788
Views
0
CrossRef citations to date
0
Altmetric
Research paper

Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of Musa acuminata under both infected and chemical perturbated conditions

ORCID Icon, , , , , & show all
Article: 2269675 | Received 31 Jul 2023, Accepted 08 Oct 2023, Published online: 10 Nov 2023

References

  • Indian Council of Agricultural Research (ICAR). Banana. Pdf (accessed on Sep 2023). https://kvk.icar.gov.in/API/Content/PPupload/k0331_41.pdf
  • Ploetz RC. Management of Fusarium wilt of banana: a review with special reference to tropical race 4. Crop Protection. 2015;73:7–11. doi:10.1016/j.cropro.2015.01.007.
  • Sun J, Zhang J, Fang H, Peng L, Wei S, Li C, Zheng S, Lu J. Comparative transcriptome analysis reveals resistance-related genes and pathways in Musa acuminata banana ’Guijiao 9’ in response to Fusarium wilt. Plant Physiol Bioch. 2019;141:83–94. doi:10.1016/j.plaphy.2019.05.022.
  • Simmonds NW, Shepherd K. The taxonomy and origins of the cultivated bananas. Journal Of The Linnaian Society. 1955;55(359):302–312. doi:10.1111/j.1095-8339.1955.tb00015.x.
  • Oyeyinka BO, Jide Afolayan A. Comparative evaluation of the nutritive, mineral, and antinutritive composition of Musa sinensis L. (banana) and Musa paradisiaca L. (plantain) fruit compartments. Plants. 2019;8(12):598. doi:10.3390/plants8120598.
  • Munusamy U, Zaidi K. Elucidation of Musa acuminata cv. Berangan root infection by FOC (tropical race 4) by RNA sequencing and analysis. Asian Journal Of Plant Science & Research. 2021;11(3):96–112.
  • Stover RH. Variation and cultivar nomenclature in Musa, AAA group, Cavendish subgroup. Fruits. 1988;43:353–357.
  • Mohapatra D, Mishra S, Sutar N. Banana and its by-product utilisation: an overview. J Sci Ind Res India. 2010;69:323–329.
  • Alzate Acevedo S, Díaz Carrillo ÁJ, Flórez-López E, Grande-Tovar CD. Recovery of banana waste-loss from production and processing: a contribution to a circular economy. Molecules. 2021;26(17):5282. doi:10.3390/molecules26175282.
  • Huang H, Zhang X, Zhang Y, Yi G, Xie J, Viljoen A, Wang W, Mostert D, Fu G, Peng C. FocECM33, a GPI-anchored protein, regulates vegetative growth and virulence in Fusarium oxysporum f. sp. cubense tropical race 4. Fungal Biol. 2022;126(3):213–223. doi:10.1016/j.funbio.2021.12.005.
  • Thangavelu R, Edwin Raj E, Pushpakanth P, Loganathan M, Uma S. Draft genome of Fusarium oxysporum f. sp. cubense strain tropical race-4 infecting Cavendish (AAA) group of banana in India. Plant Disease. 2021;105(2):481–483. doi:10.1094/PDIS-06-20-1170-A.
  • Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M. MAPMAN: a user‐driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal. 2004;37(6):914–939. doi:10.1111/j.1365-313X.2004.02016.x.
  • Zhan N, Kuang M, He W, Deng G, Liu S, Li C, Roux N, Dita M, Yi G, Sheng O. Evaluation of resistance of banana genotypes with AAB genome to Fusarium wilt tropical race 4 in China. J Fungus. 2022;8(12):1274. doi:10.3390/jof8121274.
  • Guo L, Han L, Yang L, Zeng H, Fan D, Zhu Y, Feng Y, Wang G, Peng C, Jiang X, et al. Genome and transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. cubense causing banana vascular wilt disease. PloS One. 2014;9(4):e95543. doi:10.1371/journal.pone.0095543.
  • Kaushal M, Mahuku G, Swennen R. Comparative transcriptome and expression profiling of resistant and susceptible banana cultivars during infection by Fusarium oxysporum. Int J Mol Sci. 2021;22(6):3002. doi:10.3390/ijms22063002.
  • Li C, Deng G, Yang J, Viljoen A, Jin Y, Kuang R, Zuo C, Lv Z, Yang Q, Sheng O, et al. Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4. Bmc Genomics. 2012;13(1):374. doi:10.1186/1471-2164-13-374.
  • Niu Y, Hu B, Li X, Chen H, Takáč T, Šamaj J, Xu C. Comparative digital gene expression analysis of tissue-cultured plantlets of highly resistant and susceptible banana cultivars in response to Fusarium oxysporum. Int J Mol Sci. 2018;19(2):350. doi:10.3390/ijms19020350.
  • An B, Hou X, Guo Y, Zhao S, Luo H, He C, Wang Q. The effector SIX8 is required for virulence of Fusarium oxysporum f. sp. cubense tropical race 4 to Cavendish banana. Fungal Biol. 2019;123(5):423–430. doi:10.1016/j.funbio.2019.03.001.
