Genome-wide Identification and Expression Analysis Under Low-temperature Stress of Histone Gene Family in Eggplant (Solanum melongena)
LIN Hui1, HUANG Jian-Du2, CHEN Ji-Bing2, WANG Yi-Kui3, ZHU Hai-Sheng1,*, WEN Qing-Fang1,*
1 Fujian Key Laboratory of Vegetable Genetics and Breeding, Fujian Engineering Research Center for Vegetables, Crops Research Institute, Fujian Academy of Agricultural Science, Fuzhou 350013, China; 2 Fuzhou Institute of Vegetable Science, Fuzhou 350111, China; 3 Vegetable Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
Abstract Histones are essential components of chromatin and play an important role in developmental regulation, and resistance to stress. In order to explore the characteristics under cold stress in eggplant (Solanum melongena), in this study, the genome-wide identification of Histone genes and bioinformatics analysis were carried out in eggplant, the transcriptome data were mined to analyze the expression pattern of SmHistones in 2 different resistant eggplant (epl008 and eplck) leaves under low temperature stress. The results showed that a total of 40 SmHistones genes were identified in eggplant, which were unevenly distributed on 9 chromosomes. The members of SmHistone gene family were classified into 5 subgroups (H1, H2A, H2B, H3 and H4). Members of the same groups had similar physical and chemical properties, gene/protein structure, and conserved motifs. Intraspecific collinearity analysis showed that there was a collinear relationship among 6 pairs of SmHistones. The results of promoter elements analysis indicated that a large number of abiotic stress response cis-acting elements, such as low temperature responsive elements and drought responsive elements existed in promoter sequences of Smhistones. Transcriptome and qRT-PCR analysis revealed that 36 Smhistones were differentially expressed under low temperature stress and were significantly upregulated in eggplant epl008. The induced expression of SmHistone3 under low temperature stress was significant, revealing that it may be closely related to the cold metabolic response. This study provides a theoretical basis in breeding of eggplant with high tolerance to low temperature stress.
LIN Hui,HUANG Jian-Du,CHEN Ji-Bing, et al. Genome-wide Identification and Expression Analysis Under Low-temperature Stress of Histone Gene Family in Eggplant (Solanum melongena)[J]. 农业生物技术学报, 2024, 32(9): 1996-2008.
[1] 徐渴, 王伟伟, 武宁静, 等. 2021. 小麦OFP基因家族鉴定及其低温胁迫的表达分析[J]. 农业生物技术学报, 29(9): 1665-1677. (Xu K, Wang W W, Wu N J, et al.2021. Identification of OFP gene family and their expression analysis under low-temperature stress in wheat (Triticum aestivum)[J]. Journal of Agricultural Biotechnology, 29(9): 1665-1677.) [2] 王宝强, 朱晓林, 魏小红, 等. 2021. 番茄钙调蛋白结合转录因子CAMTA家族基因的鉴定及其低温胁迫下表达模式的分析[J]. 农业生物技术学报, 29(05): 871-884. (Wang B Q, Zhu X L, Wei X H, et al.2021. Identification of calmodulin-binding transcription factor CAMTA gene family and its expression analysis under low-temperature stress in tomato (Solanum lycopersicum)[J]. Journal of Agricultural Biotechnology, 29(05): 871-884.) [3] 张高原, 魏兵强. 2020. 甜瓜WRKY基因家族鉴定及其响应低温胁迫的表达分析[J]. 农业生物技术学报, 28(10): 1761-1775. (Zhang G Y, Wei B Q.2020. Identification of WRKY gene family and their expression analysis under low-temperature stress in melon (Cucumis melo)[J]. Journal of Agricultural Biotechnology, 28(10): 1761-1775.) [4] 张静, 苗佳敏, 李玉珠, 等. 2022. 植物组蛋白H3的研究进展[J]. 草原与草坪, 42(04): 147-157. (Zhang J, Miao J M, Li Y Z, et al.2022. Research progress of plant histone H3[J]. Grassland and Turf, 42(04): 147-157.) [5] 张娅欣. 2021. 竹子组蛋白对染色质结构和基因表达的调控[D]. 博士学位论文, 福建农林大学, 导师: 顾连峰, pp. 4-7. (Zhang Y X.2021. Histone regulation of chromatinstructure and gene expression in bamboos[D]. Thesis for Ph.D., Fujian Agriculture and Forestry University, Supervisor: Gu L F, pp. 4-7.) [6] Ascencio-Ibáñez J T, Sozzani R, Lee T J, et al.2008. Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection[J]. Plant Physiology, 148(1): 436-454. [7] Bailey T L, Johnson J, Grant C E, et al.2015. The MEME suite[J]. Nucleic Acids Research, 43(W1): W39-49. [8] Chen C, Chen H, Zhang Y, et al.2020. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8): 1194-1202. [9] Chen J, Hu Y, Yu Y, et al.2019. Quantitative analysis of post-translational modifications of histone H3 variants during the cell cycle[J]. Analytica Chimica Acta, 1080: 116-126. [10] Comai L, Maheshwari S, Marimuthu M P A.2017. Plant centromeres[J]. Current Opinion in Plant Biology, 36: 158-167. [11] Ding D, Zhang L, Wang H, et al.2009. Differential expression of miRNAs in response to salt stress in maize roots[J]. Annals of Botany, 103: 29-38. [12] Giaimo B D, Ferrante F, Herchenröther A, et al.2019. The histone variant H2A.Z in gene regulation[J]. Epigenetics Chromatin, 12(1): 37. [13] He K X, Cao X F, Deng X.2021. Histone methylation in epigenetic regulation and temperature responses[J]. Current Opinion in Plant Biology, 61: 102001. [14] Hirakawa H, Shirasawa K, Miyatake K,et al.2014. Draft genome sequence of eggplant (Solanum melongena L.): The representative solanum species indigenous to the old world[J]. DNA Research, 21(6): 649-660. [15] Hu Y F, Lai Y.2015. Identification and expression analysis of rice histone genes[J]. Plant Physiology and Biochemistry , 86: 55-65. [16] Huang S Z, Zhang A, Jin J B, et al.2019. Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress respons[J]. New Phytologist, 223: 1372-1387. [17] Jiang D, Berger F.2017. Histone variants in plant transcriptional regulation[J]. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, 1860(1): 123-130. [18] Jiang D, Borg M, Lorković ZJ, et al.2020. The evolution and functional divergence of the histone H2B family in plants[J]. PLOS Genetics, 16(7): e1008964. [19] Krzywinski M, Schein J, Birol I, et al.2009. Circos: An information aesthetic for comparative genomics[J]. Genome Research, 19(9): 1639-1645. [20] Kumar S V, Wigge P A.2010. H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis[J]. Cell, 140(1): 136-147. [21] Lawrence M, Daujat S, Schneider R.2016. Lateral thinking: How histone modifications regulate gene expression[J]. Trends in Genetics, 32(1): 42-56. [22] Lescot M, Déhais P, Thijs G, et al.2002. 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, 30(1): 325-327. [23] Letunic I, Bork P.2021. Interactive Tree of life (iTOL) v5: An online tool for phylogenetic tree display and annotation[J]. Nucleic Acids Research, 49(W1): W293-W296. [24] Liu J, Wang B, Li Y.2020. RNA sequencing analysis of low temperature and low light intensity-responsive transcriptomes of zucchini (Cucurbita pepo L.)[J]. Scientia Horticulturae, 265: 109263. [25] Lu S, Wang J, Chitsaz F, et al.2020. CDD/SPARCLE: The conserved domain database in 2020[J]. Nucleic Acids Research, 48(D1): D265-D268. [26] March-Díaz R, García-Domínguez M, Lozano-Juste J, et al.2008. Histone H2A.Z and homologues of components of the SWR1 complex are required to control immunity in Arabidopsis[J]. The Plant Journal, 53(3): 475-87. [27] Osakabe A, Molaro A.2023. Histone renegades: Unusual H2A histone variants in plants and animals[J]. Seminars in Cell & Developmental Biology, 135: 35-42. [28] Ramamoorthy R, Jiang S Y, Kumar N, et al.2008. A comprehensive transcriptional profiling of the WRKY gene family in rice under various abiotic and phytohormone treatments[J]. Plant Cell Physio, 49(6): 865-879. [29] Saini D K, Kaushik P.2019. Visiting eggplant from a biotechnological perspective: A review[J]. Scientia Horticulturae, 253: 327-340. [30] Sharma A, Singh K, Almasan A.2012. Histone H2AX phosphorylation: A marker for DNA damage[J].Methods in Molecular Biology, 920: 613-26. [31] Shaytan A K, Landsman D, Panchenko A R.2015. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers[J]. Current Opinion in Structural Biology, 32: 48-57. [32] Shen Y, Silva N C E, Audonnet L, et al.2014. Over-expression of histone H3K4 demethylase gene JMJ15 enhances salt tolerance in Arabidopsis[J]. Frontiers in Plant Science, 5: 290. [33] Tamura K, Stecher G, Kumar S.2020. MEGA11: Molecular evolutionary genetics analysis version 11[J]. International Journal of Biological Macromolecules, 38(7): 3022-3027. [34] Tian Y, Zeng H, Wu J, et al.2022. Screening DHHCs of S-acylated proteins using an OsDHHC cDNA library and bimolecular fluorescence complementation in rice[J]. The Plant Journal, 110(6): 1763-1780. [35] Wang L, Guo K, Li Y, et al.2010. Expression profiling and integrative analysis of the CESA/CSL superfamily in rice[J]. BMC Plant Biology, 10: 282. [36] Wang Q, Fan L, Su X, et al.2022. Genome-wide characterization of Histone gene family and expression profiling during microspore development in radish (Raphanus sativus L.)[J]. Gene, 815: 146180. [37] Wang Y, Li Y, Zhou F, et al.2023. Genome-wide characterization, phylogenetic and expression analysis of Histone gene family in cucumber (Cucumis sativus L.)[J]. International Journal of Biological Macromolecules, 230: 123401. [38] Wang Y, Tang H, Debarry J D, et al.2012. MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic Acids Research, 40(7): e49. [39] Wei Q, Wang J, Wang W, et al.2020. A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant[J]. Horticulture Research, 7(1): 153. [40] Xu G X, Guo C C, Shan HY, et al.2012. Divergence of duplicate genes in exon-intron structure[J]. PNAS, 109(4): 1187-1192. [41] Yang Y, Liu J, Zhou X H, et al.2020. Transcriptomics analysis unravels the response to low temperature in sensitive and tolerant eggplants[J].Scientia Horticulturae, 271: 109468. [42] Zhang H, Zhu J, Gong Z, et al.2022. Abiotic stress responses in plants[J]. Nature Reviews. Genetics, 23(2): 104-119. [43] Zhao F, Zhang H, Zhao T, et al.2021. The histone variant H3.3 promotes the active chromatin state to repress flowering in Arabidopsis[J].Plant Physiology, 186(4): 2051-2063. [44] Zhu Y, Wu N N, Song W L, et al.2014. Soybean (Glycine max) expansin gene superfamily origins: Segmental and tandem duplication events followed by divergent selection among subfamilies[J]. BMC Plant Biology, 14: 93.
