研究论文

巨桉HDAC基因家族的全基因组鉴定与分析

  • LING Teng-hong ,
  • HUANG Zhi-qing ,
  • XIE Jin-cong ,
  • WU Ai-min
展开
  • (华南农业大学林学与风景园林学院,广东 广州 510642)

收稿日期: 2025-04-08

  录用日期: 2025-05-09

  网络出版日期: 2025-10-13

基金资助

科技部科技创新2030-重大项目(2023ZD04057)

Genome-wide Identification and Analysis of the HDAC Gene Family in Eucalyptus grandis

  • 凌腾泓,黄稚清,谢进聪,吴蔼民
Expand
  • (College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, Guangdong China)

Received date: 2025-04-08

  Accepted date: 2025-05-09

  Online published: 2025-10-13

摘要

基于全基因组序列对巨桉Eucalyptus grandis组蛋白去乙酰化酶(Histone Deacetylase, HDAC)基因家族成员进行鉴定和生物信息学分析,并结合转录组数据分析EgHDAC家族在幼叶、成熟叶、茎、根、花、木质部、韧皮部和形成层的表达情况。结果表明,巨桉HDAC家族可分为RPD3/HDA1、HD2和SIR2亚家族,共含15个成员,均为亲水性蛋白。亚细胞预测定位主要在细胞核和细胞质中。EgHDACs启动子序列包含许多光响应性、激素响应性、应激响应性和植物生长相关元件。EgHDT1和EgHDA2/4/7/8/11在幼叶、成熟叶、茎、根、花、木质部、韧皮部和形成层组织中均高表达,而EgHDA5仅在叶片中高表达。在茉莉酸、水杨酸和盐胁迫处理下,EgHDT1、EgHDA4和EgHDA5均有不同程度的表达。在进化过程中,EgHDACs既具有保守性,又具有特异性,可能参与巨桉的生长发育,并响应茉莉酸处理、水杨酸处理和盐胁迫,体现对环境的适应与调节能力。

本文引用格式

LING Teng-hong , HUANG Zhi-qing , XIE Jin-cong , WU Ai-min . 巨桉HDAC基因家族的全基因组鉴定与分析[J]. 亚热带植物科学, 2025 , 54(4) : 365 -377 . DOI: 10.3969/j.issn.1009-7791.2025.04.001

Abstract

The histone deacetylase (HDAC) gene encodes a class of proteins associated with histone deacetylation and is related to growth, development, and stress response. In this study, we conducted a genome-wide identification and bioinformatics analysis of the Eucalyptus grandis HDAC family members and analyzed the expression patterns of the EgHDAC family in the young leaves, mature leaves, stems, roots, flowers, xylem, phloem, and cambium based on transcriptome data. The results showed that the EgHDAC family could be divided into the RPD3/HDA1, HD2, and SIR2 subfamilies, comprising a total of 15 members, all of which are hydrophilic proteins. Subcellular localization prediction mainly located these proteins in the nucleus and cytoplasm. The promoter sequences of EgHDACs contained many elements responsive to light, hormones, stress, and plant growth. The E. grandis HDAC family genes EgHDT1 and EgHDA2/4/7/8/11 were highly expressed in the young leaves, mature leaves, stems, roots, flowers, xylem, phloem, and cambium tissues, while EgHDA5 was highly expressed only in the leaves. Under treatments with jasmonic acid, salicylic acid, and salt stress, EgHDT1, EgHDA4, and EgHDA5 exhibited varying degrees of expression changes. During the course of evolution, EgHDACs have both conservation and specificity, and they are likely involved in the growth and development of E. grandis, as well as responding to jasmonic acid treatment, salicylic acid treatment, and salt stress, thereby demonstrating the ability to adapt to and regulate the environment.

