Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials and Transcriptome Sequencing
2.2. Identification of SUV Gene Family
2.3. Phylogenetic Analysis
2.4. Chromosomal Mapping and Gene Structure
2.5. Protein Properties Prediction and Conserved Motif Analysis
2.6. The Syntenic Genes, Duplication Types and Transposable Elements Analysis
2.7. Cis-Elements and SUV Genes Expression
3. Results
3.1. Identification, Characterization of SUV Gene Family and the Protein Properties Prediction
3.2. The Phylogenetic Relationship Analysis of SUV Proteins
3.3. Gene Structure and Protein Conserved Domain
3.4. Chromosomal Localization of SUV Genes
3.5. Syntenic and Duplicated Gene Analysis
3.6. The Gene Duplication Types and Transposable Elements Analysis
3.7. Cis-Acting Elements in the Promoter Region of SUV Gene Family
3.8. Expression Patterns of SUV Gene Family in Different Tissues
4. Discussion
4.1. Compared with Its Diploid Ancestors, SUV Gene Family in B. napus Amplified during Allopolyploidization
4.2. Some Orthologous Genes of SUV Gene Family in Arabidopsis Were Lost in B. napus and Its Diploid Ancestors during Evolution
4.3. The Gene Structure of SUV Gene Family Was Conserved during the Allopolyploidization Process
4.4. The Expression Patterns of SUV Genes in B. napus Were Changed
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
- Jenuwein, T.; Laible, G.; Dorn, R.; Reuter, G. SET domain proteins modulate chromatin domains in eu- and heterochromatin. Cell. Mol. Life Sci. 1998, 54, 80–93. [Google Scholar] [CrossRef]
- Sarma, S.; Lodha, M. Phylogenetic relationship and domain organisation of SET domain proteins of Archaeplastida. BMC Plant. Biol. 2017, 17, 238. [Google Scholar] [CrossRef] [Green Version]
- Ng, D.W.; Wang, T.; Chandrasekharan, M.B.; Aramayo, R.; Kertbundit, S.; Hall, T.C. Plant SET domain-containing proteins: Structure, function and regulation. Biochim. Biophys. Acta 2007, 1769, 316–329. [Google Scholar] [CrossRef] [Green Version]
- Pontvianne, F.; Blevins, T.; Pikaard, C.S. Arabidopsis histone lysine methyltransferases. Adv. Bot. Res. 2010, 53, 1–22. [Google Scholar] [CrossRef] [Green Version]
- Baumbusch, L.O.; Thorstensen, T.; Krauss, V.; Fischer, A.; Naumann, K.; Assalkhou, R.; Schulz, I.; Reuter, G.; Aalen, R.B. The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res. 2001, 29, 4319–4333. [Google Scholar] [CrossRef]
- Springer, N.M.; Napoli, C.A.; Selinger, D.A.; Pandey, R.; Cone, K.C.; Chandler, V.L.; Kaeppler, H.F.; Kaeppler, S.M. Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant. Physiol. 2003, 132, 907–925. [Google Scholar] [CrossRef] [Green Version]
- Zhang, L.; Ma, H. Complex evolutionary history and diverse domain organization of SET proteins suggest divergent regulatory interactions. New Phytol. 2012, 195, 248–263. [Google Scholar] [CrossRef]
- Zhu, X.; Ma, H.; Chen, Z. Phylogenetics and evolution of Su(var)3-9 SET genes in land plants: Rapid diversification in structure and function. BMC Evol. Biol. 2011, 11, 63. [Google Scholar] [CrossRef] [Green Version]
