Genome-wide identification, characterization and expression pattern analysis of TIFY family members in Artemisia argyi.
Artemisia
/ genetics
Plant Proteins
/ genetics
Phylogeny
Gene Expression Regulation, Plant
Multigene Family
Gene Expression Profiling
Stress, Physiological
/ genetics
Genome, Plant
Transcription Factors
/ genetics
Plant Growth Regulators
/ metabolism
Promoter Regions, Genetic
Chromosomes, Plant
/ genetics
Artemisia argyi
Abiotic stress
Gene expression
Phytohormone treatment
TIFY
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
03 Oct 2024
03 Oct 2024
Historique:
received:
06
05
2024
accepted:
30
09
2024
medline:
4
10
2024
pubmed:
4
10
2024
entrez:
3
10
2024
Statut:
epublish
Résumé
Plant-specific TIFY proteins play crucial roles in regulating plant growth, development, and various stress responses. However, there is no information available about this family in Artemisia argyi, a well-known traditional medicinal plant with great economic value. A total of 34 AaTIFY genes were identified, including 4 TIFY, 22 JAZ, 5 PPD, and 3 ZML genes. Structural, motif scanning, and phylogenetic relationships analysis of these genes revealed that members within the same group or subgroup exhibit similar exon-intron structures and conserved motif compositions. The TIFY genes were unevenly distributed across the 15 chromosomes. Tandem duplication events and segmental duplication events have been identified in the TIFY family in A. argyi. These events have played a crucial role in the gene multiplication and compression of different subfamilies within the TIFY family. Promoter analysis revealed that most AaTIFY genes contain multiple cis-elements associated with stress response, phytohormone signal transduction, and plant growth and development. Expression analysis of roots and leaves using RNA-seq data revealed that certain AaTIFY genes showed tissue-specific expression patterns, and some AaTIFY genes, such as AaTIFY19/29, were found to be involved in regulating salt and saline-alkali stresses. In addition, RT-qPCR analysis showed that TIFY genes, especially AaTIFY19/23/27/29, respond to a variety of hormonal treatments, such as MeJA, ABA, SA, and IAA. This suggested that TIFY genes in A. argyi regulate plant growth and respond to different stresses by following different hormone signaling pathways. Taken together, our study conducted a comprehensive identification and analysis of the TIFY gene family in A. argyi. These findings suggested that TIFY might play an important role in plant development and stress responses, which laid a valuable foundation for further understanding the function of TIFY genes in multiple stress responses and phytohormone crosstalk in A. argyi.
Sections du résumé
BACKGROUND
BACKGROUND
Plant-specific TIFY proteins play crucial roles in regulating plant growth, development, and various stress responses. However, there is no information available about this family in Artemisia argyi, a well-known traditional medicinal plant with great economic value.
RESULTS
RESULTS
A total of 34 AaTIFY genes were identified, including 4 TIFY, 22 JAZ, 5 PPD, and 3 ZML genes. Structural, motif scanning, and phylogenetic relationships analysis of these genes revealed that members within the same group or subgroup exhibit similar exon-intron structures and conserved motif compositions. The TIFY genes were unevenly distributed across the 15 chromosomes. Tandem duplication events and segmental duplication events have been identified in the TIFY family in A. argyi. These events have played a crucial role in the gene multiplication and compression of different subfamilies within the TIFY family. Promoter analysis revealed that most AaTIFY genes contain multiple cis-elements associated with stress response, phytohormone signal transduction, and plant growth and development. Expression analysis of roots and leaves using RNA-seq data revealed that certain AaTIFY genes showed tissue-specific expression patterns, and some AaTIFY genes, such as AaTIFY19/29, were found to be involved in regulating salt and saline-alkali stresses. In addition, RT-qPCR analysis showed that TIFY genes, especially AaTIFY19/23/27/29, respond to a variety of hormonal treatments, such as MeJA, ABA, SA, and IAA. This suggested that TIFY genes in A. argyi regulate plant growth and respond to different stresses by following different hormone signaling pathways.
