Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation (Dianthus caryophyllus)
Abstract
:1. Introduction
2. Results
2.1. Identification of DcaHsfs in Carnation
2.2. Phylogenetic and Sequence Conservation Analysis of DcaHsfs
2.3. Structural and Motif Analysis of DcaHsfs
2.4. Cis-Acting Element Analysis in the Promoters of DcaHsfs
2.5. The Expression Pattern of DcaHsfs in Different Tissues and Flower Development
2.6. DcaHsfs Response to Various Stresses
3. Discussion
3.1. Characterization of the Carnation Hsf Genes Family
3.2. Cis-Element Analysis in the Promoters of DcaHsfs
3.3. Structural Analysis of DcaHsfs
3.4. DcaHsfs Involvement in Carnation Development Processes
3.5. DcaHsfs are Involved in Carnation Stress Response
4. Materials and Methods
4.1. Identification and Characterization of Hsf Genes in D. caryophyllus
4.2. Phylogenetic Analysis
4.3. Structural and Motif Analyses of DcaHsf Genes
4.4. Cis-acting Element Analysis of DcaHsfs
4.5. Plant Materials, Growth Conditions, and Stress Treatments
4.6. RNA Isolation and Expression Analysis of DcaHsf Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
ABA | Abscisic acid |
ABRE | ABA-responsive element |
APX | Ascorbate peroxidase |
CA | Calyx |
CAT | Catalase |
DBD | DNA-binding domains |
ERE | Ethylene-responsive element |
F | Flower |
FS | Flowering stages |
HSE | Heat shock element |
Hsf | Heat shock transcription factor |
MEME | Multiple Em for Motif Elicitation |
ML | Mature leaf |
MW | Molecular weight |
NES | Nuclear export signals |
NLS | Nuclear localization signals |
OV | Ovary |
PEG | Polyethylene glycol |
qRT-PCR | Quantitative real-time PCR |
R | Root |
RD | Repressor domains |
ROS | Reactive oxygen species |
S | Stem |
SA | Salicylic acid |
ST | Stigma |
TFs | Transcription factors |
YL | Young leaf |
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Protein Name | Gene ID | Subfamily | Size | I.I. | Stability | A.I. | n.c.r. (%) | p.c.r.(%) | GRAVY | pI | MW (kDa) |
---|---|---|---|---|---|---|---|---|---|---|---|
DcaHsf-A1 | Dca57201.1 | A1 | 488 | 55.97 | U | 66.72 | 69 | 47 | −0.690 | 4.74 | 54.49 |
DcaHsf-A2a | Dca14360.1 | A2 | 380 | 59.24 | U | 83.55 | 59 | 45 | −0.503 | 5.12 | 42.96 |
DcaHsf-A2b | Dca52568.1 | A2 | 359 | 58.97 | U | 80.03 | 57 | 43 | −0.548 | 5.05 | 40.55 |
DcaHsf-A3 | Dca41810.1 | A3 | 244 | 64.58 | U | 67.33 | 67 | 50 | −0.566 | 4.98 | 51.75 |
DcaHsf-A4 | Dca23163.1 | A4 | 390 | 47.75 | U | 71.95 | 59 | 47 | −0.859 | 5.7 | 44.99 |