- Satish, M.; Nivya, M.A.; Abhishek, S.; Nakarakanti, N.K.; Shivani, D.; Vani, M.V.; Rajakumara, E. Computational characterization of substrate and product specificities, and functionality of S-adenosylmethionine binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize. Proteins 2018, 86, 21–34. [Google Scholar] [CrossRef] [Green Version]
- Schotta, G.; Ebert, A.; Krauss, V.; Fischer, A.; Hoffmann, J.; Rea, S.; Jenuwein, T.; Dorn, R.; Reuter, G. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 2002, 21, 1121–1131. [Google Scholar] [CrossRef]
- Nakayama, J.; Rice, J.C.; Strahl, B.D.; Allis, C.D.; Grewal, S.I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 2001, 292, 110–113. [Google Scholar] [CrossRef] [Green Version]
- Tschiersch, B.; Hofmann, A.; Krauss, V.; Dorn, R.; Korge, G.; Reuter, G. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 1994, 13, 3822–3831. [Google Scholar] [CrossRef]
- Johnson, L.M.; Law, J.A.; Khattar, A.; Henderson, I.R.; Jacobsen, S.E. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet. 2008, 4, e1000280. [Google Scholar] [CrossRef]
- Qian, Y.; Xi, Y.; Cheng, B.; Zhu, S.; Kan, X. Identification and characterization of the SET domain gene family in maize. Mol. Biol. Rep. 2014, 41, 1341–1354. [Google Scholar] [CrossRef]
- Huang, Y.; Liu, C.; Shen, W.H.; Ruan, Y. Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family. BMC Plant Biol. 2011, 11, 175. [Google Scholar] [CrossRef] [Green Version]
- Dong, H.; Liu, D.; Han, T.; Zhao, Y.; Sun, J.; Lin, S.; Cao, J.; Chen, Z.H.; Huang, L. Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication. Sci. Rep. 2015, 5, 16851. [Google Scholar] [CrossRef] [Green Version]
- Lu, Z.; Huang, X.; Ouyang, Y.; Yao, J. Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice. PLoS ONE 2013, 8, e65426. [Google Scholar] [CrossRef] [Green Version]
- Batra, R.; Gautam, T.; Pal, S.; Chaturvedi, R.D.; Jan, I.; Balyan, H.S.; Gupta, P.K. Identification and characterization of SET domain family genes in bread wheat (Triticum aestivum L.). Sci. Rep. 2020, 10, 14624. [Google Scholar] [CrossRef]
- Li, W.; Yan, J.; Wang, S.; Wang, Q.; Wang, C.; Li, Z.; Zhang, D.; Ma, F.; Guan, Q.; Xu, J. Genome-wide analysis of SET-domain group histone methyltransferases in apple reveals their role in development and stress responses. BMC Genom. 2021, 22, 283. [Google Scholar] [CrossRef]
- Naumann, K.; Fischer, A.; Hofmann, I.; Krauss, V.; Phalke, S.; Irmler, K.; Hause, G.; Aurich, A.C.; Dorn, R.; Jenuwein, T.; et al. Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J. 2005, 24, 1418–1429. [Google Scholar] [CrossRef]
- Liu, Z.W.; Shao, C.R.; Zhang, C.J.; Zhou, J.X.; Zhang, S.W.; Li, L.; Chen, S.; Huang, H.W.; Cai, T.; He, X.J. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet. 2014, 10, e1003948. [Google Scholar] [CrossRef] [Green Version]
- Johnson, L.M.; Du, J.; Hale, C.J.; Bischof, S.; Feng, S.; Chodavarapu, R.K.; Zhong, X.; Marson, G.; Pellegrini, M.; Segal, D.J.; et al. SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation. Nature 2014, 507, 124–128. [Google Scholar] [CrossRef] [Green Version]