CONCLUSION
CONCLUSIONS
Taken together, our study conducted a comprehensive identification and analysis of the TIFY gene family in A. argyi. These findings suggested that TIFY might play an important role in plant development and stress responses, which laid a valuable foundation for further understanding the function of TIFY genes in multiple stress responses and phytohormone crosstalk in A. argyi.
Identifiants
pubmed: 39363209
doi: 10.1186/s12864-024-10856-4
pii: 10.1186/s12864-024-10856-4
doi:
Substances chimiques
Plant Proteins
0
Transcription Factors
0
Plant Growth Regulators
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
925Subventions
Organisme : the Key Scientific Research Project of Higher Education Institutions in Henan Province
ID : 22A360012
Organisme : Key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources
ID : 2060302
Organisme : Chinese herbal medicine industry technology system of Henan Province
ID : Yucaike [2024]8
Informations de copyright
© 2024. The Author(s).
Références
Shikata M, Matsuda Y, Ando K, Nishii A, Takemura M, Yokota A, Kohchi T. Characterization of Arabidopsis ZIM, a member of a novel plant-specific GATA factor gene family. J Exp Bot. 2004;55(397):631–9.
pubmed: 14966217
doi: 10.1093/jxb/erh078
Bai Y, Meng Y, Huang D, Qi Y, Chen M. Origin and evolutionary analysis of the plant-specific TIFY transcription factor family. Genomics. 2011;98(2):128–36.
pubmed: 21616136
doi: 10.1016/j.ygeno.2011.05.002
Staswick PE. JAZing up jasmonate signaling. Trends Plant Sci. 2008;13(2):66–71.
pubmed: 18261950
doi: 10.1016/j.tplants.2007.11.011
Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G. The tify family previously known as ZIM. Trends Plant Sci. 2007;12(6):239–44.
pubmed: 17499004
doi: 10.1016/j.tplants.2007.04.004
White DWR. PEAPOD regulates lamina size and curvature in Arabidopsis. P Natl Acad Sci USA. 2006;103(35):13238–43.
doi: 10.1073/pnas.0604349103
Yu X, Chen G, Tang B, Zhang J, Zhou S, Hu Z. The Jasmonate ZIM-domain protein gene SlJAZ2 regulates plant morphology and accelerates flower initiation in Solanum lycopersicum plants. Plant Sci. 2018;267:65–73.
pubmed: 29362100
doi: 10.1016/j.plantsci.2017.11.008
Ebel C, BenFeki A, Hanin M, Solano R, Chini A. Characterization of wheat (Triticum aestivum) TIFY family and role of Triticum Durum TdTIFY11a in salt stress tolerance. PLoS ONE. 2018;13(7):e0200566.
pubmed: 30021005
pmcid: 6051620
doi: 10.1371/journal.pone.0200566
Zhu D, Li R, Liu X, Sun M, Wu J, Zhang N, Zhu Y. The positive Regulatory roles of the TIFY10 proteins in plant responses to alkaline stress. PLoS ONE. 2014;9(11):e111984.
pubmed: 25375909
pmcid: 4222965
doi: 10.1371/journal.pone.0111984
Liu YL, Zheng L, Jin LG, Liu YX, Kong YN, Wang YX, et al. Genome-wide analysis of the soybean TIFY Family and Identification of GmTIFY10e and GmTIFY10g response to salt stress. Front Plant Sci. 2022;13:845314.
Peethambaran PK, Glenz R, Höninger S, Shahinul Islam SM, Hummel S, Harter K, Kolukisaoglu Ü, Meynard D, Guiderdoni E, Nick P, et al. Salt-inducible expression of OsJAZ8 improves resilience against salt-stress. BMC Plant Biol. 2018;18(1):311.
pubmed: 30497415
pmcid: 6267056
doi: 10.1186/s12870-018-1521-0
Zhang C, Yang R, Zhang T, Zheng D, Li X, Zhang ZB, Li LG, Wu ZY. ZmTIFY16, a novel maize TIFY transcription factor gene, promotes root growth and development and enhances drought and salt tolerance in Arabidopsis and Zea mays. Plant Growth Regul. 2023;100(1):149–60.
