Phenotypic and Transcriptomic Analysis of Two Pinellia ternata Varieties T2 line and T2Plus line

Scientific Reports

Volumn 10, Issue 1, 2020, Pages

  Lu, Jun ^a,c   Liu, Jian Ning ^b   Sarsaiya, Surendra ^c   Duns, Gregory Joseph ^a,d   Han, Jing ^a   Jin, Leilei ^a   Chen, Jishuang ^a,c  

^a NANJING TECH UNIVERSITY   (China)

^b Nantianmen Middle Road   (China)

^c ZUNYI MEDICAL UNIVERSITY   (China)

^d AirChem Consulting and Research   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

BIOLOGY; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MEDICINAL PLANT; METABOLISM; PHENOTYPE; PHOTOSYNTHESIS; PINELLIA; PLANT GENE; PROCEDURES;

COMPUTATIONAL BIOLOGY; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; METABOLIC NETWORKS AND PATHWAYS; PHENOTYPE; PHOTOSYNTHESIS; PINELLIA; PLANTS, MEDICINAL; TRANSCRIPTOME;

EID: 85081734430     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-020-61512-2     Document Type: Article

References (71)

1. Ji, X., Huang, B., Wang, G. & Zhang, C. ethnobotanical, phytochemical Pharmacol. profile genus Pinellia. Fitoterapia. 93, 1–17 (2014).
2. Wu, X. Y. et al. Sedative, hypnotic and anticonvulsant activities of the ethanol fraction from Rhizoma Pinelliae Praeparatum. J. Of. Ethnopharmacology. 135, 325–329 (2011).
3. Li, G. L. et al. HPV E6 down-regulation and apoptosis induction of human cervical cancer cells by a novel lipid-soluble extract (PE) from Pinellia pedatisecta Schott in vitro. J. Ethnopharmacol. 132, 56–64 (2010).
4. Kurata, K. et al. Quantitative analysis of anti-emetic principle in the tubers of Pinellia ternata by enzyme immunoassay. Planta Medica. 64, 645–648 (1998).
5. Kim, S. H. et al. IgE-mediated occupational asthma induced by herbal medicine, Banha (Pinellia ternata). Clin. Exp. Allergy. 31, 779–781 (2010).
6. Lee, M. Y. et al. Pinellia ternata Breitenbach attenuates ovalbumin-induced allergic airway inflammation and mucus secretion in a murine model of asthma. Immunopharmacol. Immunotoxicol. 35, 410–418 (2013).
7. Alix, K., Gerard, P. R., Schwarzacher, T. & Heslop-Harrison, J. S. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants (vol 120, pg 183, 2017). Ann. Of. Botany. 120, 619–619 (2017).
8. Allario, T. et al. Tetraploid Rangpur lime rootstock increases drought tolerance via enhanced constitutive root abscisic acid production. Plant. Cell And. Environment. 36, 856–868 (2013).
9. Chao, D.-Y. et al. Polyploids Exhibit Higher Potassium Uptake and Salinity Tolerance in Arabidopsis. Science. 341, 658–659 (2013).
10. Pereira, A. L. A. et al. Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response. Bmc Genomics. 15 (2014).
11. Ruiz, M. et al. Effects of salinity on diploid (2x) and doubled diploid (4x) Citrus macrophylla genotypes. Sci. Horticulturae. 207, 33–40 (2016).
12. Godfree, R. C., Marshall, D. J., Young, A. G., Miller, C. H. & Mathews, S. Empirical evidence of fixed and homeostatic patterns of polyploid advantage in a keystone grass exposed to drought and heat stress. Royal Society Open. Science. 4, 170934 (2017).
13. Hallahan, B. F. et al. Hybridity has a greater effect than paternal genome dosage on heterosis in sugar beet (Beta vulgaris). Bmc Plant Biology. 18 (2018).
14. Yun, L. et al. Callus polyploidy induction and identification of Russian wild ryegrass. Acta Prataculturae Sinica. 19, 126–131 (2010).
15. Wuerschum, T., Tucker, M. R., Reif, J. C., & Maurer, H. P. Improved efficiency of doubled haploid generation in hexaploid triticale by in vitro chromosome doubling. Bmc Plant Biology. 12 (2012).
16. Lopes Gomes, S. S. et al. Karyotype, genome size, and in vitro chromosome doubling of Pfaffia glomerata (Spreng.) Pedersen. Plant. Cell Tissue And. Organ. Culture. 118, 45–56 (2014).
17. Yang, Z. et al. Production of Autopolyploid Lowland Switchgrass Lines Through In Vitro Chromosome Doubling. Bioenergy Research. 7, 232–242 (2014).
