Biotechnology Bulletin ›› 2024, Vol. 40 ›› Issue (2): 233-244.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0874
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LI Hao(), WU Guo-qiang(), WEI Ming, HAN Yue-xin
Received:
2023-09-11
Online:
2024-02-26
Published:
2024-03-13
Contact:
WU Guo-qiang
E-mail:1044624636@qq.com;gqwu@lut.edu.cn
LI Hao, WU Guo-qiang, WEI Ming, HAN Yue-xin. Genome-wide Identification of the BvBADH Gene Family in Sugar Beet(Beta vulgaris)and Their Expression Analysis Under High Salt Stress[J]. Biotechnology Bulletin, 2024, 40(2): 233-244.
基因Gene | 正向引物序列Forward primer sequence(5'-3') | 反向引物序列Reverse primer sequence(5'-3') |
---|---|---|
BvBADH1 | GCAGTGCAACATCCAGACTC | CCCCCTCACTCTTTGCTGTT |
BvBADH2 | GTCCTGTTGTCAGCAAGGGA | GCATGGACGTGGAGACATCA |
BvBADH3 | CCAAATTGGGGGAAGTTTGTGT | TGGATCACCAACAACCCAAGA |
BvBADH4 | ACGGGGAATTTGTGGATGCT | TCATCACCCTTCCCCTTTCA |
BvBADH5 | ATTGAGCATGGCAAGCGAGA | TGCCATTCGCTCGCTCTATC |
BvBADH6 | GCCGATTTAGCACCACTTCT | GCAGAAGTGGTGCTAAATCGG |
BvBADH7 | GCATCTGATTATGGGCTGGC | CCACTCATTTTGTACCCGCC |
BvBADH8 | TCGTCGAGCCAATAACACCC | CCACCAAATGGAATGCCTGC |
BvBADH9 | GGCCAGTTCAGAGGTGAGGA | GAACTTGGACCCAAGCCTTTT |
BvACTIN | ACTGGTATTGTGCTTGACTC | ATGAGATAATCAGTGAGATC |
Table 1 Sequences of primers used for RT-qPCR in this study
基因Gene | 正向引物序列Forward primer sequence(5'-3') | 反向引物序列Reverse primer sequence(5'-3') |
---|---|---|
BvBADH1 | GCAGTGCAACATCCAGACTC | CCCCCTCACTCTTTGCTGTT |
BvBADH2 | GTCCTGTTGTCAGCAAGGGA | GCATGGACGTGGAGACATCA |
BvBADH3 | CCAAATTGGGGGAAGTTTGTGT | TGGATCACCAACAACCCAAGA |
BvBADH4 | ACGGGGAATTTGTGGATGCT | TCATCACCCTTCCCCTTTCA |
BvBADH5 | ATTGAGCATGGCAAGCGAGA | TGCCATTCGCTCGCTCTATC |
BvBADH6 | GCCGATTTAGCACCACTTCT | GCAGAAGTGGTGCTAAATCGG |
BvBADH7 | GCATCTGATTATGGGCTGGC | CCACTCATTTTGTACCCGCC |
BvBADH8 | TCGTCGAGCCAATAACACCC | CCACCAAATGGAATGCCTGC |
BvBADH9 | GGCCAGTTCAGAGGTGAGGA | GAACTTGGACCCAAGCCTTTT |
BvACTIN | ACTGGTATTGTGCTTGACTC | ATGAGATAATCAGTGAGATC |
基因名称 Gene name | 基因登录号 Gene ID | CDS /bp | 相对分子量 Mw/kD | 亲水性平均值 GRAVY | 等电点 pI | 脂肪指数 Aliphatic index | 氨基酸数目 Protein length/aa | 不稳定指数 Instability index |
---|---|---|---|---|---|---|---|---|
BvBADH1 | Bv5_ 116250_aodi | 1 500 | 54.72 | -0.077 | 5.45 | 88.78 | 500 | 32.48 |
BvBADH2 | Bv5_ 116230_ntjn | 1 512 | 54.78 | -0.062 | 5.37 | 88.51 | 503 | 31.62 |
BvBADH3 | Bv8_ 195870_rfyd | 1 509 | 54.69 | -0.081 | 5.24 | 87.45 | 502 | 28.42 |
BvBADH4 | Bv8_ 195860_yiyp | 1 506 | 54.25 | -0.079 | 5.60 | 89.00 | 501 | 22.07 |
BvBADH5 | Bv8_ 195850_giqy | 1 509 | 54.34 | -0.039 | 6.01 | 88.05 | 502 | 25.97 |
BvBADH6 | Bv5_ 116750_zqhy | 1 605 | 58.11 | -0.111 | 6.65 | 85.90 | 534 | 31.08 |
