Comparative Genomics of the Small Heat Shock Protein Family in Angiosperms
Received date: 2020-12-25
Accepted date: 2021-03-25
Online published: 2021-03-24
Small heat shock protein (sHSP) can respond to environmental stresses and regulate plant growth and development. In this study, 33 NcsHSPs, 24 OssHSPs, 17 AtsHSPs and 47 VvsHSPs were found in waterlily, rice, Arabidopsis, and grape, respectively. The sHSP family can be divided into 12 subfamilies, and different subfamily had different number of sHSP members, conserved motifs, gene structures and number of duplicated genes. Then, 12 gene duplication events in tle sHSP fanily were identified from 4 model angiosperms of sHSP family. The segmental and tandem duplication events were related to the gene expansion in the sHSP family, and the segmental duplication events occurred earlier than the tandem duplication events. Moreover, sHSP members in Arabidopsis and grape had the highest orthologous similarity, followed by sHSP members in waterlily and grape. Furthermore, sHSP family in angiosperms evolved towards sHSP members with smaller length of amino acid, lower molecular weight, simpler gene structure, and concentrated chromosomal localization. Besides, some sHSP members may be related to plant growth and development in waterlily, rice, Arabidopsis, and grape. Above all, these results could lay vital foundations on comparative genomics of the sHSP family in four model angiosperms and advance the sHSP family in other angiosperms.
Key words： sHSP family; comparative genomics; expansion; gene expression
Kai Fan, Fangting Ye, Zhijun Mao, Xinfeng Pan, Zhaowei Li, Wenxiong Lin . Comparative Genomics of the Small Heat Shock Protein Family in Angiosperms[J]. Chinese Bulletin of Botany, 2021 , 56(3) : 245 -261 . DOI: 10.11983/CBB20209
| 1 | 何福林, 张斌 (2019). 银杏(Ginkgo biloba) GbHsp20基因家族的鉴定及系统进化分析. 分子植物育种 17, 7368-7376. |
| 2 | 黄祥富, 黄上志, 傅家瑞 (1999). 植物热激蛋白的功能及其基因表达的调控. 植物学通报 16, 530-536. |
| 3 | 栗振义, 龙瑞才, 张铁军, 杨青川, 康俊梅 (2016). 植物热激蛋白研究进展. 生物技术通报 32(2), 7-13. |
| 4 | 刘德立 (1996). 植物热激蛋白及其功能. 植物学通报 13, 14-19. |
| 5 | 张宁, 姜晶, 史洁玮 (2017). 番茄HSP20基因家族的全基因组鉴定、系统进化及表达分析. 沈阳农业大学学报 48, 137-144. |
| 6 | 张奇艳, 雷忠萍, 宋银, 海江波, 贺道华 (2019). 陆地棉扩展蛋白基因的鉴定与特征分析. 中国农业科学 52, 3713-3732. |
| 7 | Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004). The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4, 10. |
| 8 | Chen CJ, Chen H, Zhang Y, Thomas HR, Frank MH, He YH, Xia R (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant 13, 1194-1202. |
| 9 | Dafny-Yelin M, Tzfira T, Vainstein A, Adam Z (2008). Non-redundant functions of sHSP-CIs in acquired thermotolerance and their role in early seed development in Arabidopsis. Plant Mol Biol 67, 363-373. |
| 10 | Fan K, Chen YR, Mao ZJ, Fang Y, Li ZW, Lin WW, Zhang YQ, Liu JP, Huang JW, Lin WX (2020a). Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max. BMC Genomics 21, 465. |
| 11 | Fan K, Mao ZJ, Zheng JX, Chen YR, Li ZW, Lin WW, Zhang YQ, Huang JW, Lin WX (2020b). Molecular evolution and expansion of the KUP family in the allopolyploid cotton species Gossypium hirsutum and Gossypium barbadense. Front Plant Sci 11, 545042. |
| 12 | Fan K, Shen H, Bibi N, Li F, Yuan SN, Wang M, Wang XD (2015). Molecular evolution and species-specific expansion of the NAP members in plants. J Integr Plant Biol 57, 673-687. |
| 13 | Fan K, Wang M, Miao Y, Ni M, Bibi N, Yuan SN, Li F, Wang XD (2014). Molecular evolution and expansion analysis of the NAC transcription factor in Zea mays. PLoS One 9, e111837. |
