Identification and Expression Analysis of HDAC and HAT gene families in Xanthoceras sorbifolium

doi:10.7525/j.issn.1673-5102.2026.01.005

Abstract

Abstract:

Histone deacetylases（HDACs） and histone acetyltransferases（HATs） are a group of reversible enzymes that catalyze histone acetylation/deacetylation， playing crucial roles in plant growth and development. This study aimed to investigate the characteristics of histone deacetylase（XsHDAC） and histone acetyltransferase（XsHAT） family member genes and proteins in Xanthoceras sorbifolium， with a focus on their expression patterns during seed embryo development. Genome-wide identification of XsHDACs and XsHATs family members in X. sorbifolium was conducted. Bioinformatics analyses were performed to examine their physicochemical properties， gene structure， conserved motifs， chromosomal localization， synteny， and cis-acting elements. The expression patterns of XsHDACs and XsHATs genesin different tissues and during seed embryo development were analyzed using quantitative real-time PCR. A total of 15 XsHDACs genes（belonging to the RPD3/HDA1， HD2， and SIR2 subfamilies） and eight XsHATs genes（belonging to the GNAT， MYST， CBP， and TAF_II250 subfamilies） were identified from the X. sorbifolium genome. These genes were distributed across nine different chromosomes. Physicochemical analysis of XsHDACs and XsHATs family members revealed that most proteins in both families were hydrophilic and acidic. Subcellular localization predictions indicated that XsHDACs and XsHATs family proteins were primarily localized in the nucleus. Phylogenetic analysis showed a close evolutionary relationship between X. sorbifolium and Litchi chinensis， both belonging to the Sapindaceae family. Protein structure predictions demonstrated that XsHDACs and XsHATs family members were rich in random coils and α-helices. Cis-acting element analysis revealed that the promoters of XsHDACs and XsHATs genescontain elements related to seed development， light response， hormone signaling， and stress responses. Quantitative real-time PCR revealed that most XsHDACs and XsHATs members were highly expressed in the embryo of seed， with increased expression levels during late-stage embryogenesis. The XsHDACs and XsHATs gene families exhibited both evolutionary conservation and specificity. The expression results suggested their potential crucial roles in the embryonic development and oil biosynthesis in X. sorbifolium.

Key words: Xanthoceras sorbifolium, histone deacetylase, histone acetyltransferase, gene family, gene expression analysis

CLC Number:

Q786

Mengmeng CHENG, Bin GE, Beisen KOU, Wenbin GUAN, Hai LU, Huihong GUO, Hui LI. Identification and Expression Analysis of HDAC and HAT gene families in Xanthoceras sorbifolium[J]. Bulletin of Botanical Research, 2026, 46(1): 51-66.

Figures/Tables 11

Table 1

Table2

Physicochemical properties of proteins encoded by XsHDACs and XsHATs gene family members

亚家族 Subfamily	基因名称 Gene name	基因编号 Gene ID	基因序列长度 Gene sequence length/bp	氨基酸数目 Amino acids number	染色体 Chromosome			等电点 pI	疏水性 Hydroph- obicity	亚细胞定位 Subcellular localization
亚家族 Subfamily	基因名称 Gene name	基因编号 Gene ID	基因序列长度 Gene sequence length/bp	氨基酸数目 Amino acids number	编号No.	起始位置 Starting	结束位置 Ending	等电点 pI	疏水性 Hydroph- obicity	亚细胞定位 Subcellular localization
RPD3/HDA1	XsHDA5	XS13G0000300.1	31 469	1 346	13	42 083	73 551	7.04	-0.231	细胞核
	XsHDA6	XS13G0205600.1	6 511	715	13	18 440 192	18 446 702	5.88	-0.281	叶绿体
	XsHDA8	XS10G0208600.1	4 094	378	10	27 324 779	27 328 872	5.38	-0.181	细胞骨架
	XsHDA9	XS10G0189900.1	9 672	459	10	25 563 436	25 573 107	5.16	-0.343	细胞质
	XsHDA14	XS08G0082900.1	1 687	175	8	10 694 904	10 696 590	5.28	0.054	细胞质
	XsHDA15	XS13G0012000.1	110 820	581	13	999 640	1 010 459	6.09	-0.423	细胞核
	XsHDA19a	XS06G0265200.1	6 258	499	6	31 591 565	31 597 822	5.11	-0.567	细胞核
	XsHDA19b	XS06G0266100.1	11 068	467	6	31 988 618	31 999 685	5.79	-0.397	细胞质
SIR	XsSRT2	XS01G0117000.1	11 080	447	1	13 708 191	13 719 270	8.17	-0.159	细胞核
	XsSRT4	XS08G0254700.1	6 286	372	8	29 422 597	29 428 882	8.72	-0.219	无
	XsSRT6a	XS01G0117200.1	7 465	472	1	1 374 249	13 749 961	7.88	0.107	细胞质膜
	XsSRT6b	XS15G0181700.1	6 828	448	15	18 691 280	18 698 107	9.11	-0.260	细胞核
HD2	XsHDT1a	XS12G0010700.1	4 221	326	12	1 014 407	1 018 627	4.87	-1.055	细胞核
	XsHDT1b	XS10G0185900.1	3 539	274	10	25 235 716	25 239 254	5.3	-0.821	细胞核
	XsHDT3	XS13G0226100.1	4 773	608	13	21 330 954	21 335 726	5.14	-0.977	细胞核
GNAT	XsHAG1	XS01G0275100.1	9 344	616	1	28 219 065	28 228 408	5.99	-0.603	细胞核
	XsHAG2	XS04G0216600.1	3 258	466	4	27 534 203	27 537 460	5.55	-0.246	细胞骨架
	XsHAG3	XS13G0078200.1	5 775	1 005	13	7 261 674	7 267 448	7.13	-0.255	细胞骨架
MYST	XsHAM1	XS07G0161100.1	1 674	456	7	14 445 643	14 453 353	6.99	-0.613	细胞核
MYST	XsHAM2	XS07G0161400.1	5 973	456	7	14 513 828	14 521 582	8.23	-0.436	细胞核
CBP	XsHAC1	XS13G0220600.1	2 360	1 793	13	20 139 040	20 151 359	8.36	-0.678	细胞核
TAF_II250	XsHAF1	XS13G0224500.1	9 596	1 101	13	20 139 040	20 151 359	9.17	-0.734	无
TAF_II250	XsHAF2	XS12G0000500.1	5 412	1 803	12	20 139 040	20 151 359	5.81	-0.675	无

