Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Identification of the Expansin Gene Family in Three Basic Diploid Species of Brassica
2.2. Phylogenetic and Structural Analyses of BrEXPs, BolEXPs, and BniEXPs
2.3. Chromosomal Distribution, Duplication Mechanism and Retained Proportion in Three Basic Species of Brassica
2.4. Coding Sequence and Promoter Evolution Analyses of Expansin Genes in the Three Species of Brassica
2.5. Expression Patterns of Expansin Family Members in Various Tissues and Organs of B. rapa, B. nigra, and B. oleracea
3. Discussion
3.1. Scale of Expansin Families after WGT in B. rapa, B. oleracea, and B. nigra
3.2. Conservative and Large Family Size of EXLB in Three Basic Species of Brassica
3.3. Promoter Divergence is Closely Related to the Coding Sequence Evolution of Expansin Genes in Three Basic Species of Brassica
3.4. Speculative Roles of Expansin Genes during Reproductive Development
4. Materials and Methods
4.1. Identification and Physicochemical Property Predictions of Expansin Family Members in Three Basic Diploid Species of Brassica
4.2. Phylogenetic Genetic Tree Construction and Structural Analysis
4.3. Chromosome Location, Synteny and Retained Rate Analysis
4.4. Evolution Analysis of Coding Sequences and Promoters
4.5. Expression Analysis of Expansin Family Members
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
BrEXPs | B. rapa expansin genes |
BolEXPs | B. oleracea expansin genes |
BniEXPs | B. nigra expansin genes |
GMS | genic male sterile |
Ka | nonsynonymous substitution rate |
Ks | synonymous substitution rate |
Mw | molecular weights |
MYA | million years ago |
PGs | polygalacturonases genes |
pIs | isoelectric points |
qRT-PCR | quantitative reverse transcription polymerase chain reaction |
WGT | whole genome triplication |
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Species | EXPA | EXPB | EXLA | EXLB | Total | References |
---|---|---|---|---|---|---|
Algae | ||||||
Micrasterias denticulata | 4′EXP’ | [22] | ||||
Moss | ||||||
Physcomitrella patens | 28 | 7 | 0 | 0 | 34 | [23] |
Fern | ||||||
Selaginella moellendorffi | 15 | 2 | 0 | 0 | 17 | [34] |
Gymnosperm | ||||||
Pinus taeda | 6 | 1 | 1 | 1 | 9 | [5] |
Angiosperms | ||||||
Monocotyledon | ||||||
Rice | 33 | 18 | 4 | 1 | 56 | [5] |
Maize | 36 | 48 | 4 | 0 | 88 | [24] |
Triticum aestivum | 52 | 42 | 4 | 0 | 98 | [35] |
Dicotyledon | ||||||
Cruciferae | ||||||
Arabidopsis thaliana | 26 | 6 | 3 | 1 | 36 | [5] |
Brassica rapa | 41 | 10 | 2 | 3 | 56 | |
Brassica oleracea | 41 | 12 | 2 | 3 | 58 | |
Brassica nigra | 47 | 9 | 2 | 2 | 60 | |
Solanaceae | ||||||
Tobacco | 36 | 6 | 3 | 7 | 52 | [26] |
Tomato | 25 | 8 | 1 | 4 | 38 | [36] |
Potato | 24 | 5 | 1 | 6 | 36 | [18] |
Leguminosae | ||||||
Soybean | 49 | 9 | 2 | 15 | 75 | [25] |
Salicaceae | ||||||
Poplar | 27 | 3 | 2 | 4 | 36 | [37] |
Amborellaceae | ||||||
