Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis
Abstract
:1. Introduction
2. Results
2.1. Identification of NF-YB Genes in Cotton
2.2. Phylogenetic Analysis of the NF-YB Gene Family
2.3. Chromosomal Distribution and Synteny Analysis of GhNF-YB Genes
2.4. Gene Structure and Analysis of Conserved Motifs
2.5. Analyses of Tissue-Specific Expression Patterns of 50 G. hirsutum NF-YB Genes
2.6. Overexpression of GhDNF-YB22 in Cotton Affects Embryogenesis
3. Discussion
3.1. Variation in the NF-YB Gene Family in G. hirsutum
3.2. Expression Patterns of NF-YB Genes in G. hirsutum
3.3. Role of GhDNF-YB22 in Embryogenesis
4. Materials and Methods
4.1. Identification of the NF-YB Gene Family
4.2. Phylogenetic Analyses
4.3. Chromosome Locations and Collinearity Analyses
4.4. Estimating Ka/Ks Rates
4.5. Analysis of Transposable Elements
4.6. Gene Structure and Conserved Motifs Analysis
4.7. Gene Expression Heat Map
4.8. RNA Isolation and qRT-PCR Verification
4.9. Gene Cloning and Transformation into Cotton
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Homologous Pairs | Ka | Ks | Ka/Ks | |
---|---|---|---|---|
Gh_ANF-YB21 | Gh_ANF-YB19 | 0.071 | 0.376 | 0.189 |
Gh_ANF-YB11 | Gh_ANF-YB1 | 0.025 | 0.563 | 0.044 |
Gh_ANF-YB14 | Gh_ANF-YB2 | 0.061 | 0.621 | 0.098 |
Gh_ANF-YB20 | Gh_ANF-YB10 | 0.203 | 1.113 | 0.182 |
Gh_DNF-YB23 | Gh_DNF-YB3 | 0.067 | 0.486 | 0.139 |
Gh_DNF-YB21 | Gh_DNF-YB19 | 0.183 | 0.474 | 0.386 |
Gh_DNF-YB11 | Gh_DNF-YB1 | 0.025 | 0.481 | 0.052 |
Gh_DNF-YB14 | Gh_DNF-YB2 | 0.083 | 0.500 | 0.165 |
Gh_DNF-YB20 | Gh_DNF-YB10 | 0.245 | 0.846 | 0.289 |
Type | Elements | Number of Elements | Length Occupied (bp) | Percentage of Sequence (%) | Number of Elements | Length Occupied (bp) | Percentage of Sequence (%) |
---|---|---|---|---|---|---|---|
10,000 bp region | 2000 bp region | ||||||
DNA transposons | 1 | 91 | 0.10 | 0 | 0 | 0 | |
CMC-EnSpm | 0 | 0 | 0 | 0 | 0 | 0 | |
MULE-MuDR | 0 | 0 | 0 | 0 | 0 | 0 | |
PIF-Harbinger | 0 | 0 | 0 | 0 | 0 | 0 | |
TcMar-Pogo | 0 | 0 | 0 | 0 | 0 | 0 | |
hAT | 0 | 0 | 0 | 0 | 0 | 0 | |
hAT-Ac | 1 | 91 | 0.10 | 0 | 0 | 0 | |
hAT-Charlie | 0 | 0 | 0 | 0 | 0 | 0 | |
hAT-Tag1 | 0 | 0 | 0 | 0 | 0 | 0 | |
hAT-Tip100 | 0 | 0 | 0 | 0 | 0 | 0 | |
Retroelements | 53 | 17,673 | 18.90 | 3 | 1038 | 7.43 | |
LINE: | 10 | 2923 | 3.13 | 1 | 91 | 0.65 | |
L1 | 10 | 2923 | 3.13 | 1 | 91 | 0.65 | |
LTR: | 43 | 14,750 | 15.78 | 2 | 947 | 6.78 | |
Caulimovirus | 0 | 0 | 0 | 0 | 0 | 0 | |
Copia | 33 | 12,359 | 13.22 | 2 | 947 | 6.7 | |
Gypsy | 10 | 2391 | 2.56 | 0 | 0 | 0 | |
RC: | 0 | 0 | 0 | 0 | 0 | 0 | |
Helitron | 0 | 0 | 0 | 0 | 0 | 0 | |
DNA | 1 | 72 | 0.08 | 0 | 0 | 0 | |
Low_complexity | 166 | 9514 | 10.18 | 47 | 2479 | 17.74 | |
Simple_repeat | 586 | 25176 | 26.93 | 221 | 8121 | 58.12 | |
Unspecified | 151 | 49452 | 52.90 | 16 | 3681 | 26.35 | |
tRNA | 1 | 30 | 0.03 | 0 | 0 | 0 |
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Chen, Y.; Yang, Z.; Xiao, Y.; Wang, P.; Wang, Y.; Ge, X.; Zhang, C.; Zhang, X.; Li, F. Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis. Int. J. Mol. Sci. 2018, 19, 483. https://doi.org/10.3390/ijms19020483
Chen Y, Yang Z, Xiao Y, Wang P, Wang Y, Ge X, Zhang C, Zhang X, Li F. Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis. International Journal of Molecular Sciences. 2018; 19(2):483. https://doi.org/10.3390/ijms19020483
Chicago/Turabian StyleChen, Yanli, Zhaoen Yang, Yanqing Xiao, Peng Wang, Ye Wang, Xiaoyang Ge, Chaojun Zhang, Xianlong Zhang, and Fuguang Li. 2018. "Genome-Wide Analysis of the NF-YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF-YB22 in Embryogenesis" International Journal of Molecular Sciences 19, no. 2: 483. https://doi.org/10.3390/ijms19020483