| 14 | Guo CL, Guo RR, Xu XZ, Gao M, Li XQ, Song JY, Zheng Y, Wang XP (2014). Evolution and expression analysis of the grape (Vitis vinifera L.) WRKY gene family. J Exp Bot 6, 1513-1528. |
| 15 | Guo LM, Li J, He J, Liu H, Zhang HM (2020). A class I cytosolic HSP20 of rice enhances heat and salt tolerance in different organisms. Sci Rep 10, 1383. |
| 16 | Guo M, Liu JH, Lu JP, Zhai YF, Wang H, Gong ZH, Wang SB, Lu MH (2015). Genome-wide analysis of the CaHsp20 gene family in pepper: comprehensive sequence and expression profile analysis under heat stress. Front Plant Sci 6, 806. |
| 17 | Ji XR, Yu YH, Ni PY, Zhang GH, Guo DL (2019). Genome-wide identification of small heat-shock protein (HSP20) gene family in grape and expression profile during berry development. BMC Plant Biol 19, 433. |
| 18 | Jiao YN, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain M, McNeal J, Rolf M, Ruzicka DR, Wafula E, Wickett NJ, Wu XL, Zhang Y, Wang J, Zhang YT, Carpenter EJ, Deyholos MK, Kutchan TM, Chanderbali AS, Soltis PS, Stevenson DW, McCombie R, Pires JC, Wong GKS, Soltis DE, DePamphilis DW (2012). A genome triplication associated with early diversification of the core eudicots. Genome Biol 13, R3. |
| 19 | Key JL, Lin CY, Chen YM (1981). Heat shock proteins of higher plants. Proc Natl Acad Sci USA 78, 3526-3530. |
| 20 | Lamesch P, Berardini TZ, Li DH, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40, D1202-D1210. |
| 21 | Li JB, Zhang J, Jia HX, Li Y, Xu XD, Wang LJ, Lu MZ (2016). The Populus trichocarpa PtHSP17.8 involved in heat and salt stress tolerances. Plant Cell Rep 35, 1587-1599. |
| 22 | Li JB, Zhang J, Jia HX, Yue ZQ, Lu MZ, Xin XB, Hu JJ (2018). Genome-wide characterization of the sHsp gene family in Salix suchowensis reveals its functions under different abiotic stresses. Int J Mol Sci 19, 3246. |
| 23 | Li Q, Zhang N, Zhang LS, Ma H (2015). Differential evolution of members of the rhomboid gene family with conservative and divergent patterns. New Phytol 206, 368-380. |
| 24 | Ma W, Guan XY, Li J, Pan RH, Wang LY, Liu FJ, Ma HY, Zhu SJ, Hu J, Ruan YL, Chen XY, Zhang TZ (2019). Mitochondrial small heat shock protein mediates seed germination via thermal sensing. Proc Natl Acad Sci USA 116, 4716-4721. |
| 25 | Ma W, Zhao T, Li J, Liu BL, Fang L, Hu Y, Zhang TZ (2016). Identification and characterization of the GhHsp20 gene family in Gossypium hirsutum. Sci Rep 6, 32517. |
| 26 | Maere S, de Bodt S, Raes J, Casneuf T, van Montagu M, Kuiper M, van de Peer Y (2005). Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci USA 102, 5454-5459. |
| 27 | Ouyang S, Zhu W, Hamilton J, Lin HN, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007). The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35, D883-D887. |
| 28 | Park KC, Kim NS (2010). Intron loss mediated structural dynamics and functional differentiation of the polygalacturonase gene family in land plants. Genes Genom 32, 570-577. |
| 29 | Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016). Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11, 1650-1667. |
| 30 | Sarkar NK, Kim YK, Grover A (2009). Rice sHsp genes: genomic organization and expression profiling under stress and development. BMC Genomics 10, 393. |
| 31 | Scharf KD, Siddique M, Vierling E (2001). The expanding family of Arabidopsis thaliana small heat stress proteins and a new family of proteins containing α-crystallin domains (Acd proteins). Cell Stress Chaperones 6, 225-237. |