DcaHsf-A5 | Dca19769.1 | A5 | 489 | 48.53 | U | 72.17 | 67 | 52 | −0.745 | 5.45 | 54.52 |
DcaHsf-A7 | Dca4574.1 | A7 | 425 | 48.11 | U | 67.36 | 63 | 61 | −0.771 | 6.72 | 48.91 |
DcaHsf-A9a | Dca9629.1 | A9 | 401 | 47.92 | U | 69.73 | 67 | 46 | −0.691 | 5 | 46.12 |
DcaHsf-A9b | Dca41703.1 | A9 | 331 | 36.63 | S | 69.43 | 45 | 44 | −0.805 | 6.23 | 38.21 |
DcaHsf-B1 | Dca60410.1 | B1 | 276 | 34.47 | S | 68.77 | 38 | 39 | −0.804 | 7.61 | 31.0 |
DcaHsf-B2a | Dca22545.1 | B2 | 337 | 54.72 | U | 61.64 | 35 | 29 | −0.721 | 6 | 36.48 |
DcaHsf-B2b | Dca48996.1 | B2 | 337 | 60.89 | U | 60.98 | 39 | 32 | −0.709 | 6 | 36.48 |
DcaHsf-B2c | Dca54105.1 | B2 | 318 | 61.35 | U | 68.57 | 33 | 32 | −0.592 | 5.91 | 33.80 |
DcaHsf-B3a | Dca44175.1 | B3 | 244 | 48.80 | U | 70.33 | 31 | 37 | −0.763 | 8.88 | 28.38 |
DcaHsf-B3b | Dca48010.1 | B3 | 457 | 48.40 | U | 68.96 | 31 | 37 | −0.784 | 8.88 | 28.33 |
DcaHsf-B4 | Dca39623.1 | B4 | 287 | 54.07 | U | 72.30 | 30 | 32 | −0.874 | 8.52 | 33.72 |
DcaHsf-C1 (incomplete) | Dca24054.1 | C1 | 133 | 58.77 | U | 76.24 | 21 | 22 | −0.881 | 8.01 | 15.89 |
Motif | E-Value | Width | Best Possible Match |
---|---|---|---|
Motif1 | 2.70 × 10−426 | 41 | VWDPAEFARDLLPRYFKHNNFSSFVRQLNTYGFRKVVPDRW |
Motif2 | 5.20 × 10−225 | 29 | PFLTKTYDMVDDPSTDDIVSWSEDGTSFV |
Motif3 | 1.10 × 10−187 | 29 | EFANEGFLRGQKHLLKNIKRRKTTTAHSQ |
Motif4 | 4.20 × 10−115 | 41 | GLEGENERLRRENEVLMSELVKLKQQQQNTFSLLQAMESRL |
Motif5 | 4.80 × 10−54 | 34 | QSTEWKQKQMMTFLAKAMQNPTFVQQLVQKKDER |
Motif6 | 1.60 × 10−22 | 49 | PPQQQPSTAAPTNSSDEQVISNSNSPPLAIPSVIMHRHHHHHHLYHNNN |
Motif7 | 1.20 × 10−19 | 41 | KSVKAIRVSMKRRLTSTLSAPNLNDVVEPELVRSMAVSSDN |
Motif8 | 2.60 × 10−16 | 50 | CGGGGGGSPMIFGVSIGGKRGREGGDDGGGEVVGGGEGLGATEVHDDHMH |
Motif9 | 2.60 × 10−13 | 50 | ATLDNGTDGDIKEQKVDDSMPPEIDTNVGDVSQTSWEELLWAEDEEGFRQ |
Motif10 | 7.70 × 10−10 | 29 | MRELSIKGLFDDHDDDDECGIIMRRKMTK |
Motif11 | 1.50 × 10−9 | 13 | PKPMEGLNEMNPP |
Motif12 | 1.80 × 10−5 | 41 | DSDGDDGNNKNRPKLFGVRLDLQDESERKRRKKLALDYTRT |
Motif13 | 5.20 × 10−8 | 21 | NNNNNNNVVITRKNNENEMNN |
Motif14 | 1.40 × 10−4 | 29 | PVENVVPESGNWGEDVEDLIEQLGFLGPM |
Motif15 | 1.80 × 10−4 | 21 | MTAVLVTVSDLVSSSTTSSSS |
Motif16 | 2.10 × 10−4 | 29 | MSPPPSPPAEEKPEKLTAVVVGGGGGETQ |
Motif17 | 1.70 × 10−3 | 21 | AAPSRVNDAVWTQLLTLPRGS |
Motif18 | 2.90 × 10−3 | 10 | GFRKVDPDKW |
Motif19 | 1.30 × 10−2 | 23 | TSTTCTCTPLSTESPQLGLQLSP |
Motif20 | 1.00 × 10−2 | 19 | YWYDFDGEDEVELEERVPC |
Gene Name | DBD | HR-A/B | NLS | NES | RD | AHA |
---|---|---|---|---|---|---|
DcaHsf-A1 | 31–124 | 162–182/201–212 | N.D. | (403) L | N.D. | N.D. |
