Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Physicochemical Properties Analysis of BvBBXs
2.2. Chromosome Localization Analysis of BvBBXs
2.3. Domain Analysis of BvBBXs
2.4. Analysis of Gene Structures and Conserved Motifs of BvBBx Genes
2.5. Alignment and Phylogenetic Analysis BvBBXs
2.6. Analysis of Cis-Acting Elements of BvBBXs’ Promoters
2.7. Analisis of BvBBx Genes’ Potential Role in Leaf Spot Disease Resistance
2.7.1. Infection Experiment
2.7.2. Sampling Treatment
2.7.3. Quantitative Real-Time PCR (RT-qPCR) Analysis
2.8. Data Analysis
3. Results
3.1. Identification and Physicochemical Properties of B-Box Gene Family in Sugar Beet Genome
3.2. Chromosome Localization Analysis of B-Box Gene Family in Sugar Beet
3.3. Domain Analysis of Sugar Beet B-Box Family Members
3.4. Analysis of Gene Structure and Protein Conserved Motifs of Sugar Beet B-Box Family Members
3.5. Classification and Phylogenetic Analysis of Family Members
3.6. Cis-Acting Element Analysis
3.7. Expression Analysis of BvBBXs Gene in Highly Resistant and Susceptible Varieties
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Reagent | Amount |
---|---|
TB Green Premix Ex Taq II (2×) | 10 μL |
PCR Forward Primer (10 μM) | 0.8 μL |
PCR Reverse Primer (10 μM) | 0.8 μL |
ROX Reference Dye (50×) | 0.4 μL |
DNA Templates | 2 μL |
Sterile Water | Filling to 20 μL |
Gene | Forward Primer (5′–3′) | Reverse Primer (5′–3′) |
---|---|---|
BvBBX01 | AGACGCGCCGAAAAAGAAAA | GGGCGTTCCTATTCCCTCG |
BvBBX02 | AAAAGATTTAGCGTTGACCACC | TGTTGATGGTCTATGTGAGTCCC |
BvBBX03 | CTTCTGCTGCTTGCAAACCT | GATGAGCGCTTACACTGTGAC |
BvBBX04 | CTGATGGTTTGCGGCAAGAG | ACTGACCTGATCTGCACATTT |
BvBBX05 | TGATGGGATGACACGAACGG | TCATCACGCCATGTGGAACA |
BvBBX06 | GCAACGACGTATTGCGAGTC | CCAGATGCAGTCCAAGGTGT |
BvBBX07 | TTTTTCCCGTGCTGTGTGGG | CAAGACAATTGAACTCCGTACCA |
BvBBX08 | TTCCGGATTCGTCTTGATCCC | ATGTTCACCCTTTTGCTTGGT |
BvBBX09 | TTCCACACTGACCATCCCAC | TGCCTTCAGGGATGTGATCG |
BvBBX10 | TTCCACACTGACCATCCCAC | TGCGAGACTGAAGATGTTACCT |
BvBBX11 | CCACCACCGTACCTTTCTCC | TTCCGGCGAAGACGATTCTC |
BvBBX12 | TCAACTTTCCTTTATCTCAACCACA | CGAATTCGTGTTTCCGTCTGG |
BvBBX13 | ACCTCAATGCATCAAATCTTCCA | TCCAGATTTTGCGGGTTCAGT |
BvBBX14 | ACAACAAGGAGATCTTTCGGGG | GGCTCGGTAACCCTGTAAACT |
BvBBX15 | TGTTTCTCGATGCTAATTCGAGG | CGACATGCATGAAAAGCAAACG |
BvBBX16 | TCCCATGGGTAGACCATTTGC | GGCCAACCCAAAACTAACTGC |
BvBBX17 | TCTATGCCTTGCAATAGCCCT | CCCAAGTTCGGGCCTACTTT |
BvActin | ACTGGTATTGTGCTTGACTC | ATGAGATAATCAGTGAGATC |
Gene Name | Gene Symbol | Accession Number | Protein Length | pI | MW (Da) | Chr. Location | Exon No. | Subcellular Localization |
---|---|---|---|---|---|---|---|---|
BvBBX01 | LOC104888895 | XM_010674009.2 | 328 | 6.06 | 35915.31 | 1 | 3 | Nucleus. |
BvBBX02 | LOC104907374 | XM_010696302.2 | 368 | 5.41 | 40858.69 | 2 | 2 | Nucleus. |
BvBBX03 | LOC104906002 | XM_010694679.2 | 384 | 6.1 | 41702.13 | 2 un | 2 | Nucleus. |
BvBBX04 | LOC104888829 | XM_010673928.2 | 246 | 4.94 | 27226.69 | 3 | 3 | Nucleus. |
BvBBX05 | LOC104891303 | XM_010676978.2 | 312 | 5.44 | 33737.74 | 4 | 3 | Nucleus. |
BvBBX06 | LOC104907254 | XM_010696160.2 | 201 | 4.12 | 22061.55 | 4 un | 1 | Nucleus. |
BvBBX07 | LOC104896645 | XM_010683418.2 | 443 | 6.7 | 49495.5 | 6 | 6 | Nucleus. |
BvBBX08 | LOC104897491 | XM_010684375.2 | 517 | 5.64 | 57633.24 | 6 | 4 | Nucleus. |
