Identification of bHLH transcription factors in moso bamboo (<i>Phyllostachys edulis</i>) and their expression analysis under drought and salt stress

Xu Xiu-Rong; Yang Ke-Bin; Wang Si-Ning; Gao Zhi-Min

doi:10.11913/PSJ.2095-0837.2019.50610

Plant Science Journal > 2019 > 37(5): 610-620. > DOI: 10.11913/PSJ.2095-0837.2019.50610 CSTR: 32231.14.PSJ.2095-0837.2019.50610

Xu Xiu-Rong, Yang Ke-Bin, Wang Si-Ning, Gao Zhi-Min. Identification of bHLH transcription factors in moso bamboo (Phyllostachys edulis) and their expression analysis under drought and salt stress[J]. Plant Science Journal, 2019, 37(5): 610-620. DOI: 10.11913/PSJ.2095-0837.2019.50610

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Identification of bHLH transcription factors in moso bamboo (Phyllostachys edulis) and their expression analysis under drought and salt stress

State Forestry Administration/Beijing Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China

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This work was supported by a grant from the Sub-Project of the National Science and Technology Support Plan of the Twelfth Five-Year in China (2015BAD04B0101).

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Received Date: February 14, 2019
Available Online: October 31, 2022
Published Date: October 27, 2019

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Abstract

The transcription factors of the bHLH family have important regulatory effects on plant growth and development. Here, Phyllostachys edulis (Carr.) Lehaie was used as experimental material to understand the characteristics of bHLH family members in bamboo and explore their expression patterns under adverse conditions. Bioinformatics were used to identify and systematically analyze the bHLH family members at the genomic level, and their expression patterns in different tissues and expression of several bHLH genes under high salt and drought stress conditions were further analyzed. Our results identified 153 bHLH transcription factor genes (PebHLH001-PebHLH153) with complete conserved domains in Ph. edulis. The number of introns in PebHLHs ranged from 0 to 14. The drought and salt stress related cis-acting elements were found in the promoters of 137 PebHLHs. The length of the proteins encoded by PebHLHs ranged from 134 aa (PebHLH005) to 1401 aa (PebHLH083) with molecular weights of 13.4 to 152.6 kD, respectively. Based on phylogenetic analysis of bHLHs in Ph. edulis and Oryza sativa L., 153 PebHLHs were clustered into 17 subgroups, with the C subgroup containing the highest number (42). According to expression profile analysis of transcriptome data, 151 PebHLHs exhibited different expression levels in different tissues and growth stages of Ph. edulis. Real-time quantitative polymerase chain reaction (PCR) showed that 14 PebHLHs were up-regulated and two PebHLHs were down-regulated after drought stress, whereas 13 were up-regulated and three were down-regulated after salt stress. However, there were some differences in the expression patterns of 16 PebHLHs, indicating that they may play different roles in response to drought and salt stress.
- Phyllostachys edulis,
- bHLH gene family,
- Gene identification,
- Stress,
- Expression analysis

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References (38)