参考文献

[1] Zhang Z, Zeng Y, Hou J, Li L. Advances in understanding the roles of plant HAT and HDAC in non-histone protein acetylation and deacetylation [J]. Planta, 2024, 260(4): 93.
[2] Chen X, Ding A B, Zhong X. Functions and mechanisms of plant histone deacetylases [J]. Science China (Life Sciences), 2020, 63(2): 206–216.
[3] Xu Q, Liu Q, Chen Z, Yue Y, Liu Y, Zhao Y, Zhou D X. Histone deacetylases control lysine acetylation of ribosomal proteins in rice [J]. Nucleic Acids Research, 2021, 49(8): 4613–4628.
[4] Sendra R, Rodrigo I, Salvador M L, Franco L. Characterization of pea histone deacetylases [J]. Plant Molecular Biology, 1988, 11(6): 857–866.
[5] Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aime S, Soltis D E, Miles N W, Melkonian M, Deyholos M K, Leebens-Mack J H, Chase M W, Rothfels C J, Stevenson D W, Graham S W, Wang X, Wu S, Pires J C, Edger P P, Yan Z, Xie Y, Carpenter E J, Wong G, Wendehenne D, Nicolas-Frances V. The evolution of HD2 proteins in green plants [J]. Trends in Plant Science, 2016, 21(12): 1008–1016.
[6] Tahir M S, Tian L. HD2-type histone deacetylases: unique regulators of plant development and stress responses [J]. Plant Cell Reports, 2021, 40(9): 1603–1615.
[7] Zhao X, Wang H, Zhang B, Cheng Y, Ma X. Over expression of histone deacetylase gene 84KHDA909 from poplar confers enhanced tolerance to drought and salt stresses in Arabidopsis [J]. Plant Science, 2022, 324: 111434.
[8] Zhang M, Teixeira D S J, Yu Z, Wang H, Si C, Zhao C, He C, Duan J. Identification of histone deacetylase genes in Dendrobium officinale and their expression profiles under phytohormone and abiotic stress treatments [J]. Peer Journal, 2020, 8: e10482.
[9] Luxmi R, Garg R, Srivastava S, Sane A P. Expression of the SIN3 homologue from banana, MaSIN3, suppresses ABA responses globally during plant growth in Arabidopsis [J]. Plant Science, 2017, 264: 69–82.
[10] Li C, Xu J, Li J, Li Q, Yang H. Involvement of Arabidopsis histone acetyltransferase HAC family genes in the ethylene signaling pathway [J]. Plant and Cell Physiology, 2014, 55(2): 426–435.
[11] Hou J, Ren R, Xiao H, Chen Z, Yu J, Zhang H, Shi Q, Hou H, He S, Li L. Characteristic and evolution of HAT and HDAC genes in Gramineae genomes and their expression analysis under diverse stress in Oryza sativa [J]. Planta, 2021, 253(3): 72.
[12] Gao S, Li L, Han X, Liu T, Jin P, Cai L, Xu M, Zhang T, Zhang F, Chen J, Yang J, Zhong K. Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum [J]. Bmc Genomics, 2021, 22(1): 49.
[13] Tobias P A, Christie N, Naidoo S, Guest D I, Kulheim C. Identification of the Eucalyptus grandis chitinase gene family and expression characterization under different biotic stress challenges [J]. Tree Physiology, 2017, 37(5): 565–582.
[14] Fan S, Wang J, Lei C, Gao C, Yang Y, Li Y, An N, Zhang D, Han M. Identification and characterization of histone modification gene family reveal their critical responses to flower induction in apple [J]. BMC Plant Biology, 2018, 18(1): 173.
[15] Kaminski K, Ludwiczak J, Pawlicki K, Alva V, Dunin-Horkawicz S. pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models [J]. Bioinformatics, 2023, 39(10): 579.
[16] Peek A L, Rebbeck T J, Leaver A M, Foster S L, Refshauge K M, Puts N A, Oeltzschner G. A comprehensive guide to MEGA–PRESS for GABA measurement [J]. Analytical Biochemistry, 2023, 669: 115113.
[17] Wascher M, Kubatko L. Consistency of SVDQuartets and maximum likelihood for coalescent-based species tree stimation [J]. Systematic Biology, 2021, 70(1): 33–48.
[18] Zhou T, Xu K, Zhao F, Liu W, Li L, Hua Z, Zhou X. itol.toolkit accelerates working with iTOL (Interactive Tree of Life) by an automated generation of annotation files [J]. Bioinformatics, 2023, 39(6): 339.
