Genomic Characterization and Expressional Profiles of Autophagy-Related Genes (ATGs) in Oilseed Crop Castor Bean (Ricinus communis L.)
Abstract
1. Introduction
2. Results
2.1. Identification of Genes Encoding ATG Proteins in Castor Bean
2.2. Expression Profiles of RcATGs in Various Tissues
2.3. Expression Profiles of ATGs in Developing Seeds
2.4. Expression and Involvement of Autophagy in Mediating Storage Lipid Decomposition during Seed Germination
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. Identification of ATGs in Castor Bean
4.3. Bioinformatic Analysis and Phylogenetic Construction
4.4. Analysis of RNA-seq Data
4.5. RNA Extraction and qPCR
4.6. Determination of Lipid Content
4.7. Transmission Electron Microscopy
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Gene | Arabidopsis ID | Gene | Castor Bean ID | No. of Amino Acid Residues | Mw(kDa) | PI | E-value to Arabidopsis |
---|---|---|---|---|---|---|---|
ATG1/13 Kinase Complex | |||||||
AtATG1a | AT3G61960 | RcATG1a | 30076.m004465 | 676 | 75.1 | 5.90 | 4.4 × 10−66 |
AtATG1b | AT3G53930 | RcATG1b | 29973.m000397 | 694 | 76.9 | 6.44 | 7.6 × 10−62 |
AtATG1c | AT2G37840 | ||||||
AtATG1t | AT1G49180 | RcATG1t | 29659.m000143 | 321 | 36.6 | 8.29 | 1.2 × 10−88 |
AtATG13a | AT3G49590 | RcATG13a | 30098.m001725 | 621 | 69.4 | 8.81 | 3.5 × 10−103 |
AtATG13b | AT3G18770 | RcATG13b | 30206.m000754 | 342 | 39.5 | 9.59 | 3 × 10−83 |
RcATG13c | 30206.m000753 | 220 | 23.9 | 5.42 | 2.1 × 10−26 | ||
AtATG11 | AT4G30790 | RcATG11 | 30114.m000524 | 1145 | 129.2 | 5.73 | 0 |
AtATG101 | AT5G66930 | RcATG101 | 29676.m001649 | 205 | 24.1 | 5.94 | 7.9 × 10−76 |
PI3 Kinase Complex | |||||||
AtVPS34 | AT1G60490 | RcVPS34 | 29631.m001016 | 813 | 93 | 6.48 | 0 |
AtATG6 | AT3G61710 | RcATG6 | 29742.m001430 | 523 | 59.9 | 5.85 | 2.1 × 10−201 |
AtVPS15 | AT4G29380 | RcVPS15 | 29912.m005424 | 1455 | 163.5 | 7.00 | 0 |
ATG9/2/18 Complex | |||||||
AtATG2 | AT3G19190 | RcATG2 | 29801.m003197 | 1989 | 218.4 | 5.43 | 0 |
AtATG9 | AT2G31260 | RcATG9 | 29584.m000241 | 864 | 99.7 | 6.32 | 8.4 × 10−301 |
AtATG18a | AT3G62770 | RcATG18a | 30129.m000356 | 447 | 49 | 6.59 | 3.6 × 10−32 |
AtATG18b | AT4G30510 | RcATG18b | 28612.m000123 | 349 | 38 | 8.86 | 7.1 × 10−146 |
AtATG18c | AT2G40810 | RcATG18c | 29729.m002396 | 598 | 67 | 7.56 | 1.2 × 10−81 |
AtATG18d | AT3G56440 | RcATG18d | 30128.m008811 | 330 | 36.6 | 9.33 | 1.6 × 10−70 |
AtATG18e | AT5G05150 | RcATG18e | 28166.m001060 | 891 | 96.9 | 6.44 | 0 |
AtATG18f | AT5G54730 | RcATG18f | 29703.m001515 | 1016 | 110.7 | 6.25 | 3 × 10−115 |