References

[1]	Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family[J]. Plant Cell, 2003, 15(8):1749-1770.
[2]	Murre C, Mccaw PS, Baltimore D. A new DNA binding and dimerization motif in immunoglobulin enhancer bin-ding, daughterless, MyoD, and myc proteins[J]. Cell, 1989, 56(5):777-783.
[3]	Atchley WR, Terhalle W, Dress A. Positional dependence, cliques, and predictive motifs in the bHLH protein domain[J]. J Mol Evol, 1999, 48(5):501-516.
[4]	Sailsbery JK, Dean RA. Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites[J]. BMC Evol Biol, 2012, 12(1):154.
[5]	Li XX, Duan XP, Jiang HX, Sun YJ, Tang YP, et al. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis[J]. Plant Physiol, 2006, 141(4):1167-1184.
[6]	Bailey PC, Martin C, Toledo-Ortiz G, Quail PH, Huq E, et al. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana[J]. Plant Cell, 2003, 15(11):2497-2502.
[7]	Song XM, Huang ZN, Duan WK, Ren J, Liu TK, et al. Genome-wide analysis of the bHLH transcription factor family in Chinese cabbage (Brassica rapa L. ssp. Peki-nensis (Lour.) Olsson)[J]. Mol Genet Genomics, 2014, 289(1):77-91.
[8]	Niu X, Guan YX, Chen SK, Li HF. Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon[J]. BMC Genomics, 2017, 18(1):619.
[9]	Mao K, Dong QL, Li C, Liu CH, Ma FW. Genome wide identification and characterization of apple bHLH transcription factors and expression analysis in response to drought and salt stress[J]. Front Plant Sci, 2017, 8:480.
[10]	Kondou Y, Nakazawa M, Kawashima M, Ichikawa T, Yoshizumi T, et al. RETARDED GROWTH OF EMBRYO1, a new basic helix-loop-helix protein, expresses in endosperm to control embryo growth[J]. Plant Physiol, 2008, 147(4):1924-1935.
[11]	Arnaud N, Girin T, Sorefan K, Fuentes S, Wood TA, et al. Gibberellins control fruit patterning in Arabidopsis thaliana[J]. Genes Dev, 2010, 24(19):2127-2132.
[12]	Heisler MG, Atkinson A, Bylstra YH, Walsh R, Smyth DR. SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein[J]. Development, 2001, 128(7):1089-1098.
[13]	Sorensen AM, Kröber S, Unte US, Huijser P, Dekker K, et al. The Arabidopsis ABORTED MICROSPORES (AMS) gene encodes a MYC class transcription factor[J]. Plant J, 2010, 33(2):413-423.
[14]	何洁, 顾秀容, 魏春华, 杨小振, 李好, 等. 西瓜bHLH转录因子家族基因的鉴定及其在非生物胁迫下的表达分析[J]. 园艺学报, 2016, 43(2):281-294. He J, Gu XR, Wei CH, Yang XZ, Li H, et al. Identification and expression analysis under abiotic stresses of the bHLH transcription factor gene family in watermelon[J]. Acta Horticulturae Sinica, 2016, 43(2):281-294.
[15]	Cui X, Wang YX, Liu ZW, Wang WL, Li H, et al. Transcriptome-wide identification and expression profile analysis of the bHLH family genes in Camellia sinensis[J]. Funct Integr Genomics, 2018, 18(5):489-503.
[16]	Zhai Y, Zhang L, Xia C, Fu S, Zhao G, et al. The wheat transcription factor, TabHLH39, improves tolerance to multiple abiotic stressors in transgenic plants[J]. Biochem Biophys Res Commun, 2016, 473(4):1321-1327.
[17]	Wang FB, Zhu H, Chen DH, Li ZJ, Peng RH, et al. A grape bHLH transcription factor gene, VvbHLH1, increases the accumulation of flavonoids and enhances salt and drought tolerance in transgenic Arabidopsis thaliana[J]. Plant Cell Tiss Organ Cult, 2016, 125(2):387-398.
[18]	Peng ZH, Lu Y, Li LB, Zhao Q, Feng Q, et al. The draft genome of the fast growing non-timber forest species moso bamboo (Phyllostachys heterocycla)[J]. Nat Genet, 2013, 45(4):456-461.
[19]	Wu M, Liu HL, Han GM, Cai RH, Pan F, et al. A moso bamboo WRKY gene PeWRKY83 confers salinity tolerance in transgenic Arabidopsis plants[J]. Sci Rep, 2017, 7(1):11721.
[20]	Li L, Mu SH, Cheng ZC, Cheng YW, Zhang Y, et al. Characterization and expression analysis of the WRKY gene family in moso bamboo[J]. Sci Rep, 2017, 7(1):6675.