| 32 | Shazadee H, Khan N, Wang JJ, Wang CC, Zeng JG, Huang ZY, Wang XY (2019). Identification and expression profiling of protein phosphatases (PP2C) gene family in Gossypium hirsutum L. Int J Mol Sci 20, 1395. |
| 33 | Sun WN, Bernard C, Van De Cotte B, Van Montagu M, Verbruggen N (2010). At-HSP17.6A, encoding a small heat-shock protein in Arabidopsis, can enhance osmotolerance upon overexpression. Plant J 27, 407-415. |
| 34 | The French-Italian Public Consortium for Grapevine Genome Characterization (2007). The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463-467. |
| 35 | van Montfort RLM, Basha E, Friedrich KL, Slingsby C, Vierling E (2001). Crystal structure and assembly of a eukaryotic small heat shock protein. Nat Struct Biol 8, 1025-1030. |
| 36 | Wang L, Zhang SL, Zhang XM, Hu XY, Guo CL, Wang XP, Song JY (2018). Evolutionary and expression analysis of Vitis vinifera OFP gene family. Plant Syst Evol 304, 995-1008. |
| 37 | Wang WX, Vinocur B, Shoseyov O, Altman A (2004). Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci 9, 244-252. |
| 38 | Waters ER, Vierling E (2020). Plant small heat shock proteins—evolutionary and functional diversity. New Phytol 227, 24-37. |
| 39 | Zhai MZ, Sun YD, Jia CX, Peng SB, Liu ZX, Yang GY (2016). Over-expression of JrsHSP17.3 gene from Juglans regia confer the tolerance to abnormal temperature and NaCl stresses. J Plant Biol 59, 549-558. |
| 40 | Zhang K, Han YT, Zhao FL, Hu Y, Gao YR, Ma YF, Zheng Y, Wang YJ, Wen YQ (2015). Genome-wide identification and expression analysis of the CDPK gene family in grape, Vitis spp. BMC Plant Biol 15, 164. |
| 41 | Zhang LS, Chen F, Zhang XT, Li Z, Zhao YY, Lohaus R, Chang XJ, Dong W, Ho SYW, Liu X, Song AX, Chen JH, Guo WL, Wang ZJ, Zhuang YY, Wang HF, Chen XQ, Hu J, Liu YH, Qin Y, Wang K, Dong SS, Liu Y, Zhang SZ, Yu XX, Wu Q, Wang LS, Yan XQ, Jiao YN, Kong HZ, Zhou XF, Yu CW, Chen YC, Li F, Wang JH, Chen W, Chen XL, Jia QD, Zhang C, Jiang YF, Zhang WB, Liu GH, Fu JY, Chen F, Ma H, van de Peer Y, Tang HB (2020a). The water lily genome and the early evolution of flowering plants. Nature 577, 79-84. |
| 42 | Zhang LS, Wu SD, Chang XJ, Wang XJ, Zhao YP, Xia YP, Trigiano RN, Jiao YN, Chen F (2020b). The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. Plant Cell Environ 43, 2847-2856. |
| 43 | Zhang N, Shi JW, Zhao HY, Jiang J (2018). Activation of small heat shock protein (SlHSP17.7) gene by cell wall invertase inhibitor (SlCIF1) gene involved in sugar metabolism in tomato. Gene 679, 90-99. |
| 44 | Zhao P, Wang DD, Wang RQ, Kong NN, Zhang C, Yang CH, Wu WT, Ma HL, Chen Q (2018). Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress. BMC Genomics 19, 61. |
| 45 | Zhu W, Lu MH, Gong ZH, Chen RG (2011). Cloning and expression of a small heat shock protein gene CaHSP24 from pepper under abiotic stress. Afr J Biotechnol 10, 4968-4975. |
| 46 | Zhu YX, Yan HW, Wang YY, Feng L, Chen Z, Xiang Y (2016). Genome duplication and evolution of heat shock transcription factor (HSF) gene family in four model angiosperms. J Plant Growth Regul 35, 903-920. |
| 47 | Zhuo XK, Zheng TX, Zhang ZY, Zhang YC, Jiang LB, Ahmad S, Sun LD, Wang J, Cheng TR, Zhang QX (2018). Genome-wide analysis of the NAC transcription factor gene family reveals differential expression patterns and cold-stress responses in the woody plant Prunus mume. Genes (Basel) 9, 494. |
/
| 〈 |
|
〉 |
Home