doi: 10.1007/s10725-022-00946-2
Wang X, Li N, Zan T, Xu K, Gao S, Yin Y, Yao M, Wang F. Genome-wide analysis of the TIFY family and function of CaTIFY7 and CaTIFY10b under cold stress in pepper (Capsicum annuum L). Front Plant Sci. 2023;14:1308721.
pubmed: 38078112
pmcid: 10702603
doi: 10.3389/fpls.2023.1308721
Qi TC, Song SS, Ren QC, Wu DW, Huang H, Chen Y, Fan M, Peng W, Ren CM, Xie DX. The Jasmonate-ZIM-Domain Proteins Interact with the WD-Repeat/bHLH/MYB complexes to regulate jasmonate-mediated anthocyanin Accumulation and Trichome initiation in Arabidopsis thaliana. Plant Cell. 2011;23(5):1795–814.
pubmed: 21551388
pmcid: 3123955
doi: 10.1105/tpc.111.083261
Zhou Y, Sun W, Chen J, Tan H, Xiao Y, Li Q, Ji Q, Gao S, Chen L, Chen S, et al. SmMYC2a and SmMYC2b played similar but irreplaceable roles in regulating the biosynthesis of tanshinones and phenolic acids in Salvia miltiorrhiza. Sci Rep-Uk. 2016;6(1):22852.
doi: 10.1038/srep22852
Pei T, Ma P, Ding K, Liu S, Jia Y, et al. SmJAZ8 acts as a core repressor regulating JA-induced biosynthesis of salvianolic acids and tanshinones in Salvia miltiorrhiza hairy roots. J Exp Bot. 2017;69(7):1663–1678.
doi: 10.1093/jxb/erx484
Shi M, Zhou W, Zhang J, Huang S, Wang H, Kai G. Methyl jasmonate induction of tanshinone biosynthesis in Salvia miltiorrhiza hairy roots is mediated by JASMONATE ZIM-DOMAIN repressor proteins. Sci Rep-Uk. 2016;6(1):20919.
doi: 10.1038/srep20919
Zhu J, Yan X, Liu S, Xia X, An Y, Xu Q, et al. Alternative splicing of CsJAZ1 negatively regulates flavan-3-ol biosynthesis in tea plants. Plant J. 2022;110:243–261.
pubmed: 35043493
doi: 10.1111/tpj.15670
Committee NP. Pharmacopoeia of the people’s Republic of China. Beijing, China: Chinese Medical Science and Technology; 2020.
Liu Y, He Y, Wang F, Xu R, Yang M, Ci Z, Wu Z, Zhang D, Lin J. From longevity grass to contemporary soft gold: explore the chemical constituents, pharmacology, and toxicology of Artemisia Argyi H.Lév. & vaniot essential oil. J Ethnopharmacol. 2021;279:114404.
pubmed: 34246739
doi: 10.1016/j.jep.2021.114404
Song X, Wen X, He J, Zhao H, Li S, Wang M. Phytochemical components and biological activities of Artemisia Argyi. J Funct Foods. 2019;52:648–662.
doi: 10.1016/j.jff.2018.11.029
Zhou M, Zheng L, Geng T, Wang Y, Peng M, Hu F, et al. Effect of fermented Artemisia argyi on Egg Quality, Nutrition, and Flavor by Gut bacterial mediation. Animals. 2023;13(23):3678.
Chen H, Guo M, Dong S, Wu X, Zhang G, He L, Jiao Y, Chen S, Li L, Luo H. A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity. Plant Commun. 2023;4(3):100516.
pubmed: 36597358
pmcid: 10203441
doi: 10.1016/j.xplc.2023.100516
Jia HU, Yanting G, Yanmei LI. Research progress in protein post-translational modification. Sci Bull. 2006;51(6):633–645.
doi: 10.1007/s11434-006-0633-3
Singh V, Ram M, Kumar R, Prasad R, Roy BK, Singh KK. Phosphorylation: implications in Cancer. Protein J. 2017;36(1):1–6.
pubmed: 28108801
doi: 10.1007/s10930-017-9696-z
Darzentas N. Circoletto: visualizing sequence similarity with Circos. Bioinformatics. 2010;26(20):2620.
pubmed: 20736339
doi: 10.1093/bioinformatics/btq484
Sun P, Shi Y, Valerio AGO, Borrego EJ, Luo Q, Qin J, Liu K, Yan Y. An updated census of the maize TIFY family. PLoS ONE. 2021;16(2):e0247271.
pubmed: 33621269
pmcid: 7901733
doi: 10.1371/journal.pone.0247271
Shen J, Zou Z, Xing H, Duan Y, Zhu X, Ma Y, et al. Genome-wide analysis reveals stress and hormone responsive patterns of JAZ Family genes in Camellia Sinensis. Int J Mol Sci. 2020;21(7):2433.