- Rajakumara, E.; Nakarakanti, N.K.; Nivya, M.A.; Satish, M. Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain. Sci. Rep. 2016, 6, 20161. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Li, X.; Harris, C.J.; Zhong, Z.; Chen, W.; Liu, R.; Jia, B.; Wang, Z.; Li, S.; Jacobsen, S.E.; Du, J. Mechanistic insights into plant SUVH family H3K9 methyltransferases and their binding to context-biased non-CG DNA methylation. Proc. Natl. Acad. Sci. USA 2018, 115, E8793–E8802. [Google Scholar] [CrossRef] [Green Version]
- Gu, D.; Ji, R.; He, C.; Peng, T.; Zhang, M.; Duan, J.; Xiong, C.; Liu, X. Arabidopsis histone methyltransferase SUVH5 is a positive regulator of light-mediated seed germination. Front. Plant. Sci. 2019, 10, 841. [Google Scholar] [CrossRef]
- Xu, L.; Jiang, H. Writing and reading histone H3 lysine 9 methylation in Arabidopsis. Front. Plant Sci. 2020, 11, 452. [Google Scholar] [CrossRef] [PubMed]
- Li, S.; Liu, L.; Li, S.; Gao, L.; Zhao, Y.; Kim, Y.J.; Chen, X. SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation. Nucleic Acids Res. 2016, 44, 608–620. [Google Scholar] [CrossRef] [Green Version]
- Rahman, M.A.; Kristiansen, P.E.; Veiseth, S.V.; Andersen, J.T.; Yap, K.L.; Zhou, M.M.; Sandlie, I.; Thorstensen, T.; Aalen, R.B. The Arabidopsis histone methyltransferase SUVR4 binds ubiquitin via a domain with a four-helix bundle structure. Biochemistry 2014, 53, 2091–2100. [Google Scholar] [CrossRef] [Green Version]
- Zhou, H.; Liu, Y.; Liang, Y.; Zhou, D.; Li, S.; Lin, S.; Dong, H.; Huang, L. The function of histone lysine methylation related SET domain group proteins in plants. Protein Sci. 2020, 29, 1120–1137. [Google Scholar] [CrossRef]
- Song, X.; Wei, Y.; Xiao, D.; Gong, K.; Sun, P.; Ren, Y.; Yuan, J.; Wu, T.; Yang, Q.; Li, X.; et al. Brassica carinata genome characterization clarifies U’s triangle model of evolution and polyploidy in Brassica. Plant Physiol. 2021, 186, 388–406. [Google Scholar] [CrossRef] [PubMed]
- Liu, S.; Liu, Y.; Yang, X.; Tong, C.; Edwards, D.; Parkin, I.A.; Zhao, M.; Ma, J.; Yu, J.; Huang, S.; et al. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat. Commun. 2014, 5, 3930. [Google Scholar] [CrossRef] [PubMed]
- Town, C.D.; Cheung, F.; Maiti, R.; Crabtree, J.; Haas, B.J.; Wortman, J.R.; Hine, E.E.; Althoff, R.; Arbogast, T.S.; Tallon, L.J.; et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 2006, 18, 1348–1359. [Google Scholar] [CrossRef] [Green Version]
- Wang, X.; Wang, H.; Wang, J.; Sun, R.; Wu, J.; Liu, S.; Bai, Y.; Mun, J.H.; Bancroft, I.; Cheng, F.; et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 2011, 43, 1035–1039. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Chalhoub, B.; Denoeud, F.; Liu, S.; Parkin, I.A.; Tang, H.; Wang, X.; Chiquet, J.; Belcram, H.; Tong, C.; Samans, B.; et al. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014, 345, 950–953. [Google Scholar] [CrossRef] [Green Version]
- Li, M.; Wang, R.; Wu, X.; Wang, J. Homoeolog expression bias and expression level dominance (ELD) in four tissues of natural allotetraploid Brassica napus. BMC Genom. 2020, 21, 330. [Google Scholar] [CrossRef] [PubMed]
- Cheng, F.; Liu, S.; Wu, J.; Fang, L.; Sun, S.; Liu, B.; Li, P.; Hua, W.; Wang, X. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol. 2011, 11, 136. [Google Scholar] [CrossRef] [Green Version]
