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| Genome-wide Identification and Expression Analysis of PIN Gene Family in Dendrobium catenatum |
| WANG Hao1,2, JIANG Wei-Wei1,2, GUO Ying-Chun1,2, SI Jin-Ping1,2,*, CHEN Dong-Hong1,2,* |
1 State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China;
2 National Innovation Alliance of Dendrobium catenatum Industry/Engineering Technology Research Center of Dendrobium catenatum of National Forestry and Grassland Administration, Hangzhou 311300, China |
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Abstract Auxin export carrier PIN-FORMED (PIN) family members mainly mediate auxin polar transport and asymmetric distribution. To better understand Dendrobium catenatum PIN (DcPIN) gene family, the present study performed genome-wide identification of DcPIN members, and further analyzed their phylogenetic relationships, gene structure, protein conserved motifs and domain composition, promoter cis-acting element, and expression profiles of both tissues and stress responses by means of bioinformatics and transcriptome data. The results showed that D. catenatum contained 21 DcPIN members that were divided into 7 clades. Among them, PIN9 clade was specific to monocot and contained high number of DcPIN9 genes in D. catenatum, which might be strongly relevant to its unique lifestyle and living environment. The upstream DcPIN promoters were rich in cis-regulatory elements related to hormones, light, development, and stress response. Transcriptome data showed the expression of DcPIN genes in different tissues could be totally divided into specific expression and constitutive expression. Transcriptome and qRT-PCR analysis under different treatments showed DcPIN1a/9a/9d/9g were in response to cold, DcPIN9a/9f/9h in response to drought, DcPIN3a/9a/9d/9h in response to JA, and DcPIN1c/3a/9a in response to the infection of Southern Blight pathogen Sclerotium delphinii. This result provides a theoretical basis for further investigating the function of D. catenatum PIN genes in the growth and development and environmental adaptation.
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Received: 17 February 2021
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Corresponding Authors:
* donghong.chen@zafu.edu.cn; lssjp@163.com
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[1] Bielach A, Hrtyan M, Tognetti V B.2017. Plants under stress: Involvement of auxin and cytokinin[J]. International Journal of Molecular Sciences, 18(7): 1427.
[2] Cazzonelli C I, Vanstraelen M, Simon S, et al.2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development[J]. PLOS ONE, 8: e70069.
[3] Chen Q Y, Chen D H, Shi Y, et al.2019. Occurrence regularity of Dendrobium catenatum southern blight disease[J]. China Journal of Chinese Materia Medica, 44(09): 1789-1792. (in Chinese)
[4] Chen C, Chen H, Zhang Y, et al.2020a. TBtools: An integrative tool kit developed for interactive analyses of big biological data[J]. Molecular Plant, 13(8): 1194-1202.
[5] Chen D H, Qiu H L, Huang Y, et al.2020b. Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum[J]. BMC Plant Biology, 20(1): 40.
[6] Dal Bosco C, Dovzhenko A, Liu X, et al.2012. The endoplasmic reticulum localized PIN8 is a pollen-specific auxin carrier involved in intracellular auxin homeostasis[J]. Plant Journal, 71(5): 860-870.
[7] Friml J.2003. Auxin transport-shaping the plant[J]. Current Opinion in Plant Biology, 6(1): 7-12.
[8] Galweiler L, Guan C, Muller A, et al.1998. Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue[J]. Science, 282(5397): 2226-2230.
[9] Gales C, Kowalski-Chauvel A, Dufour M N, et al.2000. Mutation of Asn-391 within the conserved NPXXY motif of the cholecystokinin B receptor abolishes Gq protein activation without affecting its association with the receptor[J]. Journal of Biological Chemistry, 275(23): 17321-17327.
[10] Ganguly A, Park M, Kesawat M S, et al.2014. Functional analysis of the hydrophilic loop in intracellular trafficking of Arabidopsis PIN-FORMED proteins[J]. Plant Cell, 26(4): 1570-1585.
[11] He P, Zhao P, Wang L, et al.2017. The PIN gene family in cotton (Gossypium hirsutum): Genome-wide identification and gene expression analyses during root development and abiotic stress responses[J]. BMC Genomics 18(1): 507.
[12] Kim D, Langmead B, Salzberg S L.2015. HISAT: A fast spliced aligner with low memory requirements[J]. Nature Methods, 12(4): 357-360.
[13] Korver R A, Koevoets I T, Testerink C.2018. Out of shape during stress: A key role for auxin[J]. Trends in Plant Science, 23(9): 783-793.
[14] Krecek P, Skupa P, Libus J, et al.2009. The PIN-FORMED (PIN) protein family of auxin transporters[J]. Genome Biology, 10(12): 249.
[15] Krogh A, Larsson B, von Heijne G, et al.2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes[J]. Journal of Molecular Biology, 305(3): 567-580.
[16] Kumar S, Stecher G, Tamura K.2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Molecular Biology and Evolution, 33(7): 1870-1874.
[17] Lee H, Ganguly A, Lee R D, et al.2020. Intracellularly localized PIN-FORMED8 promotes lateral root emergence in Arabidopsis[J]. Frontiers in Plant Science, 10: 1808.
[18] Li G, Song H, Li B, et al.2015. Auxin Resistant1 and PIN-FORMED2 protect lateral root formation in Arabidopsis under iron stress[J]. Plant Physiology, 169(4): 2608-2623.
[19] Li Y, Zhu J, Wu L, et al.2019. Functional divergence of PIN1 paralogous genes in rice[J]. Plant & Cell Physiology, 60(12): 2720-2732.
[20] Lu G, Coneva V, Casaretto J A, et al.2015. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution[J]. Plant Journal, 83(5): 913-925.