DcaHsf-A2a | 40–154 | 183–201/222–233 | (147–156) KTIKRRRNVT (258–267) AGMKRRLTST | N.D. | N.D. | (329–338) QTSWEELLWA |
DcaHsf-A2b | 40–133 | 162–180/201–212 | (126–137) LLKTIKRRRNVT (237–246) AGMKRRLTST | (232–237) LDITHL | N.D. | (308–317) QTSWEELLWA |
DcaHsf-A3 | 37–148 | 181–199/220–230 | N.D. | (319) L | N.D. | N.D. |
DcaHsf-A4 | 11–104 | 139–157/178–189 | (204–213) HDRKRRFSRP | N.D. | N.D. | (325–334) DVFWEQFLTE |
DcaHsf-A5 | 20–113 | 138–156/177–187 | (206–217) LSAYNKKRRLPP | N.D. | ND | (438–447) DLFWEQFLTE |
DcaHsf-A7 | 40–133 | 164–182/203–213 | (126–140) LLKNIKRRKNPSQTF (237–246) LSKKRRRPIE | N.D. | ND | (322–331) DDFWEDLLNE |
DcaHsf-A9a | 87–180 | 202–220/241–251 | (173–184) LLKSIKRKRHGS (275–285) RVSKKRRLAST | (204) LDQEALKVEI | ND | N.D. |
DcaHsf-A9b | 95–188 | 210–228/249–259 | (181–192) LLKSIKRKRHGS (283–293) RVSKKRRLAST | (217–221) LKVEI | ND | N.D. |
DcaHsf-B1 | 6–99 | 125–131 | N.D. | (155–157) LEL | (220-226) KLFGVWL | N.D. |
DcaHsf-B2a | 32–125 | 151–169/190–200 | N.D. | N.D. | ND | N.D. |
DcaHsf-B2b | 32–125 | 151–169/190–200 | N.D. | N.D. | ND | N.D. |
DcaHsf-B2c | 26–119 | 145–153/172–178 | N.D. | (197–202) KENMSL | (284–290) KLFGVSI | N.D. |
DcaHsf-B3a | 29–122 | 147–152 | (5–30) SIKGLFDDHDDDDECGIIMRRKMTKP (178–187) NAMKRKCQEL (207–235) KNRPKLFGVRLDLQDESERKRRKKLALDY | (222–238) LDLQDESERKRRKKLAL | (216–222) KLFGVRL | N.D. |
DcaHsf-B3b | 29–122 | 147–152 | (5–30) SIKGLFDDHDDDDECGIIMRRKMTKP (178–187) NAMKRKCQEL (207–235) KNRPKLFGVRLDLQDESERKRRKKLALDY | N.D. | (216–222) KLFGVRL | N.D. |
DcaHsf-B4 | 12–105 | 131–149/163–166 | (275–283) HSKKRLHLA | N.D. | (268–274) RLFGVPL | N.D. |
DcaHsf-C1 (not full) | 1–44 | 73–89/98–108 | N.D. | (66) L | N.D. | N.D. |
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Li, W.; Wan, X.-L.; Yu, J.-Y.; Wang, K.-L.; Zhang, J. Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation (Dianthus caryophyllus). Int. J. Mol. Sci. 2019, 20, 5233. https://doi.org/10.3390/ijms20205233
Li W, Wan X-L, Yu J-Y, Wang K-L, Zhang J. Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation (Dianthus caryophyllus). International Journal of Molecular Sciences. 2019; 20(20):5233. https://doi.org/10.3390/ijms20205233
Chicago/Turabian StyleLi, Wei, Xue-Li Wan, Jia-Yu Yu, Kui-Ling Wang, and Jin Zhang. 2019. "Genome-Wide Identification, Classification, and Expression Analysis of the Hsf Gene Family in Carnation (Dianthus caryophyllus)" International Journal of Molecular Sciences 20, no. 20: 5233. https://doi.org/10.3390/ijms20205233