- Li, M.; Wang, R.; Liu, Z.; Wu, X.; Wang, J. Genome-wide identification and analysis of the WUSCHEL-related homeobox (WOX) gene family in allotetraploid Brassica napus reveals changes in WOX genes during polyploidization. BMC Genom. 2019, 20, 317. [Google Scholar] [CrossRef]
- Marchler-Bauer, A.; Bo, Y.; Han, L.; He, J.; Lanczycki, C.J.; Lu, S.; Chitsaz, F.; Derbyshire, M.K.; Geer, R.C.; Gonzales, N.R.; et al. CDD/SPARCLE: Functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017, 45, D200–D203. [Google Scholar] [CrossRef] [Green Version]
- Letunic, I.; Khedkar, S.; Bork, P. SMART: Recent updates, new developments and status in 2020. Nucleic Acids Res. 2021, 49, D458–D460. [Google Scholar] [CrossRef]
- Mistry, J.; Chuguransky, S.; Williams, L.; Qureshi, M.; Salazar, G.A.; Sonnhammer, E.L.L.; Tosatto, S.C.E.; Paladin, L.; Raj, S.; Richardson, L.J.; et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021, 49, D412–D419. [Google Scholar] [CrossRef]
- Ostergaard, L.; King, G.J. Standardized gene nomenclature for the Brassica genus. Plant Methods 2008, 4, 10. [Google Scholar] [CrossRef] [Green Version]
- Sakai, H.; Lee, S.S.; Tanaka, T.; Numa, H.; Kim, J.; Kawahara, Y.; Wakimoto, H.; Yang, C.C.; Iwamoto, M.; Abe, T.; et al. Rice Annotation Project Database (RAP-DB): An integrative and interactive database for rice genomics. Plant Cell Physiol. 2013, 54, e6. [Google Scholar] [CrossRef] [PubMed]
- Mansueto, L.; Fuentes, R.R.; Borja, F.N.; Detras, J.; Abriol-Santos, J.M.; Chebotarov, D.; Sanciangco, M.; Palis, K.; Copetti, D.; Poliakov, A.; et al. Rice SNP-seek database update: New SNPs, indels, and queries. Nucleic Acids Res. 2017, 45, D1075–D1081. [Google Scholar] [CrossRef]
- Lemoine, F.; Correia, D.; Lefort, V.; Doppelt-Azeroual, O.; Mareuil, F.; Cohen-Boulakia, S.; Gascuel, O. NGPhylogeny.fr: New generation phylogenetic services for non-specialists. Nucleic Acids Res. 2019, 47, W260–W265. [Google Scholar] [CrossRef] [Green Version]
- Letunic, I.; Bork, P. Interactive Tree of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 2021, 49, W293–W296. [Google Scholar] [CrossRef] [PubMed]
- Voorrips, R.E. MapChart: Software for the graphical presentation of linkage maps and QTLs. J. Hered. 2002, 93, 77–78. [Google Scholar] [CrossRef] [Green Version]
- Hu, B.; Jin, J.; Guo, A.Y.; Zhang, H.; Luo, J.; Gao, G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics 2015, 31, 1296–1297. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Duvaud, S.; Gabella, C.; Lisacek, F.; Stockinger, H.; Ioannidis, V.; Durinx, C. Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users. Nucleic Acids Res. 2021, 49, W216–W227. [Google Scholar] [CrossRef] [PubMed]
- Horton, P.; Park, K.J.; Obayashi, T.; Fujita, N.; Harada, H.; Adams-Collier, C.J.; Nakai, K. WoLF PSORT: Protein localization predictor. Nucleic Acids Res. 2007, 35, W585–W587. [Google Scholar] [CrossRef] [Green Version]
- Bailey, T.L.; Boden, M.; Buske, F.A.; Frith, M.; Grant, C.E.; Clementi, L.; Ren, J.; Li, W.W.; Noble, W.S. MEME SUITE: Tools for motif discovery and searching. Nucleic Acids Res. 2009, 37, W202–W208. [Google Scholar] [CrossRef]