AtATG18g | AT1G03380 | RcATG18g | 30128.m008700 | 991 | 107.6 | 5.44 | 1 × 10−113 |
AtATG18h | AT1G54710 | ||||||
ATG8/12 Conjugation System | |||||||
AtATG3 | AT5G61500 | RcATG3 | 30147.m014252 | 314 | 35.5 | 4.79 | 3.2 × 10−150 |
AtATG4a | AT2G44140 | RcATG4 | 28966.m000547 | 489 | 53.9 | 5.13 | 2.3 × 10−140 |
AtATG4b | AT3G59950 | ||||||
AtATG5 | AT5G17290 | RcATG5 | 30171.m000414 | 368 | 41.9 | 5.28 | 3.2 × 10−115 |
AtATG7 | AT5G45900 | RcATG7 | 29900.m001609 | 710 | 77.9 | 5.35 | 3.3 × 10−235 |
AtATG8a | AT4G21980 | RcATG8a | 29842.m003584 | 120 | 13.8 | 7.88 | 3.7 × 10−53 |
AtATG8b | AT4G04620 | RcATG8b | 30064.m000482 | 125 | 14.3 | 7.89 | 5.5 × 10−52 |
AtATG8c | AT1G62040 | RcATG8c | 30064.m000481 | 120 | 13.9 | 7.89 | 7 × 10−52 |
AtATG8d | AT2G05630 | RcATG8d | 29636.m000773 | 122 | 14.1 | 7.85 | 5.8 × 10−48 |
AtATG8e | AT2G45170 | RcATG8e | 30174.m008829 | 117 | 13.5 | 8.75 | 1.2 × 10−45 |
AtATG8f | AT4G16520 | RcATG8f | 30076.m004580 | 125 | 14.5 | 6.73 | 1.2 × 10−33 |
AtATG8g | AT3G60640 | RcATG8g | 29889.m003380 | 115 | 13.2 | 9.30 | 2 × 10−31 |
AtATG8h | AT3G06420 | ||||||
AtATG8i | AT3G15580 | ||||||
AtATG10 | AT3G07525 | RcAtg10 | 30178.m000879 | 233 | 26.9 | 5.25 | 7.3 × 10−57 |
AtATG12a | AT1G54210 | RcAtg12 | 29706.m001289 | 154 | 17.4 | 8.58 | 1.3 × 10−20 |
AtATG12b | AT3G13970 | ||||||
AtATG16L | AT5G50230 | RcATG16L | 30147.m013828 | 520 | 57.6 | 6.06 | 1.3 × 10−203 |
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Han, B.; Xu, H.; Feng, Y.; Xu, W.; Cui, Q.; Liu, A. Genomic Characterization and Expressional Profiles of Autophagy-Related Genes (ATGs) in Oilseed Crop Castor Bean (Ricinus communis L.). Int. J. Mol. Sci. 2020, 21, 562. https://doi.org/10.3390/ijms21020562
Han B, Xu H, Feng Y, Xu W, Cui Q, Liu A. Genomic Characterization and Expressional Profiles of Autophagy-Related Genes (ATGs) in Oilseed Crop Castor Bean (Ricinus communis L.). International Journal of Molecular Sciences. 2020; 21(2):562. https://doi.org/10.3390/ijms21020562
Chicago/Turabian StyleHan, Bing, Hui Xu, Yingting Feng, Wei Xu, Qinghua Cui, and Aizhong Liu. 2020. "Genomic Characterization and Expressional Profiles of Autophagy-Related Genes (ATGs) in Oilseed Crop Castor Bean (Ricinus communis L.)" International Journal of Molecular Sciences 21, no. 2: 562. https://doi.org/10.3390/ijms21020562
APA StyleHan, B., Xu, H., Feng, Y., Xu, W., Cui, Q., & Liu, A. (2020). Genomic Characterization and Expressional Profiles of Autophagy-Related Genes (ATGs) in Oilseed Crop Castor Bean (Ricinus communis L.). International Journal of Molecular Sciences, 21(2), 562. https://doi.org/10.3390/ijms21020562