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| Identification and Expression Analysis of NAC Gene Family in Castor (Ricinus communis) |
| LI Yan-Xiao1, XIANG Dian-Jun1,*, MAN Li-Li2, LIU Peng1 |
1 College of Agriculture, Inner Mongolia Minzu University, Tongliao 028000, China;
2 College of Life Science and Food Engineering, Inner Mongolia Minzu University, Tongliao 028000, China |
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Abstract As a unique transcriptional regulator of terrestrial plants, NAC transcription factors play an active role in plant adaptation to environment and stress resistance. In this study, a total of 74 NAC transcription factors unevenly distributed on 10 chromosomes were identified in the whole genome of castor (Ricinus communis) by bioinformatics methods, and 13 intergenic replications occurred. Phylogenetic analysis showed that RcNACs and Arabidopsis?thaliana NACs were divided into 8 subclusters, and each subcluster contained a NAM domain and a conserved motif 2, and the gene composition structure was similar. A total of 15 stress-related, hormone-responsive and growth-related promoter elements were identified in the promoter region of RcNACs. The tissue expression profile showed that the 54 RcNACs detected had obvious tissue expression specificity in castor, and 39.8% of the members were highly expressed in the male flowers of castor. The stress expression profile showed that 47.3% and 49.1% of the 61 RcNACs were up-regulated in the early stage of salt and drought stress, respectively, except for 6 genes that did not respond to drought stress and salt stress; the low-temperature expression profile showed that 64.1% of the 39 RcNACs were up-regulated in the early stage of stress. The results of qRT-RCR detection under low-temperature stress showed that 10 RcNACs responded to low-temperature for a long time, and most genes had bimodal expression patterns and peaked at 72 h, indicating that RcNACs were the response genes of castor under stress. This study can provide a theoretical reference for the regulation of RcNACs in castor abiotic stress.
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Received: 16 September 2022
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Corresponding Authors:
*xiangdianjun00@126.com
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[1] 韩雯毓, 李国瑞, 风兰, 等, 2020. 蓖麻GRAS转录因子家族的全基因组分析及逆境胁迫响应[J]. 植物遗传资源学报, 21(01): 252-259.
(Han W Y, Li G R, Feng L, et al.2020. Genome-wide analysis of GRAS transcription factors in Ricinus communis and response to abiotic stresses[J]. Journal of Plant Genetic Resources, 21(01): 252-259.)
[2] 孙利军, 周佳婧, 韩笑, 等. 2022. 番茄抗逆相关NAC基因对非生物胁迫的响应[J]. 南通大学学报(自然科学版) , 21(04): 64-70.
(Sun L J, Zhou J Q, Han X, et al.2022. Stress relative NAC genes in tomato response to abiotic stresses[J]. Journal of Nantong University (Natural Science Edition), 21(04): 64-70.)
[3] 张欢, 杨乃科, 商丽丽, 等. 2020. 甘薯抗旱相关基因IbNAC72的克隆与功能分析[J]. 作物学报, 46(11): 1649-1658.
(Zhang H, Yang N K, Shang L L, et al.2020. Cloning and functional analysis of a drought tolerance-related gene IbNAC72 in sweet potato[J]. Acta Agronomica Sinica, 46(11): 1649-1658.)
[4] 朱国立, 吴国林, 李金芹, 等,2004. 通辽市蓖麻生产现状及发展产业化对策[J]. 内蒙古农业科技,(S1): 33-34, 46.
(Zhu G L, Wu G L, Li J Q, et al.2004. Production status and development industrialization countermeasures of castor in Tongliao city[J]. Journal of Northern Agriculture,(S1): 33-34, 46.)
[5] Aida M, Ishida T, Fukaki H, et al.1997. Genes involved in organ separation in Arabidopsis: An analysis of the cup-shaped cotyledon mutant[J]. Plant Cell, 9(6): 841-857.
[6] Brown A P, Kroon J T M, Swarbreck D, et al.2012. Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways[J]. PLOS ONE, 7(2): e30100.
[7] Cipriano T D M, Morais A T, Aragão F J L.2013. Characterization of a pollen-specific and desiccation-associated AP2/ERF type transcription factor gene from castor bean (Ricinus communis L.)[J]. International Journal of Plant Biology, 4(1): e1.
[8] Diao W P, Snyder J C, Wang S B, et al.2018. Genome-wide analyses of the NAC transcription factor gene family in pepper (Capsicum annuum L.): Chromosome location, phylogeny, structure, expression patterns, cis-elements in the promoter, and interaction network[J]. International Journal of Molecular Sciences, 19(4): 1028.
[9] Guo W L, Wang S B, Chen R G, et al.2015. Characterization and expression profile of CaNAC2 pepper gene[J]. Frontiers in Plant Science, 6: 755.
[10] Han W Y, Li G R, Feng L, et al.2019. Genome-wide characterization analysis of WOX transcription factors and response to abiotic stresses in Ricinus communis L[J]. Journal of Nuclear Agricultural Sciences, 33(10): 1921.
[11] He L, Xu J Y, Wang Y C, et al.2018. Transcription factor ANAC074 binds to NRS1, NRS2, or MybSt1 element in addition to the NACRS to regulate gene expression[J]. International Journal of Molecular Sciences, 19(10): 3271.
[12] He X J, Mu R L, Cao W H, et al.2005. AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development[J]. The Plant Journal, 44(6): 903-916.
[13] Hu H C, Ma L, Chen X, et al.2022. Genome-wide identification of the NAC gene family in Zanthoxylum bungeanum and their transcriptional responses to drought stress[J]. International Journal of Molecular Sciences, 23(9): 4769.
