Transcriptome Sequencing of Solanum Nigrum Linn Reveals the Genes Related to the Biosynthesis of Flavonoids
DOI:
https://doi.org/10.18063/gse.v4i1.1172Keywords:
Transcristom, Solanum Nigrum, Next-generation Sequencing, Flavonoid, Differential Expression GenesAbstract
In this work we comprehensively compared the transcriptome profiles of ripe fruits (RFs) and unripe fruits (UFs) and identified the genes related to flavonoid biosynthesis in Solanum nigrum Linn. (S. nigrum). Firstly, 118198 unigenes with a N50 length of 1339 bp were de novo assembled. In addition, 527 genes that were differential expression in RFs and UFs have been identified, including 329 down-regulated genes and 198 up-regulated genes. Especially, 8 differential expression genes (DEGs) were identified to be involved in flavonoid biosynthesis. Coincidentally, most of the 8 flavonoid-related genes were highly expressed in RFs. Finally, we found that the differential expression of three genes that were related to the synthesis of dihydroflavonol-4-reductase (DFR), flavonoid 3’, 5’-hydroxylase (F35H) and anthocyanin synthase (ANS) was the main reason for differences in flavonoid biosynthesis between RFs and UFs of S. nigrum. This study provides some supporting information for the flavonoid accumulation in RFs. Moreover, this study can improve our understanding of the molecular mechanisms of flavonoid biosynthesis in S. nigrum.
References
Wen Zhihua. Development and Utilization of Wild Resource Solanum nigrum[J] Yunnan Agricultural Science and Technology, 2006(1):56-58.
Yuan H L, Liu X L, Liu Y J. Solanum Nigrum Polysaccharide (SNL) Extract Effects in Transplanted Tumor- bearing Mice - Erythrocyte Membrane Fluidity and Blocking of Functions[J]. Asian Pacific journal of cancer prevention: APJCP, 2014, 15(23):10469-10473.
Wang Y, Xiang L, Yi X, et al. Potential Anti-inflammatory Steroidal Saponins from the Berries of Solanum nigrum L. (European Black Nightshade)[J]. Journal of Agricultural & Food Chemistry, 2017, 65(21):4262-4272.
Taherpour A, Khodaei M M, Ameen B A H, et al. Chemical composition analysis of the essential oil of Solanumn nigrum L. by HS/ SPME method and calculation of the biochemical coefficients of the components[J]. Arabian Journal of Chemistry, 2013:S1878535213002761.
Huang Hua, Zhou Jianhua, New Development and Application of Solanum nigrum[J] Food Industry Science and Technology, 2009, 30(1).
Chen R, Feng L, Li H D, et al. Two novel oligosaccharides from Solanum nigrum[J]. Carbohydrate Research, 2009, 344(13):1775-1777.
He Jun, Zhou Chang Ji, Ma Bingzhi, et al. Research Progress on Chemical Constituents and Antitumor Pharmacological Activities of Solanum nigrum [J]. China Pharmacy, 2015, 26(31):4433-4436.
Hichri, Imène, Barrieu, François, Bogs J, et al. Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway[J]. Journal of Experimental Botany, 2011, 62(8):2465.
Meer I M V D, Stam M E, Tunen A J V, et al. Antisense Inhibition of Flavonoid Biosynthesis in Petunia Anthers Results in Male Sterility[J]. The Plant Cell, 1992, 4(3):253-262.
Cushnie T P T, Lamb A J. Antimicrobial activity of flavonoids[J]. Int J Antimicrob Agents, 2005, 26(5):343- 356.
Zhang Haifeng, Zhang Shaoliang, Zhang Chunlei, et al. Research Progress in Flavonoids with Anti-free Radical and UV Protective Effects [J] Daily Chemical Industry, 2008, 38(1):54-57.
Huang Huayi, Zha Xiliang, Research Progress on Antitumor Effects of Flavonoids [J] Chinese Journal of New Drugs and Clinical Medicine, 2002, 21(7).
Jagadeeshan S, David D, Jisha S, et al. Solanum nigrum Unripe fruit fraction attenuates Adriamycin resistance by down-regulating multi-drug resistance protein (Mdr) -1 through Jak-STAT pathway[J]. BMC Complementary and Alternative Medicine, 2017, 17(1):370.
Son Y O, Kim J, Lim J C, et al. Ripe fruit of Solanum nigrum L. inhibits cell growth and induces apoptosis in MCF-7 cells[J]. Food and chemical toxicology, 2003, 41(10): 1421-1428
Huang H C, Syu K Y, Lin J K. Chemical composition of Solanum nigrum linn extract and induction of autophagy by leaf water extract and its major flavonoids in AU565 breast cancer cells[J]. J Agric Food Chem, 2010, 58(15): 8699-8708.