Tao J, Jia H, Wu M, Zhong W, Jia D, Wang Z, Huang C. Genome-wide identification and characterization of the TIFY gene family in kiwifruit. BMC Genomics. 2022;23(1):179.
pubmed: 35247966
pmcid: 8897921
doi: 10.1186/s12864-022-08398-8
Cannon SB, Mitra A, Baumgarten A, Young ND, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004;4(1):10.
pubmed: 15171794
pmcid: 446195
doi: 10.1186/1471-2229-4-10
Maere S, De Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M, Van de Peer Y. Modeling gene and genome duplications in eukaryotes. Proceedings of the National Academy of Sciences 2005, 102(15):5454–5459.
Wang H, Leng X, Xu X, Li C. Comprehensive analysis of the TIFY gene family and its expression profiles under phytohormone treatment and abiotic stresses in roots of Populus trichocarpa. Forests. 2020;11(3):315.
Zheng LL, Wan Q, Wang HG, Guo CL, Niu XL, Zhang XF, Zhang R, Chen YH, Luo K. Genome-wide identification and expression of TIFY family in cassava (Manihot esculenta Crantz). Front Plant Sci. 2022;13:1017840.
pubmed: 36275529
pmcid: 9581314
doi: 10.3389/fpls.2022.1017840
Saha G, Park J-I, Kayum MA, Nou I-S. A genome-wide analysis reveals stress and hormone responsive patterns of TIFY Family genes in Brassica rapa. Front Plant Sci. 2016;7:936.
Liu X, Yu F, Yang G, Liu X, Peng S. Identification of TIFY gene family in walnut and analysis of its expression under abiotic stresses. BMC Genomics. 2022;23(1):190.
pubmed: 35255828
pmcid: 8903722
doi: 10.1186/s12864-022-08416-9
Wang P, Su L, Gao H, Jiang X, Wu X, Li Y, et al. Genome-wide characterization of bHLH genes in grape and analysis of their potential relevance to Abiotic Stress Tolerance and secondary Metabolite Biosynthesis. Front Plant Sci. 2018;9:64.
Meng L, Zhang T, Geng S, Scott PB, Li H, Chen S. Comparative proteomics and metabolomics of JAZ7-mediated drought tolerance in Arabidopsis. J Proteom. 2019;196:81–91.
doi: 10.1016/j.jprot.2019.02.001
Yu J, Zhang Y, Di C, Zhang Q, Zhang K, Wang C, You Q, Yan H, Dai SY, Yuan JS, et al. JAZ7 negatively regulates dark-induced leaf senescence in Arabidopsis. J Exp Bot. 2015;67(3):751–62.
pubmed: 26547795
pmcid: 4737072
doi: 10.1093/jxb/erv487
Valenzuela CE, Acevedo-Acevedo O, Miranda GS, Vergara-Barros P, Holuigue L, Figueroa CR, Figueroa PM. Salt stress response triggers activation of the jasmonate signaling pathway leading to inhibition of cell elongation in Arabidopsis primary root. J Exp Bot. 2016;67(14):4209–20.
pubmed: 27217545
pmcid: 5301928
doi: 10.1093/jxb/erw202
Grunewald W, Vanholme B, Pauwels L, Plovie E, Inzé D, Gheysen G, Goossens A. Expression of the Arabidopsis jasmonate signalling repressor JAZ1/TIFY10A is stimulated by auxin. EMBO Rep. 2009;10(8):923–8.
pubmed: 19575013
pmcid: 2726675
doi: 10.1038/embor.2009.103
Shikata M, Takemura M, Yokota A, Kohchi T. Arabidopsis ZIM, a plant-specific GATA factor, can function as a transcriptional activator. Biosci Biotechnol Biochem. 2003;67(11):2495–7.
pubmed: 14646219
doi: 10.1271/bbb.67.2495
White DWR. PEAPOD regulates lamina size and curvature in Arabidopsis. Proceedings of the National Academy of Sciences 2006, 103(35):13238–13243.