[14] Hu H H, You J, Fang Y J, et al.2008. Characterization of transcription factor gene SNAC2 conferring cold and salt tolerance in rice[J]. Plant Molecular Biology, 67(1): 169-181.
[15] Hussey S G, Mizrachi E, Spokevicius A V, et al.2011. SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus[J]. BMC Plant Biology, 11(1): 1-17.
[16] Janz D, Behnke K, Schnitzler J P, et al.2010. Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms[J]. BMC Plant Biology, 10(1): 1-17.
[17] Jensen M K, Kjaersgaard T, Nielsen M M, et al.2010. The Arabidopsis thaliana NAC transcription factor family: Structure-function relationships and determinants of ANAC019 stress signalling[J]. Biochemical Journal, 426(2): 183-196.
[18] Jin Z W, Xu W, Liu A Z, 2014. Genomic surveys and expression analysis of bZIP gene family in castor bean (Ricinus communis L.)[J]. Planta, 239(2): 299-312.
[19] Kikuchi K, Ueguchi-Tanaka M, Yoshida K T, et al.2000. Molecular analysis of the NAC gene family in rice[J]. Molecular and General Genetics MGG, 262(6): 1047-1051.
[20] Kim Y S, Kim S G, Park J E, et al.2006. A membrane-bound NAC transcription factor regulates cell division in Arabidopsis[J]. The Plant Cell, 18(11): 3132-3144.
[21] Lindemose S, Jensen M K, Vande V J, et al.2014. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana[J]. Nucleic Acids Research, 42(12): 7681-7693.
[22] Liu L, White M J, Macrae T H.1999. Transcription factors and their genes in higher plants functional domains, evolution and regulation[J]. European Journal of Biochemistry, 262(2): 247-257.
[23] Liu M Y, Ma Z T, Sun W J, et al.2019. Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)[J]. BMC Genomics, 20(1): 1-16.
[24] Liu T K, Song X M, Duan W K, et al.2014. Genome-wide analysis and expression patterns of NAC transcription factor family under different developmental stages and abiotic stresses in Chinese cabbage[J]. Plant Molecular Biology Reporter, 32(5): 1041-1056.
[25] Lu J J, Pan C, Fan W, et al.2021. A chromosome-level assembly of a wild castor genome provides new insights into the adaptive evolution in a tropical desert[J]. Genomics, Proteomics & Bioinformatics, 20(1): 42-59.
[26] Nuruzzaman M, Manimekalai R, Sharoni A M, et al.2010. Genome-wide analysis of NAC transcription factor family in rice[J]. Gene, 465(1-2): 30-44.
[27] Ooka H, Satoh K, Doi K, et al. 2003. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana[J]. DNA Research, 10(6): 239-247.
[28] Prince V E, Pickett F B, 2002. Splitting pairs: The diverging fates of duplicated genes[J]. Nature Reviews Genetics, 3(11): 827-837.
[29] Puranik S, Sahu P P, Srivastava P S, et al.2012. NAC proteins: Regulation and role in stress tolerance[J]. Trends in Plant Science, 17(6): 369-381.
[30] Ran X, Wang X, Gao X K, et al.2021. Effects of salt stress on the photosynthetic physiology and mineral ion absorption and distribution in white willow (Salix alba L.)[J]. PLOS ONE, 16(11): e0260086.
[31] Riaño-Pachón D M, Ruzicic S, Dreyer I, et al.2007. PlnTFDB: An integrative plant transcription factor database[J]. BMC Bioinformatics, 8(1): 1-10.
[32] Schneeberger K, Ossowski S, Ott F, et al.2011. Reference-guided assembly of four diverse Arabidopsis thaliana genomes[J]. Proceedings of the National Academy of Sciences of the USA, 108(25): 10249-10254.
[33] Singh S, Kudapa H, Garg V, et al.2021. Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops[J]. BMC Genomics, 22(1): 1-23.
[34] Souer E, Houwelingen A V, Kloos D, et al.1996. The no apical meristem gene of Petunia is required for pattern formation in embryos and flowers and is expressed at meristem and primordia boundaries[J]. Cell, 85(2): 159-170.
[35] Su H Y, Zhang S Z, Yuan X W, et al.2013. Genome-wide analysis and identification of stress-responsive genes of the NAM-ATAF1, 2-CUC2 transcription factor family in apple[J]. Plant Physiology and Biochemistry, 71: 11-21.
[36] Wang X Y, Liu Z W, Wu Z J, et al.2016. Transcriptome-wide identification and expression analysis of the NAC gene family in tea plant[Camellia sinensis (L.) O. Kuntze][J]. PLOS ONE, 11(11): e0166727.
[37] Wray G A, Hahn M W, Abouheif E, et al.2003. The evolution of transcriptional regulation in eukaryotes[J]. Molecular Biology and Evolution, 20(9): 1377-1419.
[38] Xie Q, Frugis G, Colgan D, et al.2000. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development[J]. Genes & Development, 14(23): 3024-3036.
[39] Xu Z Y, Kim S Y, Hyeon DO Y, et al.2013. The Arabidopsis NAC transcription factor ANAC096 cooperates with bZIP-type transcription factors in dehydration and osmotic stress responses[J]. The Plant Cell, 25(11): 4708-4724.
[40] Yu A M, Wang Z Q, Zhang Y, et al.2019. Global gene expression of seed coat tissues reveals a potential mechanism of regulating seed size formation in castor bean[J]. International Journal of Molecular Sciences, 20(6): 1282.
[41] Zhang H, Jin J P, Tang L, et al.2011. PlantTFDB 2.0: Update and improvement of the comprehensive plant transcription factor database[J]. Nucleic Acids Research, 39(suppl_1): D1114-D1117. |
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