 | 0 |
SbPMEI33 | Sobic.005G212900 | I | 1-24 | 1707 | Nuc | vacu: 7, nucl: 2, extr: 2, golg: 2 | 568 | 59.99 | 5.26 | 0 |
SbPMEI34 | Sobic.006G004300 | II | 1-27 | 645 | C.M | chlo: 7, extr: 3, vacu: 3 | 214 | 22.83 | 10.66 | 0 |
SbPMEI35 | Sobic.006G079100 | I | 1-21 | 660 | C.M | extr: 9, vacu: 3, chlo: 2 | 219 | 22.88 | 8.24 | 0 |
SbPMEI36 | Sobic.006G094000 | III | 1-57 | 714 | C.M | chlo: 10, mito: 3 | 237 | 25.01 | 9.47 | 0 |
SbPMEI37 | Sobic.006G194800 | I | 1-21 | 567 | C.M | chlo: 6, extr: 6, cyto: 1 | 188 | 19.84 | 6.42 | 0 |
SbPMEI38 | Sobic.006G194900 | I | 1-21 | 534 | C.M | extr: 8, chlo: 4, nucl: 1 | 177 | 18.27 | 6.72 | 0 |
SbPMEI39 | Sobic.007G008000 | I | 1-25 | 723 | C.M, Nuc | chlo: 13 | 240 | 23.74 | 7.69 | 0 |
SbPMEI40 | Sobic.007G008100 | I | 1-25 | 681 | C.M, Nuc | chlo: 12, cyto: 1 | 226 | 22.94 | 8.32 | 0 |
SbPMEI41 | Sobic.007G008200 | I | 1-18 | 660 | C.M | chlo: 12, mito: 1 | 219 | 21.84 | 6.99 | 0 |
SbPMEI42 | Sobic.007G036000 | I | 1-24 | 537 | C.M | extr: 10, chlo: 1, plas: 1, vacu: 1 | 178 | 18.77 | 4.51 | 0 |
SbPMEI43 | Sobic.007G036200 | I | 1-24 | 552 | Nuc | extr: 11, chlo: 1, vacu: 1 | 183 | 20.05 | 5.19 | 0 |
SbPMEI44 | Sobic.008G129800 | I | 1-31 | 684 | C.M | extr: 10, chlo: 1, cyto: 1, mito: 1 | 227 | 23.45 | 9.17 | 0 |
SbPMEI45 | Sobic.008G154500 | III | 1-22 | 507 | C.M | chlo: 10, cyto: 3 | 180 | 17.97 | 5.28 | 0 |
SbPMEI46 | Sobic.008G154600 | III | 1-19 | 555 | C.M | extr: 11, vacu: 3 | 184 | 18.65 | 4.59 | 0 |
SbPMEI47 | Sobic.008G154700 | III | 1-26 | 591 | C.M | extr: 8, chlo: 3, cyto: 2 | 196 | 19.03 | 5.71 | 0 |
SbPMEI48 | Sobic.008G154801 | III | 1-49 | 711 | Nuc | chlo: 5, cyto: 2, mito: 2, nucl: 1, plas: 1, extr: 1, vacu: 1 | 237 | 23.96 | 6.58 | 1 |
SbPMEI49 | Sobic.008G154900 | III | 1-23 | 576 | C.M | chlo: 5, extr: 5, cyto: 2, mito: 1 | 191 | 18.71 | 4.90 | 0 |
SbPMEI50 | Sobic.009G091600 | I | 1-30 | 555 | C.M | extr: 7, chlo: 3, vacu: 3 | 184 | 19.99 | 9.24 | 0 |
SbPMEI51 | Sobic.009G216400 | III | 1-24 | 567 | C.M, Nuc | extr: 8, vacu: 4, chlo: 1 | 188 | 20.66 | 5.83 | 1 |
SbPMEI52 | Sobic.010G006900 | II | 1-31 | 567 | C.M | extr: 13 | 188 | 19.46 | 5.36 | 1 |
SbPMEI53 | Sobic.010G007600 | I | 1-26 | 708 | Nuc | extr: 5, chlo: 4, vacu: 4 | 235 | 25.08 | 4.93 | 0 |
SbPMEI54 | Sobic.010G261000 | II | 1-21 | 609 | C.M | chlo: 6, extr: 3, cyto: 2, vacu: 2 | 202 | 20.55 | 9.35 | 0 |
SbPMEI55 | Sobic.010G261100 | II | 1-29 | 654 | C.M | chlo: 14 | 217 | 21.62 | 9.60 | 0 |
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Ren, A.; Ahmed, R.I.; Chen, H.; Han, L.; Sun, J.; Ding, A.; Guo, Y.; Kong, Y. Genome-Wide Identification, Characterization and Expression Patterns of the Pectin Methylesterase Inhibitor Genes in Sorghum bicolor. Genes 2019, 10, 755. https://doi.org/10.3390/genes10100755
Ren A, Ahmed RI, Chen H, Han L, Sun J, Ding A, Guo Y, Kong Y. Genome-Wide Identification, Characterization and Expression Patterns of the Pectin Methylesterase Inhibitor Genes in Sorghum bicolor. Genes. 2019; 10(10):755. https://doi.org/10.3390/genes10100755
Chicago/Turabian StyleRen, Angyan, Rana Imtiaz Ahmed, Huanyu Chen, Linhe Han, Jinhao Sun, Anming Ding, Yongfeng Guo, and Yingzhen Kong. 2019. "Genome-Wide Identification, Characterization and Expression Patterns of the Pectin Methylesterase Inhibitor Genes in Sorghum bicolor" Genes 10, no. 10: 755. https://doi.org/10.3390/genes10100755