[21]	Wu HL, Lü H, Li L, Liu J, Mu SH, et al. Genome-wide analysis of the AP2/ERF transcription factors family and the expression patterns of DREB genes in moso bamboo (Phyllostachys edulis)[J]. PLoS One, 2015, 10(5):e0126657.
[22]	Yang KB, Li Y, Wang SN, Xu XR, Sun HY, et al. Genome-wide identification and expression analysis of the MYB transcription factor in moso bamboo (Phyllostachys edulis)[J]. PeerJ, 2019, 6:e6242.
[23]	Wu M, Li Y, Chen D, Liu H, Zhu DY, et al. Genome-wide identification and expression analysis of the IQD gene fa-mily in moso bamboo (Phyllostachys edulis)[J]. Sci Rep, 2016, 6:24520.
[24]	Pan F, Wang Y, Liu HL, Wu M, Chu WY, et al. Genome-wide identification and expression analysis of SBP-like transcription factor genes in moso bamboo (Phyllostachys edulis)[J]. BMC Genomics, 2017, 18(1):486.
[25]	Zhang YT, Tang DQ, Lin XC, Ding MQ, Tong ZK. Genome-wide identification of MADS-box family genes in moso bamboo (Phyllostachys edulis) and a functional analysis of PeMADS5 in flowering[J]. BMC Plant Biol, 2018, 18(1):176.
[26]	何龙燕, 刘武阳, 娄永峰, 肖复明. 毛竹GRF转录因子家族的全基因组鉴定与分析[J]. 植物科学学报, 2018, 36(5):713-720. He LY, Liu WY, Lou YF, Xiao FM. Genome wide identication and analysis of the GRF transcription factor family in moso bamboo (Phyllostachys edulis)[J]. Plant Science Journal, 2018, 36(5):713-720.
[27]	郭安源, 朱其慧, 陈新, 罗静初. GSDS:基因结构显示系统[J]. 遗传, 2007, 29(8):1023-1026. Guo AY, Zhu QH, Chen X, Luo JC. GSDS:a gene structure display server[J]. Hereditas, 2007, 29(8):1023-1026.
[28]	Liu HL, Wu M, Li F, Gao YM, Chen F, Xiang Y. TCP transcription factors in moso bamboo (Phyllostachys edulis):Genome-wide identification and expression analysis[J]. Front Plant Sci, 2018, 9:1263.
[29]	Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J]. Nucleic Acids Res, 2002, 30(1):325-327.
[30]	Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, et al. ExPASy:SIB bioinformatics resource portal[J]. Nucleic Acids Res, 2012, 40:597-603.
[31]	Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. MEME SUITE:tools for motif discovery and searching[J]. Nucleic Acids Res, 2009, 37:202-208.
[32]	Fan CJ, Ma JM, Guo QR, Li XT, Wang H, et al. Selection of reference genes for real-time quantitative PCR in bamboo (Phyllostachys edulis)[J]. PLoS One, 2013, 8(2):e56573.
[33]	Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2^-ΔΔCt Method[J]. Methods, 2001, 25(4):402-408.
[34]	赵广枝, 孙化雨, 赵韩生, 高志民. 毛竹基因组测序及数据应用研究现状[J]. 世界竹藤通讯, 2015, 13(3):8-13. Zhao GZ, Sun HY, Zhao HS, Gao ZM. Research status of genomic sequencing and data application of Phyllostachys edulis[J]. World Bamboo and Rattan, 2015, 13(3):8-13.
[35]	Zhao HS, Gao ZM, Wang L, Wang JL, Wang SB, et al. Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)[J]. Gigascience, 2018, 7(10):1-12.
[36]	Chen XR, Xiong R, Liu HL, Wu M, Chen F, et al. Basic helix-loop-helix gene family:Genome wide identification, phylogeny, and expression in moso bamboo[J]. Plant Physiol Bioch, 2018, 132(11):104-119.
[37]	Yamaguchi-Shinozaki K, Shinozaki K. The plant hormone abscisic acid mediates the drought-induced expression but not the seed-specific expression of rd22, a gene responsive to dehydration stress in Arabidopsis thaliana[J]. Mol Gen Genet, 1993, 238(1-2):17-25.
[38]	王昕嘉, 李昆志. 植物bHLH转录因子参与非生物胁迫信号通路研究进展[J]. 生命科学, 2015, 27(2):209-216. Wang XJ, Li KZ. Progress of plant bHLH transcription factors involved in abiotic stress signaling pathways[J]. Chinese Bulletin of Life Sciences, 2015, 27(2):209-216.

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Identification of bHLH transcription factors in moso bamboo (Phyllostachys edulis) and their expression analysis under drought and salt stress

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