- Chen, C.; Chen, H.; Zhang, Y.; Thomas, H.R.; Frank, M.H.; He, Y.; Xia, R. TBtools: An integrative toolkit developed for interactive analyses of big biological data. Mol. Plant 2020, 13, 1194–1202. [Google Scholar] [CrossRef] [PubMed]
- Kohany, O.; Gentles, A.J.; Hankus, L.; Jurka, J. Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinform. 2006, 7, 474. [Google Scholar] [CrossRef] [Green Version]
- Rombauts, S.; Déhais, P.; Van Montagu, M.; Rouzé, P. PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res. 1999, 27, 295–296. [Google Scholar] [CrossRef] [Green Version]
- Li, B.; Dewey, C.N. RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011, 12, 323. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Fischer, A.; Hofmann, I.; Naumann, K.; Reuter, G. Heterochromatin proteins and the control of heterochromatic gene silencing in Arabidopsis. J. Plant. Physiol. 2006, 163, 358–368. [Google Scholar] [CrossRef]
- Thorstensen, T.; Fischer, A.; Sandvik, S.V.; Johnsen, S.S.; Grini, P.E.; Reuter, G.; Aalen, R.B. The Arabidopsis SUVR4 protein is a nucleolar histone methyltransferase with preference for monomethylated H3K9. Nucleic Acids Res. 2006, 34, 5461–5470. [Google Scholar] [CrossRef] [Green Version]
- Cheng, F.; Wu, J.; Fang, L.; Wang, X. Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Front. Plant Sci. 2012, 3, 198. [Google Scholar] [CrossRef] [Green Version]
- Qiao, X.; Li, Q.; Yin, H.; Qi, K.; Li, L.; Wang, R.; Zhang, S.; Paterson, A.H. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol. 2019, 20, 38. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rensing, S.A. Gene duplication as a driver of plant morphogenetic evolution. Curr. Opin. Plant Biol. 2014, 17, 43–48. [Google Scholar] [CrossRef] [PubMed]
- Wang, Y.; Tan, X.; Paterson, A.H. Different patterns of gene structure divergence following gene duplication in Arabidopsis. BMC Genom. 2013, 14, 652. [Google Scholar] [CrossRef] [Green Version]
- Lallemand, T.; Leduc, M.; Landès, C.; Rizzon, C.; Lerat, E. An overview of duplicated gene detection methods: Why the duplication mechanism has to be accounted for in their choice. Genes 2020, 11, 1046. [Google Scholar] [CrossRef] [PubMed]
- Panchy, N.; Lehti-Shiu, M.; Shiu, S.H. Evolution of gene duplication in plants. Plant Physiol. 2016, 171, 2294–2316. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Albalat, R.; Cañestro, C. Evolution by gene loss. Nat. Rev. Genet. 2016, 17, 379–391. [Google Scholar] [CrossRef] [PubMed]
- Jiao, Y.; Wickett, N.J.; Ayyampalayam, S.; Chanderbali, A.S.; Landherr, L.; Ralph, P.E.; Tomsho, L.P.; Hu, Y.; Liang, H.; Soltis, P.S.; et al. Ancestral polyploidy in seed plants and angiosperms. Nature 2011, 473, 97–100. [Google Scholar] [CrossRef] [PubMed]
- Bowers, J.E.; Chapman, B.A.; Rong, J.; Paterson, A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003, 422, 433–438. [Google Scholar] [CrossRef]
- Lysak, M.A.; Koch, M.A.; Pecinka, A.; Schubert, I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 2005, 15, 516–525. [Google Scholar] [CrossRef] [Green Version]
- Jiang, D.; Li, G.; Chen, G.; Lei, J.; Cao, B.; Chen, C. Genome-wide identification and expression profiling of 2OGD superfamily genes from three Brassica plants. Genes 2021, 12, 1399. [Google Scholar] [CrossRef]