Andrade Galan AG, Doll J, Saile SC, Wünsch M, Roepenack-Lahaye Ev, Pauwels L, Goossens A, Bresson J, Zentgraf U. The Non-JAZ TIFY protein TIFY8 of Arabidopsis thaliana interacts with the HD-ZIP III Transcription Factor REVOLUTA and regulates Leaf Senescence. Int J Mol Sci. 2023;24(4):3079.
pubmed: 36834490
pmcid: 9967580
doi: 10.3390/ijms24043079
Oblessuc PR, Obulareddy N, DeMott L, Matiolli CC, Thompson BK, Melotto M. JAZ4 is involved in plant defense, growth, and development in Arabidopsis. Plant J. 2020;101(2):371–83.
pubmed: 31557372
doi: 10.1111/tpj.14548
An X-H, Hao Y-J, Li E-M, Xu K, Cheng C-G. Functional identification of apple MdJAZ2 in Arabidopsis with reduced JA-sensitivity and increased stress tolerance. Plant Cell Rep. 2017;36(2):255–65.
pubmed: 27844101
doi: 10.1007/s00299-016-2077-9
Wu H, Ye HY, Yao RF, Zhang T, Xiong LZ. OsJAZ9 acts as a transcriptional regulator in jasmonate signaling and modulates salt stress tolerance in rice. Plant Sci. 2015;232:1–12.
pubmed: 25617318
doi: 10.1016/j.plantsci.2014.12.010
Heidari P, Ahmadizadeh M, Izanlo F, Nussbaumer T. In silico study of the CESA and CSL gene family in Arabidopsis thaliana and Oryza sativa: focus on post-translation modifications. Plant Gene. 2019;19:100189.
doi: 10.1016/j.plgene.2019.100189
Rizvi MZ, Ansari SA, Ansari MI. ABA: metabolism, regulation, and functions in crop abiotic stress tolerance. In: Ansari, S.A., Ansari, M.I., Husen, A. (eds) Augmenting Crop Productivity in stress environment. Springer, Singapore, 2022.
Zhang YC, Gao M, Singer SD, Fei ZJ, Wang H, Wang XP. Genome-wide identification and analysis of the TIFY Gene family in grape. PLoS ONE. 2013;8(12):10.
Seo JS, Joo J, Kim MJ, Kim YK, Nahm BH, Song SI, Cheong JJ, Lee JS, Kim JK, Do Choi Y. OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice. Plant J. 2011;65(6):907–21.
pubmed: 21332845
doi: 10.1111/j.1365-313X.2010.04477.x
Li H, Hu Y, Li A, Wang X, Hou P, Wang C, Chen K, Zhao C. A highly sensitive electrochemical impedance immunosensor for indole-3-acetic acid and its determination in sunflowers under salt stress. Rsc Adv. 2017;7(86):54416–21.
doi: 10.1039/C7RA09979G
Benjamins R, Scheres B. Auxin: the looping star in plant development. Annu Rev Plant Biol. 2008;59:443–65.
pubmed: 18444904
doi: 10.1146/annurev.arplant.58.032806.103805
Chen Q, Sun J, Zhai Q, Zhou W, Qi L, Xu L, Wang B, Chen R, Jiang H, Qi J, et al. The Basic Helix-Loop-Helix transcription factor MYC2 directly represses PLETHORA expression during jasmonate-mediated modulation of the Root Stem Cell Niche in Arabidopsis. Plant Cell. 2011;23(9):3335–52.
pubmed: 21954460
pmcid: 3203420
doi: 10.1105/tpc.111.089870
Kang G, Li G, Guo T. Molecular mechanism of salicylic acid-induced abiotic stress tolerance in higher plants. Acta Physiol Plant. 2014;36(9):2287–97.