Table2

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Table 3

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基因名称 Gene name	正向引物（5′→3′） Forward primer（5′→3′）	反向引物（5′→3′） Reverse primer（5′→3′）
XsGAPDHF	GCCAAGACTATCCAACCT	GCAACCACATCAACATCAT
XsHDA5	ACGCTGCCATTCCTCAAAGA	ATGCAGACTCCGATGAACCC
XsHDA6	AGATCAACCGTCCCTTCCCT	AGAAGCCGAAAAGCCCATCA
XsHDA8	CCGGGCTTTCTTGACGTTCT	CCCGCTTTGTCTGCTTCAAC
XsHDA9	GTCTACTTTGGGCCCAACCA	GTCAGCTGAGTGGAATTGCG
XsHDA14	AGTCACTTGTTGCAGCTGGA	AGCCCATGTACACGTTGAGT
XsHDA15	TGCTGGGTGAAAATCCTGGA	GCCCGCCGTACCTTCTTAAT
XsHDA19a	GCACTTGGTATGGACGTGGA	TGGACACTAGGTGCATGCTG
XsHDA19b	ACCTGGTGCTGTGGTTCTTC	TCCACGTCCATACCAAGTGC
XsSRT2	ACGATATTGGGCAAGGAGCT	ACAGTCCCATGCAACTCAAGT
XsSRT4	TGTCGGATCTCAGTTCCTGG	GGGCTTTCACTTGGTCCTGA
XsSRT6a	TGCACCTGTAAACGCCACTA	TGTCGGATCTCAGTTCCTGG
XsSRT6b	AGGCTACGCAGAGAAGCTCT	ATACCTGCACCCGTGAACAC
XsHDT1a	AGTCGTGAGGTTGAAAGTGACA	AGCCTTCTTATCAGGAACCGG
XsHDT1b	AAAGCAGGCACTCCTCAGAC	TAGAGCACCATCAGACCCGA
XsHDT3	GCCCAGAACATAAGCCAGGA	ACTTTTCTCCTCTGCCAGCT
XsHAG1	GCCACCTCTTCCATCCACAA	AGTCCTCAGCATCAGAGTCG
XsHAG2	ATTTGTCCCTCCTGCCAGTG	GCTTCCCAGCAGTTCCTGAA
XsHAG3	TTGATGGAAGAGGCAGAGCG	TCGGGTTGGTTGAGGCATTT
XsHAM1	TTGGCATGCATCCTCACCTT	ACTCAACAGCCCAAGGTCAG
XsHAM2	AGGAGGCTTGATGAATGGGTG	GTTCACGTAAACTGGCAGCA
XsHAC1	GAGTAATGCCGGGTGATGGA	GATGGAGGCTTTACATGCGC
XsHAF1	CGTGGGAAGCAGGAGAACTT	TCAGCAAGCATTTCTCGCTC
XsHAF2	GGTGAGTGTGTGGCAGTTCT	TGGAAGCGGTGTGGAAACTT

蛋白名称 Protein name	α-螺旋 α-helix/%	延伸链 Extended strand/%	不规则卷曲 Random coil/%
XsHDA5	34.18	10.25	55.57
XsHDA6	36.22	13.43	50.35
XsHDA8	37.83	15.87	46.30
XsHDA9	34.89	11.56	53.56
XsHDA14	30.29	21.14	48.57
XsHDA15	37.52	11.19	51.29
XsHDA19a	37.68	11.02	51.30
XsHDA19b	34.69	11.19	53.75
XsSRT2	30.65	11.02	58.17
XsSRT4	29.84	11.56	59.14
XsSRT6a	28.18	13.35	58.47
XsSRT6b	29.24	9.38	61.38
XsHDT1a	11.04	12.58	76.38
XsHDT1b	8.76	16.79	74.45
XsHDT3	9.54	13.98	76.48
XsHAG1	29.71	7.63	62.66
XsHAG2	44.42	13.09	42.49
XsHAG3	46.67	12.04	41.29
XsHAM1	32.24	13.16	54.61
XsHAM2	38.28	15.91	45.81
XsHAC1	26.49	5.13	68.38
XsHAF1	47.23	4.09	48.68
XsHAF2	40.82	4.83	54.35