- Clark, J.W.; Donoghue, P.C.J. Whole-genome duplication and plant macroevolution. Trends Plant Sci. 2018, 23, 933–945. [Google Scholar] [CrossRef] [Green Version]
- Babula-Skowrońska, D. Functional divergence of Brassica napus BnaABI1 paralogs in the structurally conserved PP2CA gene subfamily of Brassicaceae. Genomics 2021, 113, 3185–3197. [Google Scholar] [CrossRef]
- Mun, J.H.; Kwon, S.J.; Yang, T.J.; Seol, Y.J.; Jin, M.; Kim, J.A.; Lim, M.H.; Kim, J.S.; Baek, S.; Choi, B.S.; et al. Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol. 2009, 10, R111. [Google Scholar] [CrossRef] [Green Version]
- Lim, K.Y.; Soltis, D.E.; Soltis, P.S.; Tate, J.; Matyasek, R.; Srubarova, H.; Kovarik, A.; Pires, J.C.; Xiong, Z.; Leitch, A.R. Rapid chromosome evolution in recently formed polyploids in Tragopogon (Asteraceae). PLoS ONE 2008, 3, e3353. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gaeta, R.T.; Pires, J.C.; Iniguez-Luy, F.; Leon, E.; Osborn, T.C. Genomic changes in resynthesized Brassica napus and their effect on gene expression and phenotype. Plant Cell 2007, 19, 3403–3417. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Rajakumara, E.; Law, J.A.; Simanshu, D.K.; Voigt, P.; Johnson, L.M.; Reinberg, D.; Patel, D.J.; Jacobsen, S.E. A dual flip-out mechanism for 5mC recognition by the Arabidopsis SUVH5 SRA domain and its impact on DNA methylation and H3K9 dimethylation in vivo. Genes Dev. 2011, 25, 137–152. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Gallego-Bartlomé, J. DNA methylation in plants: Mechanisms and tools for targeted manipulation. New Phytol. 2020, 227, 38–44. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Pu, M.; Chen, J.; Tao, Z.; Miao, L.; Qi, X.; Wang, Y.; Ren, J. Regulatory network of miRNA on its target: Coordination between transcriptional and post-transcriptional regulation of gene expression. Cell Mol. Life Sci. 2019, 76, 441–451. [Google Scholar] [CrossRef]
- Pope, S.D.; Medzhitov, R. Emerging principles of gene expression programs and their regulation. Mol. Cell 2018, 71, 389–397. [Google Scholar] [CrossRef] [Green Version]
Gene Name | |log2FC| in Stems | |log2FC| in Leaves | |log2FC| in Flowers | |log2FC| in Siliques |
---|---|---|---|---|
SUVH2 | 0.83 | 2.42 | 0.42 | 0.64 |
SUVH5 | 0.71 | 0.17 | 0.48 | 0.33 |
SUVH6 | 2.33 | 0.72 | 1.45 | 1.53 |
SUVR2 | 0.69 | 2.45 | 0.43 | 1.29 |
SUVR3 | 3.70 | 3.32 | 2.61 | 2.36 |
SUVR5 | 2.46 | 1.07 | 2.98 | 2.31 |
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. |
© 2021 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/).
Share and Cite
Hu, M.; Li, M.; Wang, J. Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors. Genes 2021, 12, 1848. https://doi.org/10.3390/genes12121848
Hu M, Li M, Wang J. Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors. Genes. 2021; 12(12):1848. https://doi.org/10.3390/genes12121848
Chicago/Turabian StyleHu, Meimei, Mengdi Li, and Jianbo Wang. 2021. "Comprehensive Analysis of the SUV Gene Family in Allopolyploid Brassica napus and Its Diploid Ancestors" Genes 12, no. 12: 1848. https://doi.org/10.3390/genes12121848