Genome-Wide Identification and Evolution of HECT Genes in Soybean
Abstract
:1. Introduction
2. Results
2.1. Identification of Homologous to the E6-Associated Protein (E6-AP) Carboxyl Terminus (HECT) Gene Family in Soybean
Gene Symbol | Gene Locus | Chromosome | Gene Start | Gene Stop | Amino Acids |
---|---|---|---|---|---|
Gma01 | Glyma02g38020 | 2 | 43347265 | 43364774 | 3649 |
Gma02 | Glyma03g34650 | 3 | 42000995 | 42011419 | 973 |
Gma03 | Glyma04g00530 | 4 | 285772 | 296292 | 1891 |
Gma04 | Glyma04g10481 | 4 | 8701971 | 8719496 | 3680 |
Gma05 | Glyma05g26360 | 5 | 32340858 | 32357248 | 3762 |
Gma06 | Glyma06g00600 | 6 | 309849 | 320018 | 1895 |
Gma07 | Glyma06g10360 | 6 | 7845196 | 7861448 | 3654 |
Gma08 | Glyma07g36390 | 7 | 41782618 | 41798454 | 1026 |
Gma09 | Glyma07g39546 | 7 | 44005949 | 44011941 | 867 |
Gma10 | Glyma08g09270 | 8 | 6626148 | 6642483 | 3749 |
Gma11 | Glyma10g05620 | 10 | 4408645 | 4417572 | 1557 |
Gma12 | Glyma11g11490 | 11 | 8185583 | 8196786 | 1872 |
Gma13 | Glyma12g03640 | 12 | 2443609 | 2454729 | 1877 |
Gma14 | Glyma13g19981 | 13 | 23464333 | 23472965 | 1558 |
Gma15 | Glyma14g36180 | 14 | 45377087 | 45394472 | 3652 |
Gma16 | Glyma15g14591 | 15 | 11013042 | 11048953 | 1031 |
Gma17 | Glyma17g01210 | 17 | 704329 | 710650 | 867 |
Gma18 | Glyma17g04180 | 17 | 2781543 | 2800188 | 1026 |
Gma19 | Glyma19g37310 | 19 | 44504837 | 44515898 | 1157 |
2.2. Phylogenetic Analysis of HECT Genes in Soybean
2.3. Domain Architecture and Exon-Intron Structure of the Soybean HECT Genes
2.4. Chromosome Location and Duplication of Soybean HECT Genes
Group | Gene Locus 1 | Gene Locus 2 | Ka | Ks | Ka/Ks | Mya |
---|---|---|---|---|---|---|
I | Glyma05g26360 | Glyma08g09270 | 0.02 | 0.08 | 0.25 | 6.56 |
II | Glyma02g38020 | Glyma04g10481 | 0.1 | 0.51 | 0.2 | 41.8 |
Glyma02g38020 | Glyma06g10360 | 0.09 | 0.49 | 0.18 | 40.16 | |
Glyma02g38020 | Glyma14g36180 | 0.02 | 0.09 | 0.22 | 7.38 | |
Glyma04g10481 | Glyma06g10360 | 0.04 | 0.09 | 0.44 | 7.38 | |
Glyma04g10481 | Glyma14g36180 | 0.1 | 0.5 | 0.2 | 40.98 | |
Glyma06g10360 | Glyma14g36180 | 0.09 | 0.49 | 0.18 | 40.16 | |
III | Glyma07g39546 | Glyma17g01210 | 0.03 | 0.14 | 0.21 | 11.48 |
IV | Glyma07g36390 | Glyma15g14591 | 0.09 | 0.4 | 0.23 | 32.79 |
Glyma07g36390 | Glyma17g04180 | 0.02 | 0.09 | 0.22 | 7.38 | |
Glyma15g14591 | Glyma17g04180 | 0.1 | 0.42 | 0.24 | 34.43 | |
V | Glyma03g34650 | Glyma19g37310 | 0.03 | 0.07 | 0.43 | 5.74 |
VI | Glyma04g00530 | Glyma06g00600 | 0.03 | 0.09 | 0.33 | 7.38 |
Glyma04g00530 | Glyma11g11490 | 0.07 | 0.55 | 0.13 | 45.08 | |
Glyma04g00530 | Glyma12g03640 | 0.07 | 0.52 | 0.13 | 42.62 | |
Glyma06g00600 | Glyma11g11490 | 0.09 | 0.55 | 0.16 | 45.08 | |
Glyma06g00600 | Glyma12g03640 | 0.08 | 0.51 | 0.16 | 41.8 | |
Glyma11g11490 | Glyma12g03640 | 0.02 | 0.08 | 0.25 | 6.56 | |
VII | Glyma10g05620 | Glyma13g19981 | 0.03 | 0.1 | 0.3 | 8.2 |
2.5. Conserved Residues in the HECT Domain
2.6. Expression Patterns of Soybean HECT Genes
3. Discussion
4. Experimental Section
4.1. Identification of HECT Genes in Soybean
4.2. Phylogenetic Analysis and Gene Structure
4.3. Chromosome Location and Duplication
4.4. Calculation of Synonymous (Ks) and Nonsynonymous Substitution (Ka) to Date Duplication Events
4.5. Logos of HECT Domains and Three-Dimensional Representations of Domain Alignment
4.6. Expression Analyses
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Meng, X.; Wang, C.; Rahman, S.U.; Wang, Y.; Wang, A.; Tao, S. Genome-Wide Identification and Evolution of HECT Genes in Soybean. Int. J. Mol. Sci. 2015, 16, 8517-8535. https://doi.org/10.3390/ijms16048517
Meng X, Wang C, Rahman SU, Wang Y, Wang A, Tao S. Genome-Wide Identification and Evolution of HECT Genes in Soybean. International Journal of Molecular Sciences. 2015; 16(4):8517-8535. https://doi.org/10.3390/ijms16048517
Chicago/Turabian StyleMeng, Xianwen, Chen Wang, Siddiq Ur Rahman, Yaxu Wang, Ailan Wang, and Shiheng Tao. 2015. "Genome-Wide Identification and Evolution of HECT Genes in Soybean" International Journal of Molecular Sciences 16, no. 4: 8517-8535. https://doi.org/10.3390/ijms16048517