BvBADH7 | Bv6_ 149040_dgrz | 1 605 | 57.84 | -0.076 | 6.53 | 89.55 | 534 | 32.99 |
BvBADH8 | Bv6_ 149060_fmfu | 1 608 | 58.71 | -0.109 | 6.54 | 85.74 | 535 | 32.04 |
BvBADH9 | Bv2_047750_ktxe | 1 602 | 57.11 | 0.066 | 6.98 | 95.72 | 533 | 38.12 |
Table 2 Identification of BvBADH gene family members in sugar beet
基因名称 Gene name | 基因登录号 Gene ID | CDS /bp | 相对分子量 Mw/kD | 亲水性平均值 GRAVY | 等电点 pI | 脂肪指数 Aliphatic index | 氨基酸数目 Protein length/aa | 不稳定指数 Instability index |
---|---|---|---|---|---|---|---|---|
BvBADH1 | Bv5_ 116250_aodi | 1 500 | 54.72 | -0.077 | 5.45 | 88.78 | 500 | 32.48 |
BvBADH2 | Bv5_ 116230_ntjn | 1 512 | 54.78 | -0.062 | 5.37 | 88.51 | 503 | 31.62 |
BvBADH3 | Bv8_ 195870_rfyd | 1 509 | 54.69 | -0.081 | 5.24 | 87.45 | 502 | 28.42 |
BvBADH4 | Bv8_ 195860_yiyp | 1 506 | 54.25 | -0.079 | 5.60 | 89.00 | 501 | 22.07 |
BvBADH5 | Bv8_ 195850_giqy | 1 509 | 54.34 | -0.039 | 6.01 | 88.05 | 502 | 25.97 |
BvBADH6 | Bv5_ 116750_zqhy | 1 605 | 58.11 | -0.111 | 6.65 | 85.90 | 534 | 31.08 |
BvBADH7 | Bv6_ 149040_dgrz | 1 605 | 57.84 | -0.076 | 6.53 | 89.55 | 534 | 32.99 |
BvBADH8 | Bv6_ 149060_fmfu | 1 608 | 58.71 | -0.109 | 6.54 | 85.74 | 535 | 32.04 |
BvBADH9 | Bv2_047750_ktxe | 1 602 | 57.11 | 0.066 | 6.98 | 95.72 | 533 | 38.12 |
Fig. 2 Phylogenetic tree of BADH gene family in plants BADHs is divided into three clusters. Cluster I(black), II(red)and III. Cluster III is further divided into Cluster III a(green)and III b(gold). The dark green marks in the figure represent the BvBADH family members
顺式作用元件Cis-acting element | 功能Function | 序列Sequence | BvBADH | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ||||
ABRE | Abscisic acid-responsive element | ACGTG | 3 | 2 | 5 | 3 | 3 | 2 | 0 | 4 | 3 | |
TCA-element | Involved in salicylic acid responsiveness | CCATCTTTTT | 0 | 1 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | |
TGA-element | Auxin-responsive element | AACGAC | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | |
ARE | Anaerobic-responsive element | AAACCA | 4 | 3 | 1 | 2 | 4 | 4 | 5 | 2 | 6 | |
LTR | Low-temperature responsiveness | CCGAAA | 1 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 2 | |
Box 4 | Involved in light responsiveness | ATTAAT | 3 | 3 | 2 | 1 | 0 | 1 | 0 | 3 | 1 | |
GT1-motif | Involved in light responsiveness | GGTTAAT | 2 | 0 | 4 | 3 | 4 | 0 | 2 | 2 | 1 | |
TCT-motif | Involved in light responsiveness | TCTTAC | 6 | 0 | 2 | 1 | 1 | 1 | 1 | 2 | 0 | |
AE-box | Modul for light response | AGAAACTT | 0 | 1 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | |
O2-site | Zein metabolism regulation | GATGACATGA | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | |
G-box | Involved in light responsiveness | TACGTG | 1 | 2 | 7 | 0 | 4 | 4 | 3 | 0 | 0 |
Table 3 Analysis of cis-acting regulatory elements in the promoter of BvBADHs genes
顺式作用元件Cis-acting element | 功能Function | 序列Sequence | BvBADH | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | ||||
ABRE | Abscisic acid-responsive element | ACGTG | 3 | 2 | 5 | 3 | 3 | 2 | 0 | 4 | 3 | |
TCA-element | Involved in salicylic acid responsiveness | CCATCTTTTT | 0 | 1 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | |
TGA-element | Auxin-responsive element | AACGAC | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | |
ARE | Anaerobic-responsive element | AAACCA | 4 | 3 | 1 | 2 | 4 | 4 | 5 | 2 | 6 | |
LTR | Low-temperature responsiveness | CCGAAA | 1 | 0 | 0 | 2 | 0 | 0 | 2 | 0 | 2 | |
Box 4 | Involved in light responsiveness | ATTAAT | 3 | 3 | 2 | 1 | 0 | 1 | 0 | 3 | 1 | |
GT1-motif | Involved in light responsiveness | GGTTAAT | 2 | 0 | 4 | 3 | 4 | 0 | 2 | 2 | 1 | |
TCT-motif | Involved in light responsiveness | TCTTAC | 6 | 0 | 2 | 1 | 1 | 1 | 1 | 2 | 0 | |
AE-box | Modul for light response | AGAAACTT | 0 | 1 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | |
O2-site | Zein metabolism regulation | GATGACATGA | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | |
G-box | Involved in light responsiveness | TACGTG | 1 | 2 | 7 | 0 | 4 | 4 | 3 | 0 | 0 |
蛋白名称 Protein name | α螺旋 α-helix | 伸展主链 Extended strand | β转角 β-turn | 无规卷曲 Random coil |
---|---|---|---|---|
BvBADH1 | 43.40 | 16.40 | 7.80 | 32.40 |
BvBADH2 | 42.94 | 15.90 | 7.55 | 33.60 |
BvBADH3 | 40.84 | 17.53 | 8.17 | 33.47 |
BvBADH4 | 40.32 | 17.56 | 7.98 | 34.13 |
BvBADH5 | 39.44 | 17.73 | 8.37 | 34.46 |
BvBADH6 | 43.07 | 15.54 | 7.49 | 33.90 |
BvBADH7 | 41.76 | 15.54 | 7.87 | 34.83 |
BvBADH8 | 42.80 | 16.07 | 7.85 | 33.27 |
BvBADH9 | 48.22 | 15.01 | 8.07 | 28.71 |
Table 4 Secondary structure composition of BvBADHs proteins %
蛋白名称 Protein name | α螺旋 α-helix | 伸展主链 Extended strand | β转角 β-turn | 无规卷曲 Random coil |
---|---|---|---|---|
BvBADH1 | 43.40 | 16.40 | 7.80 | 32.40 |
BvBADH2 | 42.94 | 15.90 | 7.55 | 33.60 |
BvBADH3 | 40.84 | 17.53 | 8.17 | 33.47 |
BvBADH4 | 40.32 | 17.56 | 7.98 | 34.13 |
BvBADH5 | 39.44 | 17.73 | 8.37 | 34.46 |
BvBADH6 | 43.07 | 15.54 | 7.49 | 33.90 |
BvBADH7 | 41.76 | 15.54 | 7.87 | 34.83 |
BvBADH8 | 42.80 | 16.07 | 7.85 | 33.27 |
BvBADH9 | 48.22 | 15.01 | 8.07 | 28.71 |
Fig. 8 Relative expressions of BvBADHs in sugar beet leaves under various concentrations of NaCl The vertical bar represents the standard error(SE), n=3. The lowercase letter at the top of each bar indicates a significant deviation at the P<0.05 level
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