  • Cheng Z, Yu X, Li S, Wu Q. Genome-wide transcriptome analysis and identification of benzothiadiazole-induced genes and pathways potentially associated with defense response in banana. Bmc Genomics. 2018;19(1):1–19. doi:10.1186/s12864-018-4830-7.
  • Lefevere H, Bauters L, Gheysen G. Salicylic acid biosynthesis in plants. Front Plant Sci. 2020;11:11. https://www.frontiersin.org/articles/10.3389/fpls.2020.00338.
  • Abdel-Monaim MF, Ismail ME, Morsy KM. Induction of systemic resistance of benzothiadiazole and humic acid in soybean plants against Fusarium wilt disease. Mycobiology. 2011;39(4):290–298. doi:10.5941/MYCO.2011.39.4.290.
  • Gamez RM, Rodríguez F, Vidal NM, Ramirez S, Vera Alvarez R, Landsman D, Mariño-Ramírez L. Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006. Bmc Genomics. 2019;20(1):1–20. doi:10.1186/s12864-019-5763-5.
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–360. doi:10.1038/nmeth.3317.
  • Bates D, Mächler M, Bolker B, Walker S. Fitting linear mixed-effects models using lme4. 2014;67(1). ArXiv Preprint ArXiv:1406.5823. doi:10.18637/jss.v067.i01.
  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi:10.1186/s13059-014-0550-8.
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinform. 2008;9(1):559. [online] URL. doi:10.1186/1471-2105-9-559.
  • Yip AM, Horvath S. Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinform. 2007;8(1):1–14. doi:10.1186/1471-2105-8-22.
  • Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the dynamic tree cut package for R. Bioinformatics. 2008;24(5):719–720. doi:10.1093/bioinformatics/btm563.
  • Tian L, Chen T, Lu J, Yan J, Zhang Y, Qin P, Ding S, Zhou Y. Integrated protein–protein interaction and weighted gene co-expression network analysis uncover three key genes in hepatoblastoma. Frontiers In Cell And Developmental Biology. 2021;9:631982. doi:10.3389/fcell.2021.631982.
  • Farhadian M, Rafat SA, Panahi B, Mayack C. Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process. Sci Rep. 2021;11(1):2367. doi:10.1038/s41598-021-81888-z.
  • Kumar A, Kanak KR, Arunachalam A, Dass RS, Lakshmi PTV. Comparative transcriptome profiling and weighted gene co-expression network analysis to identify core genes in maize (Zea mays L.) silks infected by multiple fungi. Front Plant Sci. 2022;13:13. doi:10.3389/fpls.2022.985396.
  • Ge SX, Jung D, Yao R, Valencia A. ShinyGO: a graphical gene-set enrichment tool for animals and plants. Bioinformatics. 2020;36(8):2628–2629. doi:10.1093/bioinformatics/btz931.
  • Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613. doi:10.1093/nar/gky1131.
  • Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape StringApp: network analysis and visualization of proteomics data. J Proteome Res. 2018;18(2):623–632. doi:10.1021/acs.jproteome.8b00702.
  • Ghag SB, Shekhawat UKS, Ganapathi TR. Fusarium wilt of banana: biology, epidemiology and management. International Journal Of Pest Management. 2015;61(3):250–263. doi:10.1080/09670874.2015.1043972.
  • Bovie C, Ongena M, Thonart P, Dommes J. Cloning and expression analysis of cDnas corresponding to genes activated in cucumber showing systemic acquired resistance after BTH treatment. BMC Plant Biol. 2004;4(1):1–12. doi:10.1186/1471-2229-4-15.
  • Friedrich L, Lawton K, Ruess W, Masner P, Specker N, Rella MG, Meier B, Dincher S, Staub T, Uknes S. A benzothiadiazole derivative induces systemic acquired resistance in tobacco. Plant Journal. 1996;10(1):61–70. doi:10.1046/j.1365-313X.1996.10010061.x.
  • Zhang S, Xiaolu W, Cui J, Zhang F, Wan X, Liu Q, Zhong Y, Lin T. Physiological and transcriptomic analysis of Yellow leaf coloration in Populus deltoides marsh. PloS One. 2019;14(5):e0216879. doi:10.1371/journal.pone.0216879.
  • Cheng C, Liu F, Tian N, Mensah RA, Sun X, Liu J, Wu J, Wang B, Li D, Lai Z. Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing. Sci Rep. 2021;11(1):16363. doi:10.1038/s41598-021-95832-8.
  • Wang Z, Zhang J, Jia C, Liu J, Li Y, Yin X, Xu B, Jin Z. De novo characterization of the banana root transcriptome and analysis of gene expression under Fusarium oxysporum f. sp. cubense tropical race 4 infection. Bmc Genomics. 2012;13(1):650. doi:10.1186/1471-2164-13-650.
