HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress
Abstract
:1. Introduction
2. Methodology
2.1. Identification and Characterization of the HSP70 Gene Family
2.2. Phylogenetic Tree and Synteny Analysis of B.rapaHSP70 Family Proteins
2.3. B.rapaHSP70 Duplicated Gene Identification and Purity Selection Analysis
2.4. Cis-Element Analysis of B.rapaHSP70 Gene Promoters and Protein Structure
2.5. Targeted miRNA Prediction and Functional Analysis
2.6. Digital Expression Analysis of B.rapaHSP70
2.7. Plant Material and Stress Conditions
2.8. RNA Extraction and qRT-PCR Analysis
3. Results
3.1. Identification and Characteristics of HSP70 Gene Family Members in B. rapa
3.2. Evolutionary Relationship of B.rapaHSP70 Gene
3.3. B.rapaHSP70 Gene Duplication and Ka/Ks Analysis
3.4. B.rapaHSP70 Gene Duplication and Synteny Analysis of the B.rapaHSP70 Gene Family among Closely Related Species
3.5. Cis-Element Analysis in Promoter Regions of B.rapaHSP70 and Their Distribution
3.6. Prediction of the 3D Structures of B.rapaHSP70s
3.7. Genome-Wide Analysis of miRNA-Associated B.rapaHSP70 Genes
3.8. Functional Annotation Analysis of B.rapaHSP70 Genes
3.9. Expression Profiling of B.rapaHSP70 Genes in Various Tissues
3.10. B.rapaHSP70 Gene Expression in Response to Heat and Cold Stress
4. Discussion
4.1. Characterization of the B.rapaHSP70 Gene Family in B. rapa
4.2. Promoter Analysis and Gene Ontology
4.3. miRNA: Key Players in the Regulation of Stress Responses
5. Differential Expression Analysis of B.rapaHSP70 Genes in Chinese Cabbage Leaves under Heat and Cold Stress
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Transcript ID | Gene Name | Chr Position | Location Start–End | Strand | CDS(BP) | Instability Index | Protein Length (A.A) | Protein MW (KDa) | PI | GRAVY | Intron, Exon | Sub-Cellular Localization |
---|---|---|---|---|---|---|---|---|---|---|---|---|
BraA01g038810.3C | B.rapaHSP70-1 | A01 | 26269513–26272150 | Positive | 1953 | 32.26 | 650 | 71.27 | 5.13 | −0.429 | 1,2 | Cytoplasm |
BraA03g035360.3C | B.rapaHSP70-2 | A03 | 17438369–17440713 | Negative | 1958 | 33.17 | 652 | 71.38 | 5.13 | −0.443 | 1,2 | Cytoplasm |
BraA09g007150.3C | B.rapaHSP70-3 | A09 | 4091084–4093380 | Negative | 1944 | 36.12 | 647 | 70.94 | 5.04 | −0.401 | 1,2 | Cytoplasm |
BraA10g033140.3C | B.rapaHSP70-4 | A10 | 20445814–20448082 | positive | 1941 | 36.2 | 646 | 70.87 | 5.07 | −0.396 | 1,2 | Cytoplasm |
BraA10g033130.3C | B.rapaHSP70-5 | A10 | 20434824–20437099 | Negative | 1941 | 36.2 | 646 | 70.87 | 5.07 | −0.396 | 1,2 | Cytoplasm |
BraA03g043350.3C | B.rapaHSP70-6 | A03 | 21842760–21844958 | Positive | 1953 | 34.3 | 650 | 71.18 | 5.07 | −0.419 | 1,2 | Cytoplasm |
BraA09g038510.3C | B.rapaHSP70-7 | A09 | 30333133–30335310 | Positive | 1950 | 35.5 | 649 | 71.05 | 5.02 | −0.416 | 1,2 | Cytoplasm |
BraA01g027130.3C | B.rapaHSP70-8 | A01 | 17439040–17441266 | Negative | 1986 | 36.31 | 661 | 72.34 | 5.11 | −0.407 | 2,3 | Cytoplasm |
BraA08g029700.3C | B.rapaHSP70-9 | A08 | 20365638–20367590 | Positive | 1953 | 35.47 | 650 | 71.34 | 5.28 | −0.434 | 0,1 | Cytoplasm |
BraA06g012060.3C | B.rapaHSP70-10 | A06 | 6488327–6490270 | Negative | 1944 | 35.51 | 647 | 71.04 | 5.48 | −0.408 | 0,1 | Cytoplasm |