Li Y, Wang F, Jiang Q, et al. Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing[J]. Hortic Res, 2014, 1(10):10.
Mueller O M, Schroeder A, Lightfoot S, et al. RNA integrity number (RIN) - towards standardization of RNA quality assessment[J]. Cancer Research, 2004, 64.
Lambert D, Carrillo C D, Koziol A G, et al. GeneSippr: A Rapid Whole-Genome Approach for the Identification and Characterization of Foodborne Pathogens such as Priority Shiga Toxigenic Escherichia coli[J]. PLoS One, 2015, 10(4): e0122928.
Labreche K, Simeonova I, Kamoun A, et al. TCF12 is mutated in anaplastic oligodendroglioma[J]. Nature Communications, 2016, 6: 7207.
Wu A R, Neff NF, Kalisky T, et al. Quantitative assessment of single-cell RNA-sequencing methods[J]. Nature Methods, 2014, 11(1): 41-46.
Bolger A M, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data[J]. Bioinformatics, 2014, 30(15): 2114-2120.
Haas B J, Alexie P, Moran Y, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis[J]. Nature Protocols, 2013, 8(8): 1494-1512.
Grabherr M G, Haas B J, Moran Y, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nature Biotechnology, 2011, 29(7): 644.
Sim O F A, Waterhouse R M, Panagiotis I, et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs[J]. Bioinformatics, 2015, 31(19): 3210-3212.
Gentleman R . Bioconductor: open software development for computational biology and bioinformatics[J]. Genome biology, 2004, 5.
Laurent H, Stephane M, Francoise M, et al. Purification, cloning, and properties of an acyltransferase controlling shikimate and quinate ester intermediates in phenylpropanoid metabolism[J]. Journal of Biological Chemistry, 2003, 278(1): 95-103.
Hoffmann L, Besseau S, Geoffroy P, et al. Silencing of hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyltransferase affects phenylpropanoid biosynthesis[J]. Plant Cell, 2004, 16(6): 1446-1465.
Kang Yalan, Pei Jin, Liu Wei, et al. Cloning, Bioinformatics Analysis and Expression of Safflower Chalcone Synthase Gene [J] Chinese Herbal Medicine, 2014, 45(16).
Peters A, Schneider-Poetsch H A W, Schwarz H, et al. Biochemical and Immunological Characterization of Chalcone Synthase from Rye Leaves[J]. Journal of Plant Physiology, 1988, 133(2): 178-182.
Toguri T, Umemoto N, Kobayashi O, et al. Activation of anthocyanin synthesis genes by white light in eggplant hypocotyl tissues, and identification of an inducible P-450 cDNA[J]. Plant Mol Biol, 1993, 23(5): 933-946.
Martens S, Forkmann G. Cloning and expression of flavone synthase II from Gerbera hybrids[J]. The Plant journal: for cell and molecular biology, 1999, 20(5): 611-618.
Ferreyra M L F, Rius S P, Casati P. Flavonoids: biosynthesis, biological functions, and biotechnological applications[J]. Frontiers in Plant Science, 2012, 3(222): 222.
Wellmann F, Lukacin R, Moriguchi T, et al. Functional expression and mutational analysis of flavonol synthase from Citrus unshiu[J]. European journal of biochemistry, 2002, 269(16): 4134-4142.
Holton T A , Cornish E C. Genetics and Biochemistry of Anthocyanin Biosynthesis[J]. Plant Cell, 1995, 7(7):1071-1083.
Petrussa E, Braidot E, Zancani M, et al. Plant flavonoids--biosynthesis, transport and involvement in stress responses[J]. International journal of molecular sciences, 2013, 14(7): 14950-14973.
Markham K R, Gould K S, Winefield C S, et al. Anthocyanic vacuolar inclusions--their nature and significance in flower colouration[J]. Phytochemistry, 2000, 55(4): 327-336.
Séverine G, Cédric S, Laurence G. Composition and cellular localization of tannins in Cabernet Sauvignon skins during growth[J]. J Agric Food Chem, 2006, 54(25): 9465-9471.
Zhao J. Flavonoid transport mechanisms: how to go, and with whom[J]. Trends in plant science, 2015, 20(9): 576-585.
Wu Y, Guo J, Zhou Q, et al. De novo transcriptome analysis revealed genes involved in flavonoid biosynthesis, transport and regulation in Ginkgo biloba[J]. Industrial Crops and Products, 2018, 124: 226-235.
Zhang F, Gonzalez A, Zhao M, et al. A network of redundant bHLH proteins functions in all TTG1-dependent pathways of Arabidopsis[J]. Development, 2003, 130(20): 4859-4869.
Sotiropoulos A, Gineitis D, Copeland J, et al. Signal-Regulated Activation of Serum Response Factor Is Mediated by Changes in Actin Dynamics[J]. Cell, 1999, 98(2):159-169.