BvBBX09 | LOC104897745 | XM_019250497.1 | 338 | 4.58 | 37833.16 | 6 | 4 | Nucleus. |
BvBBX10 | LOC104908945 | XM_010698113.2 | 389 | 5.99 | 41552.96 | 7 un | 1 | Nucleus. |
BvBBX11 | LOC104908648 | XM_010697779.2 | 254 | 5.92 | 27896.79 | 7 un | 4 | Nucleus. |
BvBBX12 | LOC104902431 | XM_010690211.2 | 379 | 5.99 | 41552.96 | 8 | 2 | Nucleus. |
BvBBX13 | LOC104903341 | XM_010691368.2 | 412 | 4.97 | 44928.89 | 9 | 6 | Nucleus. |
BvBBX14 | LOC104904254 | XM_010692457.2 | 196 | 5.75 | 21583.28 | 9 | 6 | Nucleus. |
BvBBX15 | LOC104904288 | XM_010692495.2 | 262 | 5.77 | 29046.26 | 9 | 3 | Nucleus. |
BvBBX16 | LOC104884672 | XM_010669358.2 | 430 | 5.64 | 48855.67 | Un | 2 | Nucleus. |
BvBBX17 | LOC104884884 | XM_010669588.2 | 135 | 4.33 | 14743.74 | Un | 1 | Nucleus. |
Cis-Acting Element | Number of Genes | Functions of Cis-Acting Element |
---|---|---|
CAAT-box | 17 | common cis-acting element in promoter and enhancer regions |
TATA-box | 17 | core promoter element around −30 of transcription start |
Box 4 | 16 | part of a conserved DNA module involved in light responsiveness |
ABRE | 16 | cis-acting element involved in abscisic acid responsiveness |
G-box | 13 | cis-acting regulatory element involved in light responsiveness |
ARE | 13 | cis-acting regulatory element essential for anaerobic induction |
TCT-motif | 11 | part of a light-responsive element |
CGTCA-motif | 10 | cis-acting regulatory element involved in MeJA responsiveness |
TGACG-motif | 10 | cis-acting regulatory element involved in MeJA responsiveness |
O2-site | 9 | cis-acting regulatory element involved in zein metabolism regulation |
TCA-element | 9 | cis-acting element involved in salicylic acid responsiveness |
I-box | 8 | part of a light-responsive element |
GATA-motif | 8 | part of a light-responsive element |
GT1-motif | 8 | light-responsive element |
MBS | 7 | MYB binding site involved in drought inducibility |
TGA-element | 6 | auxin-responsive element |
TC-rich repeats | 6 | cis-acting element involved in defense and stress responsiveness |
CAT-box | 5 | cis-acting regulatory element related to meristem expression |
WUN-motif | 5 | wound-responsive element |
P-box | 5 | gibberellin-responsive element |
AE-box | 5 | part of a module for light response |
CCAAT-box | 5 | MYBHv1 binding site |
LTR | 5 | cis-acting element involved in low-temperature responsiveness |
TCCC-motif | 5 | part of a light-responsive element |
MRE | 4 | MYB binding site involved in light responsiveness |
ACE | 4 | cis-acting element involved in light responsiveness |
ATCT-motif | 3 | part of a conserved DNA module involved in light responsiveness |
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Song, H.; Ding, G.; Zhao, C.; Li, Y. Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.). Genes 2023, 14, 1248. https://doi.org/10.3390/genes14061248
Song H, Ding G, Zhao C, Li Y. Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.). Genes. 2023; 14(6):1248. https://doi.org/10.3390/genes14061248
Chicago/Turabian StyleSong, He, Guangzhou Ding, Chunlei Zhao, and Yanli Li. 2023. "Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.)" Genes 14, no. 6: 1248. https://doi.org/10.3390/genes14061248
APA StyleSong, H., Ding, G., Zhao, C., & Li, Y. (2023). Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.). Genes, 14(6), 1248. https://doi.org/10.3390/genes14061248