doi: 10.1007/s11738-014-1603-z
Nazar R, Iqbal N, Syeed S, Khan NA. Salicylic acid alleviates decreases in photosynthesis under salt stress by enhancing nitrogen and sulfur assimilation and antioxidant metabolism differentially in two mungbean cultivars. J Plant Physiol. 2011;168(8):807–15.
pubmed: 21112120
doi: 10.1016/j.jplph.2010.11.001
Khan MIR, Iqbal N, Masood A, Per TS, Khan NA. Salicylic acid alleviates adverse effects of heat stress on photosynthesis through changes in proline production and ethylene formation. Plant Signal Behav. 2013;8(11):e26374.
pubmed: 24022274
pmcid: 4091357
doi: 10.4161/psb.26374
Lian C, Yao K, Duan H, Li Q, Liu C, Yin W, et al. Exploration of ABA responsive miRNAs reveals a new hormone signaling crosstalk pathway regulating Root Growth of Populus Euphratica. Int J Mol Sci. 2018;19(5):1481.
Lian C, Lan J, Ma R, Li J, Zhang F, Zhang B, et al. Genome-wide analysis of Aux/IAA gene family in Artemisia argyi: identification, phylogenetic analysis, and determination of response to various phytohormones. Plants. 2024;13(5):564.
Gasteiger E, Hoogland C, Gattiker A, Duvaud Se, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server. In: The Proteomics Protocols Handbook. Edited by Walker JM. Totowa, NJ: Humana Press; 2005: 571–607.
Chou K-C, Shen H-B. Plant-mPLoc: A Top-Down Strategy to augment the Power for Predicting Plant Protein Subcellular Localization. PLoS ONE. 2010;5(6):e11335.
pubmed: 20596258
pmcid: 2893129
doi: 10.1371/journal.pone.0011335
Geourjon C, Deléage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics. 1995;11(6):681–4.
doi: 10.1093/bioinformatics/11.6.681
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, Heer FT, de Beer TAP, Rempfer C, Bordoli L, Lepore R, Schwede T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46(W1):W296–303.
pubmed: 29788355
pmcid: 6030848
doi: 10.1093/nar/gky427
Blom N, Gammeltoft S, Brunak S. Sequence and structure-based prediction of eukaryotic protein phosphorylation sites1 1Edited by F. E. Cohen. J Mol Biol. 1999;294(5):1351–62.
pubmed: 10600390
doi: 10.1006/jmbi.1999.3310
Almagro Armenteros JJ, Tsirigos KD, Sønderby CK, Petersen TN, Winther O, Brunak S, von Heijne G, Nielsen H. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat Biotechnol. 2019;37(4):420–3.
pubmed: 30778233
doi: 10.1038/s41587-019-0036-z
Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee T-h, Jin H, Marler B, Guo H, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49–49.
pubmed: 22217600
pmcid: 3326336
doi: 10.1093/nar/gkr1293
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: an integrative Toolkit developed for interactive analyses of big Biological Data. Mol Plant. 2020;13(8):1194–202.
pubmed: 32585190
doi: 10.1016/j.molp.2020.06.009
Mering Cv, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003;31(1):258–61.
doi: 10.1093/nar/gkg034
He Z, Zhang H, Gao S, Lercher MJ, Chen W-H, Hu S. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res. 2016;44(W1):W236–41.
pubmed: 27131786
pmcid: 4987921
doi: 10.1093/nar/gkw370
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. 2011 2011, 17(1):3.
Lyu F, Han F, Ge C, Mao W, Chen L, Hu H, Chen G, Lang Q, Fang C. OmicStudio: a composable bioinformatics cloud platform with real-time feedback that can generate high-quality graphs for publication. iMeta. 2023;2(1):e85.
pubmed: 38868333
pmcid: 10989813
doi: 10.1002/imt2.85
Lian CL, Zhang B, Yang JF, Lan JX, Yang H, Guo KH, et al. Validation of suitable reference genes by various algorithms for gene expression analysis in Isodon rubescens under different abiotic stresses. Sci Rep. 2022;12:19599.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001;25(4):402–408.
pubmed: 11846609
doi: 10.1006/meth.2001.1262