Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of ARF, Aux/IAA, GH3, and SAUR Genes in Upland Cotton
2.2. Phylogenetic Analysis and Gene Structure of Upland Cotton ARF, Aux/IAA, GH3, and SAUR Genes
2.3. Genomic Distribution, Collinearity and Duplication Analysis of Upland Cotton ARF, Aux/IAA, GH3, and SAUR Genes
2.4. Expression Profile Analysis of ARF, Aux/IAA, GH3, and SAUR Genes during Embryogenic Ability Acquisition of Upland Cotton Callus
2.5. Differentially Expression Analysis
2.6. Co-Expression Network Analysis
2.7. qRT-PCR Validation and Analysis
3. Results
3.1. Identification and Characterization of ARF, Aux/IAA, GH3, and SAUR Genes in Upland Cotton
3.2. Phylogenetic Analysis and Gene Structure of ARF, Aux/IAA, GH3, and SAUR Genes in Upland Cotton
3.3. Genomic Distribution and Gene Duplication of ARF, Aux/IAA, GH3, and SAUR Genes in Upland Cotton
3.4. Expression Profiling and Differentially Expression of ARF, Aux/IAA, GH3, and SAUR Genes in Upland Cotton Somatic Embryogenesis
3.5. Co-Expression of ARF, Aux/IAA, GH3, and SAUR Genes and Somatic Embryogenesis Related Genes during Cotton Somatic Embryogenesis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene Family | Domains/Motifs | Number of Genes |
---|---|---|
ARF | 71 | |
DBD, ARF-AD a, Aux/IAA | 24 | |
DBD, ARF-RD a, Aux/IAA | 47 | |
Aux/IAA | 86 | |
Domains I, II, III, IV | 67 | |
Domains I, II, III | 1 | |
Domains II, III, IV | 13 | |
Domains I, II | 1 | |
Domains I, IV | 1 | |
Domains II, III | 1 | |
Domains III, IV | 2 | |
GH3 | 63 | |
GH3 | 47 | |
2 × GH3 | 8 | |
GH3, JAR1 | 8 | |
SAUR | 194 | |
SAUR, Motifs 1 b, 2, 3 | 167 | |
SAUR, Motifs 1, 2 | 9 | |
SAUR, Motifs 1, 3 | 2 | |
SAUR, Motifs 2, 3 | 12 | |
SAUR, Motif 2 | 3 | |
SAUR, Motif 3 | 1 |
DEGs | AN_vs_AE | BN_vs_BE | AN_vs_BN | AE_vs_BE | Total | |
---|---|---|---|---|---|---|
ARF | 32 | 38 | 9 | 2 | 44 | |
up | 17 | 21 | 5 | 1 | - | |
down | 15 | 17 | 4 | 1 | - | |
Aux/IAA | 35 | 38 | 17 | 11 | 56 | |
up | 19 | 12 | 15 | 0 | - | |
down | 16 | 26 | 2 | 11 | - | |
GH3 | 14 | 17 | 4 | 1 | 23 | |
up | 9 | 8 | 2 | 0 | - | |
down | 5 | 9 | 2 | 1 | - | |
SAUR | 36 | 43 | 7 | 4 | 52 | |
up | 15 | 10 | 6 | 0 | - | |
down | 21 | 33 | 1 | 4 | - |
Auxin Early Response Family | DEGs | Number (Percentage) of DEGs Co-Expressed with | |||
---|---|---|---|---|---|
ARF | Aux/IAA | GH3 | SAUR | ||
ARF | 44 | 38 (86.4%) | 39 (88.6%) | 37 (84.1%) | 40 (90.9%) |
Aux/IAA | 56 | 39 (69.6%) | 41 (73.2%) | 39 (69.6%) | 41 (73.2%) |
GH3 | 23 | 18 (78.3%) | 19 (82.6%) | 17 (73.9%) | 20 (87.0%) |
SAUR | 52 | 48 (92.3%) | 49 (94.2%) | 45 (86.5%) | 49 (94.2%) |
SE Related Genes | Number (Percentage) of Co-Expressed Auxin Early Response Genes | |||
---|---|---|---|---|
ARF | AuxIAA | GH3 | SAUR | |
ABI3 | 14 (53.8%) | 15 (65.2%) | 8 (66.7%) | 18 (62.1%) |
AGL15 | 8 (30.8%) | 8 (34.8%) | 3 (25.0%) | 9 (31.0%) |
FUS3 | 12 (46.2%) | 13 (56.5%) | 8 (66.7%) | 16 (55.2%) |
LEC1 | 10 (38.5%) | 11 (47.8%) | 5 (41.7%) | 12 (41.4%) |
LEC2 | 1 (3.8%) | 1 (4.3%) | 1 (8.3%) | 2 (6.9%) |
PLT1 | 8 (30.8%) | 8 (34.85) | 3 (25.0%) | 11 (37.9%) |
PLT2 | 8 (30.8%) | 14 (60.9%) | 6 (50.0%) | 14 (48.3%) |
PLT3 | 5 (19.2%) | 10 (43.5%) | 1 (8.3%) | 12 (41.4%) |
PLT7 | 10 (38.5%) | 7 (30.4%) | 3 (25.0%) | 9 (31.0%) |
BBM | 2 (7.7%) | 1 (4.3%) | 1 (8.3%) | 2 (6.9%) |
PLT5 | 12 (46.2%) | 17 (73.9%) | 7 (58.3%) | 16 (55.2%) |
WUS | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) | 0 (0.0%) |
SERK3 | 9 (34.6%) | 5 (21.7%) | 3 (25.0%) | 9 (31.0%) |
SERK4 | 8 (30.8%) | 10 (43.5%) | 7 (58.3%) | 15 (51.7) |
Total | 26 | 23 | 12 | 29 |
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Sun, R.; Wang, S.; Ma, D.; Li, Y.; Liu, C. Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis. Genes 2019, 10, 730. https://doi.org/10.3390/genes10100730
Sun R, Wang S, Ma D, Li Y, Liu C. Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis. Genes. 2019; 10(10):730. https://doi.org/10.3390/genes10100730
Chicago/Turabian StyleSun, Ruibin, Shaohui Wang, Dan Ma, Yilin Li, and Chuanliang Liu. 2019. "Genome-Wide Analysis of Cotton Auxin Early Response Gene Families and Their Roles in Somatic Embryogenesis" Genes 10, no. 10: 730. https://doi.org/10.3390/genes10100730