Histone Deacetylases (HDACs) Gene Family in Sugar Beet: Identification and Functional Prediction

doi:10.11924/j.issn.1000-6850.casb2021-0767

Abstract

Abstract:

To identify vernalization-related histone deacetylases (HDACs) in sugar beet genome, HMMsearch and Blastp were employed to identify the members of BvHDACs gene family, and iqtree program was used to construct the maximum-likelihood phylogenies. The chromosome location and gene structure of BvHDACs were analyzed by TBtools. The expression pattern of BvHDACs under vernalization was measured by RNA-seq. The results showed that there were 16 BvHDACs located on 5 chromosomes. BvHDACs were classified into 3 subfamilies, namely RPD3/HDA1, SIR2 and HD2, and members from the same subfamily had similar functional domain. According to RNA-seq, the expression of several genes from RPD3/HDA1, SIR2 and HD2 significantly changed after vernalization. Especially, the expression of BvHDT1 and BvHDT2 were correlated with changes of bolting-related phenotype. The protein-protein interaction prediction showed that BvHDT1 and BvHDT2 possibly interacted with BvFLD, BvJMJ11 and BvJMJ12, which were involved in flowering and bolting. In summary, it is hypothesized that BvHDT1 and BvHDT2 may be involved in vernalization of sugar beet.

Key words: sugar beet, vernalization, histone deacetylases, gene family, bolting

CLC Number:

S566.3

WANG Linyu, JIANG Yichen, YU Qingyang, WU Zedong, PI Zhi. Histone Deacetylases (HDACs) Gene Family in Sugar Beet: Identification and Functional Prediction[J]. Chinese Agricultural Science Bulletin, 2022, 38(8): 9-16.

Figures/Tables 6

References 28

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基因编号	基因名称	亚家族	序列长度/aa	理论分子量/kDa	理论等电点	预测定位
Bv9_218010_wffu	BvHDAC1	RPD3/HDA1	500	56.0	5.00	细胞核
Bv_006940_mxka	BvHDAC2	RPD3/HDA1	352	39.1	6.40	细胞质
Bv_025910_fkmq	BvHDAC3	RPD3/HDA1	124	13.5	8.49	胞外
Bv6_132780_hazw	BvHDAC4	RPD3/HDA1	438	47.3	6.22	质体
Bv5_123480_yfcy	BvHDAC5	RPD3/HDA1	641	71.4	5.31	细胞质
Bv5_117920_htqx	BvHDAC6	RPD3/HDA1	450	50.6	5.69	细胞核
Bv5_126810_awat	BvHDAC7	RPD3/HDA1	580	63.5	5.89	细胞质
Bv7_171060_eoxy	BvHDAC8	RPD3/HDA1	377	41.5	5.66	细胞质
Bv2_044990_wqan	BvHDAC9	RPD3/HDA1	429	49.2	5.10	细胞核
Bv9_211080_qkgc	BvHDT1	HD2	286	31.0	4.76	细胞核
Bv9_211090_esde	BvHDT2	HD2	289	31.2	4.66	细胞核
Bv7_160340_ywwk	BvHDT3	HD2	298	32.2	4.63	细胞核
Bv4_090490_zpji	BvSIRT1	SIR2	496	55.6	9.22	细胞核
Bv4_078680_huzk	BvSIRT2	SIR2	389	43.4	8.89	质体
Bv_013200_xmgc	BvSIRT3	SIR2	393	43.9	8.76	细胞核
Bv_030800_itta	BvSIRT4	SIR2	182	19.6	6.04	线粒体

基因编号	基因名称	亚家族	序列长度/aa	理论分子量/kDa	理论等电点	预测定位
Bv9_218010_wffu	BvHDAC1	RPD3/HDA1	500	56.0	5.00	细胞核
Bv_006940_mxka	BvHDAC2	RPD3/HDA1	352	39.1	6.40	细胞质
Bv_025910_fkmq	BvHDAC3	RPD3/HDA1	124	13.5	8.49	胞外
Bv6_132780_hazw	BvHDAC4	RPD3/HDA1	438	47.3	6.22	质体
Bv5_123480_yfcy	BvHDAC5	RPD3/HDA1	641	71.4	5.31	细胞质
Bv5_117920_htqx	BvHDAC6	RPD3/HDA1	450	50.6	5.69	细胞核
Bv5_126810_awat	BvHDAC7	RPD3/HDA1	580	63.5	5.89	细胞质
Bv7_171060_eoxy	BvHDAC8	RPD3/HDA1	377	41.5	5.66	细胞质
Bv2_044990_wqan	BvHDAC9	RPD3/HDA1	429	49.2	5.10	细胞核
Bv9_211080_qkgc	BvHDT1	HD2	286	31.0	4.76	细胞核
Bv9_211090_esde	BvHDT2	HD2	289	31.2	4.66	细胞核
Bv7_160340_ywwk	BvHDT3	HD2	298	32.2	4.63	细胞核
Bv4_090490_zpji	BvSIRT1	SIR2	496	55.6	9.22	细胞核
Bv4_078680_huzk	BvSIRT2	SIR2	389	43.4	8.89	质体
Bv_013200_xmgc	BvSIRT3	SIR2	393	43.9	8.76	细胞核
Bv_030800_itta	BvSIRT4	SIR2	182	19.6	6.04	线粒体