  • Kochevenko A, Araújo WL, Maloney GS, Tieman DM, Do PT, Taylor MG, Klee HJ, Fernie AR. Catabolism of branched chain amino acids supports respiration but not volatile synthesis in tomato fruits. Mol Plant. 2012;5(2):366–375. doi:10.1093/mp/ssr108.
  • Hu W, Wang B, Ali MM, Chen X, Zhang J, Zheng S, Chen F. Free amino acids profile and expression analysis of core genes involved in branched-chain amino acids metabolism during fruit development of longan (Dimocarpus longan Lour.) cultivars with different aroma types. Biology. 2021;10(8):807. doi:10.3390/biology10080807.
  • Wyllie SG, Fellman JK. Formation of volatile branched chain esters in bananas (Musa sapientum L.). J Agr Food Chem. 2000;48(8):3493–3496. doi:10.1021/jf0001841.
  • Schneider M, Knuesting J, Birkholz O, Heinisch J, Scheibe R. Cytosolic GAPDH as a redox-dependent regulator of energy metabolism. BMC Plant Biol. 2018;18:1–14.
  • Wei H, Movahedi A, Yang J, Zhang Y, Liu G, Zhu S, Yu C, Chen Y, Zhong F, Zhang J. Characteristics and molecular identification of glyceraldehyde-3-phosphate dehydrogenases in poplar. Int J Biol Macromol. 2022;219:185–198. doi:10.1016/j.ijbiomac.2022.08.001.
  • Zeng H, Xie Y, Liu G, Lin D, He C, Shi H. Molecular identification of GAPDHs in cassava highlights the antagonism of MeGAPCs and MeATG8s in plant disease resistance against cassava bacterial blight. Plant Mol Biol. 2018;97(3):201–214. doi:10.1007/s11103-018-0733-x.
  • Zhang L, Liu L, Li S, Bai T, Xu S, Fan H, Yin K, He P, Wang Y, Tang W. Proteomic analysis of banana xylem sap provides insight into resistant mechanisms to Fusarium oxysporum f. sp. cubense Tropical Race 4, 05 August 2020, PREPRINT (Version 2). 2020. https://doi.org/10.21203/rs.3.rs-26869/v2].
  • Deng B, Wang X, Long X, Fang R, Zhou S, Zhang J, Peng X, An Z, Huang W, Tang W, et al. Plant hormone metabolome and transcriptome analysis of dwarf and wild-type banana. J Plant Growth Regul. 2022;41(6):476 2386–2405. doi:10.1007/s00344-021-10447-7.
  • Micheli F. Pectin methylesterases: cell wall enzymes with important roles in plant physiology. Trends Plant Sci. 2001;6(9):414–419. doi:10.1016/S1360-1385(01)02045-3.
  • Phan TD, Bo W, West G, Lycett GW, Tucker GA. Silencing of the major salt-dependent isoform of pectinesterase in tomato alters fruit softening. Plant Physiol. 2007;144(4):1960–1967. doi:10.1104/pp.107.096347.
  • Hall LN, Tucker GA, Smith CJS, Watson CF, Seymour GB, Bundick Y, Boniwell JM, Fletcher JD, Ray JA, Schuch W. Antisense inhibition of pectin esterase gene expression in transgenic tomatoes. Plant Journal. 1993;3(1):121–129. doi:10.1111/j.1365-313X.1993.tb00015.x.
  • Siddiqui NR, Muhammad A, Khan MR, Ali GM, Mahmood T, Shahzad A, Jabbar S. Differential gene expression of pectin esterase and changes in pectin during development and ripening stages of fruit in selected cultivars of banana. Food Science And Technology. 2020;40(4):827–831. doi:10.1590/fst.20719.
  • Jianping H, Baker A, Bartel B, Linka N, Mullen RT, Reumann S, Zolman BK. Plant peroxisomes: biogenesis and function. Plant Cell. 2012;24(6):2279–2303. doi:10.1105/tpc.112.096586.
  • Candar‐Cakir B, Arican E, Zhang B. Small RNA and degradome deep sequencing reveals drought‐and tissue‐specific micrornas and their important roles in drought‐sensitive and drought‐tolerant tomato genotypes. Plant Biotechnol J. 2016;14(8):465 1727–1746. doi:10.1111/pbi.12533.
  • Li W-X, Oono Y, Zhu J, He X-J, Wu J-M, Iida K, Lu X-Y, Cui X, Jin H, Zhu J-K. The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and post transcriptionally to promote drought resistance. Plant Cell. 2008;20(8):2238–2251. doi:10.1105/tpc.108.059444.
  • Wei W, Chen J-Y, Zeng Z-X, Kuang J-F, Lu W-J, Shan W. The ubiquitin 602 E3 ligase MaLUL2 is involved in high temperature-induced green ripening in banana 603 fruit. IJMS. 2020;21(24):9386. doi:10.3390/ijms21249386.