[21] Mravec J, Skupa P, Bailly A, et al.2009. Subcellular homeostasis of phytohormone auxin is mediated by the ER-localized PIN5 transporter[J]. Nature, 459(7250): 1136-1140.
[22] Okada K, Ueda J, Komaki MK, et al.1991. Requirement of the auxin polar transport system in early stages of Arabidopsis floral bud formation[J]. Plant Cell, 3(7): 677-684.
[23] Paponov I A, Teale W D, Trebar M, et al.2005. The PIN auxin efflux facilitators: Evolutionary and functional perspectives[J]. Trends in Plant Science, 10(4): 170-177.
[24] Pasternak T, Potters G, Caubergs R, et al.2005. Complementary interactions between oxidative stress and auxins control plant growth responses at plant, organ, and cellular level[J]. Journal of Experimental Botany, 56(418): 1991-2001.
[25] Pertea M, Pertea G M, Antonescu C M, et al.2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J]. Nature Biotechnology, 33(3): 290-295.
[26] Rahman A.2013. Auxin: A regulator of cold stress response[J]. Physiologia Plantarum, 147(1): 28-35.
[27] Shen C, Bai Y, Wang S, et al.2010. Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress[J]. FEBS Journal, 277(14): 2954-2969.
[28] Shen C, Yue R, Bai Y, et al.2015. Identification and analysis of Medicago truncatula auxin transporter gene families uncover their roles in responses to Sinorhizobium meliloti infection[J]. Plant & Cell Physiology, 56(10): 1930-1943.
[29] Shibasaki K, Uemura M, Tsurumi S, et al.2009. Auxin response in Arabidopsis under cold stress: Underlying molecular mechanisms[J]. Plant Cell, 21(12): 3823-3838.
[30] Si J P, Zhang Y, Luo Y B, et al.2017. Herbal textual research on relationship between Chinese medicine "Shihu" (Dendrobium spp.) and "Tiepi Shihu" (D. catenatum)[J]. China Journal of Chinese Materia Medica, 42(10): 2001-2005. (in Chinese)
[31] Sun J, Chen Q, Qi L, et al.2011. Jasmonate modulates endocytosis and plasma membrane accumulation of the Arabidopsis PIN2 protein[J]. New Phytologist, 191(2): 360-375.
[32] Sun P, Tian Q Y, Chen J, et al.2010. Aluminium-induced inhibition of root elongation in Arabidopsis is mediated by ethylene and auxin[J]. Journal of Experimental Botany, 61(2): 347-356.
[33] Tang H, Zhao T, Sheng Y, et al.2017. Dendrobium officinale Kimura et Migo: A review on its ethnopharmacology, phytochemistry, pharmacology, and industrialization[J]. Evidence-Based Complementary and Alternative Medicine, 2017: 7436259.
[34] Viaene T, Delwiche C F, Rensing S A, et al.2013. Origin and evolution of PIN auxin transporters in the green lineage[J]. Trends in Plant Science, 18(1): 5-10.
[35] Wang J R, Hu H, Wang G H, et al.2009. Expression of PIN genes in rice (Oryza sativa L.): Tissue specificity and regulation by hormones[J]. Molecular Plant, 2(4): 823-831.
[36] Wang L, Guo M, Li Y, et al.2018. LARGE ROOT ANGLE1, encoding OsPIN2, is involved in root system architecture in rice[J]. Journal of Experimental Botany, 69(3): 385-397.
[37] Wang Y, Chai C, Valliyodan B, et al.2015. Genome-wide analysis and expression profiling of the PIN auxin transporter gene family in soybean (Glycine max)[J]. BMC Genomics, 16: 951.
[38] Wisniewska J, Xu J, Seifertova D, et al.2006. Polar PIN localization directs auxin flow in plants[J]. Science, 312(5775): 883.
[39] Wu Z G, Jiang W, Chen S L, et al.2016. Insights from the cold transcriptome and metabolome of Dendrobium officinale: Global reprogramming of metabolic and gene regulation networks during cold acclimation[J]. Frontiers in Plant Science, 7: 1653.
[40] Xu M, Zhu L, Shou H, et al.2005. A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice[J]. Plant & Cell Physiology, 46: 1674-1681.
[41] Yu C, Dong W, Zhan Y, et al.2017. Genome-wide identification and expression analysis of ClLAX, ClPIN and ClABCB genes families in Citrullus lanatus under various abiotic stresses and grafting[J]. BMC Genetics, 18(1): 33.
[42] Yue R, Tie S, Sun T, et al.2015. Genome-wide identification and expression profiling analysis of ZmPIN, ZmPILS, ZmLAX and ZmABCB auxin transporter gene families in maize (Zea mays L.) under various abiotic stresses[J]. PLOS ONE, 10: e0118751.
[43] Zazimalova E, Krecek P, Skupa P, et al.2007. Polar transport of the plant hormone auxin-the role of PIN-FORMED (PIN) proteins[J]. Cellular and Molecular Life Sciences, 64(13): 1621-1637.
[44] Zhang C, Dong W, Huang Z A, et al.2018. Genome-wide identification and expression analysis of the CaLAX and CaPIN gene families in pepper (Capsicum annuum L.) under various abiotic stresses and hormone treatments[J]. Genome, 61(2): 121-130.
[45] Zhang G Q, Xu Q, Bian C, et al.2016. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution[J]. Scientific Reports, 6: 19029.
[46] Zhu Y, Si J, Guo B, et al.2010. Quantitive variation of polysaccharides content in cultivated Dendrobium candidum[J]. China Journal of Chinese Materia Medica, 35: 427-430. (in Chinese)
[47] Zou L H, Wan X, Deng H, et al.2018. RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium candidum[J]. Scientific Data, 5: 180252. |
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