Amborella trichopoda | 17 | 2 | 1 | 2 | 22 | [38] |
Vitaceae | ||||||
Grape | 20 | 4 | 1 | 4 | 29 | [39] |
Rosaceae | ||||||
Apple | 34 | 1 | 2 | 4 | 41 | [27] |
Species | Model | Estimates of Parameters | ln L | LRT p-Value |
---|---|---|---|---|
Arabidopsis thaliana | One-ratio | ω0 = 0.137 for all subfamilies | −13843.914525 | 0.4417919 |
Free-ratio | ω1 = 999.000 for EXPA | −13840.170755 | ||
ω2 = 0.439 for EXPB | ||||
ω3 = 0.124 for EXLA | ||||
ω4 = 0.045 for EXLB | ||||
Brassica rapa | One-ratio | ω0 = 0.118 for all subfamilies | −13413.618539 | 0.2491653 |
Free-ratio | ω1 = 999.000 for EXPA | −13408.224099 | ||
ω2 = 999.000 for EXPB | ||||
ω3 = 0.225 for EXLA | ||||
ω4 = 0.005 for EXLB | ||||
Brassica oleracea | One-ratio | ω0 = 0.107 for all subfamilies | −7890.958102 | 0.7815311 |
Free-ratio | ω1 = 999.000 for EXPA | −7889.207635 | ||
ω2 = 999.000 for EXPB | ||||
ω3 = 0.122 for EXLA | ||||
ω4 = 0.070 for EXLB | ||||
Brassica nigra | One-ratio | ω0 = 0.125 for all clades | −11781.483673 | 0.9198657 |
Free-ratio | ω1 = 999.000 for EXPA | −11780.551263 | ||
ω2 = 999.000 for EXPB | ||||
ω3 = 0.154 for EXLA |
EXPA | EXPB | EXLA | EXLB | ||
---|---|---|---|---|---|
A. thaliana vs. B. rapa | Ka | 0.085(0.067) a | 0.106 (0.055) | 0.072 (0.006) | 0.059 (0.005) |
Ks | 0.508(0.114) | 0.589 (0.114) | 0.493 (0.034) | 0.338 (0.077) | |
Ka/Ks | 0.149(0.090) a | 0.174 (0.070) | 0.146 (0.002) | 0.183 (0.051) | |
dSM | 0.600(0.286) | 0.747 (0.315) | 0.803 (0.062) | 0.720 (0.076) | |
A. thaliana vs. B. oleracea | Ka | 0.053(0.026) b | 0.112 (0.055) | 0.076 (0.002) | 0.069 (0.015) |
Ks | 0.487(0.093) | 0.568 (0.059) | 0.465 (0.073) | 0.329 (0.032) | |
Ka/Ks | 0.116(0.057) b | 0.202 (0.083) | 0.165 (0.021) | 0.212 (0.058) | |
dSM | 0.592(0.256) | 0.762 (0.304) | 0.775 (0.101) | 0.694 (0.059) | |
A. thaliana vs. B. nigra | Ka | 0.048(0.019) b | 0.127 (0.063) | 0.076 (0.013) | 0.061 (0.010) |
Ks | 0.486(0.100) | 0.548 (0.068) | 0.478 (0.069) | 0.340 (0.039) | |
Ka/Ks | 0.114(0.059) b | 0.207 (0.083) | 0.160 (0.003) | 0.182 (0.049) | |
dSM | 0.573(0.285) | 0.692 (0.285) | 0.738 (0.151) | 0.672 (0.100) |
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Liu, W.; Lyu, T.; Xu, L.; Hu, Z.; Xiong, X.; Liu, T.; Cao, J. Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica. Int. J. Mol. Sci. 2020, 21, 3424. https://doi.org/10.3390/ijms21103424
Liu W, Lyu T, Xu L, Hu Z, Xiong X, Liu T, Cao J. Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica. International Journal of Molecular Sciences. 2020; 21(10):3424. https://doi.org/10.3390/ijms21103424
Chicago/Turabian StyleLiu, Weimiao, Tianqi Lyu, Liai Xu, Ziwei Hu, Xingpeng Xiong, Tingting Liu, and Jiashu Cao. 2020. "Complex Molecular Evolution and Expression of Expansin Gene Families in Three Basic Diploid Species of Brassica" International Journal of Molecular Sciences 21, no. 10: 3424. https://doi.org/10.3390/ijms21103424