[19] Bailey T L, Johnson J, Grant C E, Noble W S. The MEME suite [J]. Nucleic Acids Research, 2015, 43(W1): W39–W49.
[20] Wang J, Chitsaz F, Derbyshire M K, Gonzales N R, Gwadz M, Lu S, Marchler G H, Song J S, Thanki N, Yamashita R A, Yang M, Zhang D, Zheng C, Lanczycki C J, Marchler-Bauer A. The conserved domain database in 2023 [J]. Nucleic Acids Research, 2023, 51(D1): D384–D388.
[21] Chen C, Wu Y, Li J, Wang X, Zeng Z, Xu J, Liu Y, Feng J, Chen H, He Y, Xia R. TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining [J]. Molecular Plant, 2023, 16(11): 1733–1742.
[22] Li Y C, Lu Y C. Blastp-acc: Parallel architecture and hardware accelerator design for blast-based protein sequence alignment [J]. IEEE Transactions on Biomedical Circuits and Systems, 2019, 13(6): 1771–1782.
[23] Wang Y, Tang H, Debarry J D, Tan X, Li J, Wang X, Lee T H, Jin H, Marler B, Guo H, Kissinger J C, Paterson A H. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity [J]. Nucleic Acids Research, 2012, 40(7): e49.
[24] Wang Y, Jia L, Tian G, Dong Y, Zhang X, Zhou Z, Luo X, Li Y, Yao W. shinyCircos-V2.0: Leveraging the creation of Circos plot with enhanced usability and advanced features [J]. iMeta, 2023, 2(2): e109.
[25] Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences [J]. Nucleic Acids Research, 2002, 30(1): 325–327.
[26] Tan Y, Martin T G, Harrison B C, Leinwand L A. Utility of the burmese python as a model for studying plasticity of extreme physiological systems [J]. Journal of Muscle Research and Cell Motility, 2023, 44(2): 95–106.
[27] Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable A L, Fang T, Doncheva N T, Pyysalo S, Bork P, Jensen L J, von Mering C. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest [J]. Nucleic Acids Research, 2023, 51(D1): D638–D646.
[28] Silva M A, Nascimento Júnior J C D, Thomaz D V, Maia R T, Costa Amador V, Tommaso G, Coelho G D. Comparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller? [J]. Journal of Biomolecular Structure & Dynamics, 2023, 41(18): 8927–8940.
[29] Pandey R, Müller A, Napoli C A, Selinger D A, Pikaard C S, Richards E J, Bender J, Mount D W, Jorgensen R A. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes [J]. Nucleic Acids Research, 2002, 30(23): 5036–5055.
[30] Luo Y, Shi D Q, Jia P F, Bao Y, Li H J, Yang W C. Nucleolar histone deacetylases HDT1, HDT2, and HDT3 regulate plant reproductive development [J]. Journal of Genetics and Genomics, 2022, 49(1): 30–39.
[31] Wang Q, Bao X, Chen S, Zhong H, Liu Y, Zhang L, Xia Y, Kragler F, Luo M, Li X D, Lam H M, Zhang S. AtHDA6 functions as an H3K18ac eraser to maintain pericentromeric CHG methylation in Arabidopsis thaliana [J]. Nucleic Acids Reseach, 2021, 49(17): 9755–9767.
[32] Liu K, Chen J, Sun S, Chen X, Zhao X, Hu Y, Qi G, Li X, Xu B, Miao J, Xue C, Zhou Y, Gong Z. Histone deacetylase OsHDA706 increases salt tolerance via H4K5/K8 deacetylation of OsPP2C49 in rice [J]. Journal of Integrative Plant Biology, 2023, 65(6): 1394–1407.
[33] Yang Z, Du J, Tan X, Zhang H, Li L, Li Y, Wei Z, Xu Z, Lu Y, Chen J, Sun Z. Histone deacetylase OsHDA706 orchestrates rice broad-spectrum antiviral immunity and is impeded by a viral effector [J]. Cell Reports, 2024, 43(3): 113838.
[34] Choi S M, Song H R, Han S K, Han M, Kim C Y, Park J, Lee Y H, Jeon J S, Noh Y S, Noh B. HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis [J]. Plant Journal, 2012, 71(1): 135–146.
[35] Huang X, Yip K, Nie H, Chen R, Wang X, Wang Y, Lin W, Li R. ChIP-seq and RNA-seq Reveal the involvement of histone lactylation modification in gestational diabetes mellitus [J]. Proteome Research, 2024, 23(6): 1937–1947.
[36] Guo C, Ma X, Gao F, Guo Y. Off-target effects in CRISPR/Cas9 gene editing [J]. Frontiers in Bioengineering & Biotechnology, 2023, 11: 1143157.
文章导航

/

〈 〉