BraA07g008590.3C | B.rapaHSP70-11 | A07 | 8612041–8614425 | Negative | 2010 | 30 | 669 | 73.84 | 5.08 | −0.477 | 4,5 | Endoplasmic Reticulum |
BraA03g019440.3C | B.rapaHSP70-12 | A03 | 9196468–9198979 | Positive | 2010 | 27.96 | 669 | 73.62 | 5.08 | −0.464 | 3,4 | Endoplasmic Reticulum |
BraA03g016490.3C | B.rapaHSP70-13 | A03 | 7627325–7630035 | Negative | 2010 | 27.79 | 669 | 73.63 | 5.08 | −0.468 | 5,6 | Endoplasmic Reticulum |
BraA07g020790.3C | B.rapaHSP70-14 | A07 | 17199507–17204802 | Negative | 1998 | 30.99 | 665 | 73.49 | 5.11 | −0.466 | 4,5 | Endoplasmic Reticulum |
BraA09g062470.3C | B.rapaHSP70-15 | A09 | 43345497–43348084 | Positive | 1911 | 32.8 | 636 | 70.55 | 4.94 | −0.48 | 4,5 | Endoplasmic Reticulum |
BraA02g003050.3C | B.rapaHSP70-16 | A02 | 1492088–1495420 | Positive | 2043 | 34.42 | 680 | 72.87 | 5.82 | −0.335 | 5,6 | Mitochondrial |
BraA03g003930.3C | B.rapaHSP70-17 | A03 | 1680387–1683221 | Positive | 2046 | 33.94 | 681 | 72.67 | 5.55 | −0.336 | 4,5 | Mitochondrial |
BraA08g021750.3C | B.rapaHSP70-18 | A08 | 16460538–16462970 | Negative | 2031 | 36.79 | 676 | 72.48 | 5.79 | −0.281 | 4,5 | Mitochondrial |
BraA01g015070.3C | B.rapaHSP70-19 | A01 | 7988766–7991570 | Positive | 2136 | 31.48 | 711 | 76.1 | 5.09 | −0.316 | 4,5 | Chloroplast |
BraA01g001130.3C | B.rapaHSP70-20 | A01 | 523816–526255 | Positive | 2049 | 38.26 | 682 | 73.01 | 5.56 | −0.306 | 7,8 | Mitochondrial |
BraA03g051830.3C | B.rapaHSP70-21 | A03 | 26797918–26800806 | Positive | 2133 | 27.71 | 710 | 75.91 | 5.27 | −0.316 | 7,8 | Chloroplast |
BraA08g020460.3C | B.rapaHSP70-22 | A08 | 15677635-15680441 | Negative | 2154 | 28.52 | 717 | 76.42 | 5.14 | −0.313 | 7,8 | Chloroplast |
BraA06g001280.3C | B.rapaHSP70-23 | A06 | 802745–805920 | Positive | 2457 | 39.54 | 818 | 90.29 | 5.17 | −0.402 | 8,9 | Cytoplasmic |
BraA04g004290.3C | B.rapaHSP70-24 | A04 | 2645163–2648333 | Negative | 2373 | 40.91 | 790 | 87.16 | 5.23 | −0.4 | 8,9 | Cytoplasmic |
BraA05g012280.3C | B.rapaHSP70-25 | A05 | 6664594–6666288 | Negative | 1695 | 41.55 | 564 | 60.81 | 5.39 | 0.051 | 0,1 | Chloroplast |
BraA06g008250.3C | B.rapaHSP70-26 | A06 | 4497297–4500623 | Positive | 2286 | 47.68 | 761 | 84.54 | 5.73 | −0.493 | 8,9 | Nuclear |
BraA03g047170.3C | B.rapaHSP70-27 | A03 | 23836812-23840680 | Positive | 2631 | 42.89 | 876 | 97.59 | 5.78 | −0.483 | 13,14 | Nuclear |
BraA01g019900.3C | B.rapaHSP70-28 | A01 | 10687460–10691347 | Negative | 2685 | 44.47 | 894 | 99.97 | 5.89 | −0.499 | 12,13 | Nuclear |
Seq_1 | Seq_2 | Ka | Ks | Ka_Ks | T(MYA) |
---|---|---|---|---|---|
BraA10g033140.3C | BraA10g033130.3C | 0 | 0.0983403 | 0 | 3278010.814 |
BraA09g038510.3C | BraA01g027130.3C | 0.0056856 | 0.2035601 | 0.027931049 | 6.785335295 |
BraA01g038810.3C | BraA03g035360.3C | 0.0086499 | 0.9733226 | 0.008887026 | 32.44408789 |
BraA08g029700.3C | BraA06g012060.3C | 0.0273781 | 0.7299868 | 0.037504912 | 24.33289231 |
BraA03g019440.3C | BraA03g016490.3C | 0.0035436 | 0.2455705 | 0.014430195 | 8.185684806 |
BraA03g051830.3C | BraA08g020460.3C | 0.0218032 | 0.5165388 | 0.042210144 | 17.21796007 |
BraA02g003050.3C | BraA03g003930.3C | 0.0206864 | 0.3771192 | 0.054853846 | 12.57063953 |
BraA08g021750.3C | BraA01g001130.3C | 0.0253008 | 0.4383311 | 0.057720824 | 14.61103702 |
BraA03g047170.3C | BraA01g019900.3C | 0.0506028 | 0.315182 | 0.160551192 | 10.50606656 |
BraA06g001280.3C | BraA04g004290.3C | 0.0160146 | 0.3383936 | 0.047325361 | 11.27978551 |
MicroRNAs | MicroRNA Targeting B.rapaHSP70s | |||||
---|---|---|---|---|---|---|
Bra-miRN355 | B.rapaHSP70-3 | |||||
Bra-miR390 | B.rapaHSP70-8 | |||||
Bra-miRN363 | B.rapaHSP70-10 | |||||
Bra-miR395 | B.rapaHSP70-13 | |||||
Bra-miR6032 | B.rapaHSP70-14 | |||||
Bra-miR159a | B.rapaHSP70-15 | |||||
Bra-miRN366 | B.rapaHSP70-15 | |||||
Bra-miRN368 | B.rapaHSP70-15 | |||||
Bra-miRN351 | B.rapaHSP70-16 | |||||
Bra-miRN338 | B.rapaHSP70-19 | |||||
Bra-miR397 | B.rapaHSP70-23 | |||||
Bra-miRN324 | B.rapaHSP70-25 | |||||
Bra-miR319 | B.rapaHSP70-26 | |||||
Bra-miR162 | B.rapaHSP70-21 | B.rapaHSP70-22 | ||||
Bra-miR168 | B.rapaHSP70-2 | B.rapaHSP70-13 | ||||
Bra-miR394 | B.rapaHSP70-14 | B.rapaHSP70-27 | ||||
Bra-miR396 | B.rapaHSP70-23 | B.rapaHSP70-24 | ||||
Bra-miRN329 | B.rapaHSP70-4 | B.rapaHSP70-5 | ||||
Bra-miR5714 | B.rapaHSP70-18 | B.rapaHSP70-22 | ||||
Bra-miRN271 | B.rapaHSP70-16 | B.rapaHSP70-17 | ||||
Bra-miRN375 | B.rapaHSP70-21 | B.rapaHSP70-23 | ||||
Bra-miRN316 | B.rapaHSP70-15 | B.rapaHSP70-23 | B.rapaHSP70-24 | |||
Bra-miRN347 | B.rapaHSP70-6 | B.rapaHSP70-12 | B.rapaHSP70-13 | |||
Bra-miR5717 | B.rapaHSP70-20 | B.rapaHSP70-21 | B.rapaHSP70-22 | |||
Bra-miR9556 | B.rapaHSP70-9 | B.rapaHSP70-13 | B.rapaHSP70-15 | |||
Bra-miRN371 | B.rapaHSP70-19 | B.rapaHSP70-21 | B.rapaHSP70-22 | |||
Bra-miRN373 | B.rapaHSP70-1 | B.rapaHSP70-22 | B.rapaHSP70-27 | B.rapaHSP70-28 | ||
Bra-miR172 | B.rapaHSP70-2 | B.rapaHSP70-9 | B.rapaHSP70-14 | B.rapaHSP70-23 | ||
Bra-miRN317 | B.rapaHSP70-15 | B.rapaHSP70-19 | B.rapaHSP70-27 | B.rapaHSP70-28 | ||
Bra-miRN334 | B.rapaHSP70-7 | B.rapaHSP70-8 | B.rapaHSP70-16 | B.rapaHSP70-17 | ||
Bra-miRN348 | B.rapaHSP70-3 | B.rapaHSP70-4 | B.rapaHSP70-5 | B.rapaHSP70-8 | ||
Bra-miR408 | B.rapaHSP70-6 | B.rapaHSP70-11 | B.rapaHSP70-21 | B.rapaHSP70-22 | ||
Bra-miRN379 | B.rapaHSP70-1 | B.rapaHSP70-2 | B.rapaHSP70-25 | B.rapaHSP70-27 | B.rapaHSP70-28 | |
Bra-miR858 | B.rapaHSP70-12 | B.rapaHSP70-13 | B.rapaHSP70-18 | B.rapaHSP70-19 | B.rapaHSP70-20 | B.rapaHSP70-22 |
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Tabusam, J.; Shi, Q.; Feng, D.; Zulfiqar, S.; Shen, S.; Ma, W.; Zhao, J. HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress. Cells 2022, 11, 2316. https://doi.org/10.3390/cells11152316
Tabusam J, Shi Q, Feng D, Zulfiqar S, Shen S, Ma W, Zhao J. HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress. Cells. 2022; 11(15):2316. https://doi.org/10.3390/cells11152316
Chicago/Turabian StyleTabusam, Javaria, Qiling Shi, Daling Feng, Sumer Zulfiqar, Shuxing Shen, Wei Ma, and Jianjun Zhao. 2022. "HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress" Cells 11, no. 15: 2316. https://doi.org/10.3390/cells11152316
APA StyleTabusam, J., Shi, Q., Feng, D., Zulfiqar, S., Shen, S., Ma, W., & Zhao, J. (2022). HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress. Cells, 11(15), 2316. https://doi.org/10.3390/cells11152316