18. Dong, Y.-Q. et al. Androgenesis, gynogenesis, and parthenogenesis haploids in cucurbit species. Plant. Cell Reports. 35, 1991–2019 (2016).
19. Li, X. et al. Study on Anti-Ehrlich Ascites Tumour Effect of Pinellia Ternata Polysaccharide In Vivo. Afr. J. Of. Traditional Complementary And. Alternative Medicines. 10, 380–385 (2013).
20. Lin, J., Yao, J. H., Zhou, X. W., Sun, X. F. & Tang, K. X. Expression and purification of a novel mannose-binding lectin from Pinellia ternata. Mol. Biotechnology. 25, 215–221 (2003).
21. Liu, Y., Liang, Z. & Liu, J. Use of protocorm-like bodies for studying alkaloid metabolism in Pinellia ternata. Plant. Cell Tissue And. Organ. Culture. 100, 83–89 (2010).
22. Lu, D., Luo, F., Chi, Y. & Wu, H. Determination of nucleosides in Rhizoma Pinelliae by high performance liquid chromatography. Se pu = Chin. J. chromatography. 29, 83–86 (2011).
23. Vernon, A. J. & Allison, J. C. S. A Method of Calculating Net Assimilation Rate. Nature. 200, 814–814 (1963).
24. Buckley, T. N. & Mott, K. A. Modelling stomatal conductance in response to environmental factors. Plant. Cell Environ. 36, 1691–1699 (2013).
25. Morison, J. I. L., Zeiger, E., Farquhar, G. D., & Cowan, I. R. Intercellular CO2 concentration and stomatal response to CO2. Stomatal Function. 229–251 (1987).
26. Fletcher, A. L., Sinclair, T. R. & Allen, L. H. Jr. Transpiration responses to vapor pressure deficit in well watered ‘slow-wilting’ and commercial soybean. Environ. And. Exp. Botany. 61, 145–151 (2007).
27. Wu, G. et al. Sequencing, de novo assembly and comparative analysis of Raphanus sativus transcriptome. Frontiers in plant science. 6 (2015).
28. Horemans, N., Foyer, C. H., Potters, G. & Han, A. Ascorbate function and associated transport systems in plants. Plant. Physiol. Biochemistry. 38, 531–540 (2000).
29. Noctor, G. & Foyer, C. H. ASCORBATE AND GLUTATHIONE: Keeping Active Oxygen Under Control. Annu. Rev. Plant. Physiol. Plant Mol. Biol. 49, 249–279 (1998).
30. Riechmann, J. L. et al. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science. 290, 2105–2110 (2000).
31. Mu, R.-L. et al. An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in. Arabidopsis. Cell Research. 19, 1291–1304 (2009).
32. Haga, N. et al. Mutations in MYB3R1 and MYB3R4 Cause Pleiotropic Developmental Defects and Preferential Down-Regulation of Multiple G2/M-Specific Genes in Arabidopsis. Plant. Physiology. 157, 706–717 (2011).
33. Frerigmann, H. & Gigolashvili, T. MYB34, MYB51, and MYB122 Distinctly Regulate Indolic Glucosinolate Biosynthesis in Arabidopsis thaliana. Mol. Plant. 7, 814–828 (2014).
34. Lee, S. B. & Suh, M. C. Cuticular Wax Biosynthesis is Up-Regulated by the MYB94 Transcription Factor in Arabidopsis. Plant. And. Cell Physiology. 56, 48–60 (2015).
35. Agarwal, M. et al. A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J. Of. Biol. Chemistry. 281, 37636–37645 (2006).
36. Chen, Y. et al. AtMYB14 Regulates Cold Tolerance in Arabidopsis. Plant. Mol. Biol. Reporter. 31, 87–97 (2013).
37. Lee, H. G. & Seo, P. J. The MYB96-HHP module integrates cold and abscisic acid signaling to activate the CBF-COR pathway in. Arabidopsis. Plant. Journal. 82, 962–977 (2015).
38. Nakata, M. et al. A bHLH-Type Transcription Factor, ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR/JA-ASSOCIATED MYC2-LIKE1, Acts as a Repressor to Negatively Regulate Jasmonate Signaling in Arabidopsis. Plant. Cell. 25, 1641–1656 (2013).
39. Qi, T. et al. Arabidopsis DELLA and JAZ Proteins Bind the WD-Repeat/bHLH/MYB Complex to Modulate Gibberellin and Jasmonate Signaling Synergy. Plant. Cell. 26, 1118–1133 (2014).
40. Liu, W. et al. bHLH122 is important for drought and osmotic stress resistance in Arabidopsis and in the repression of ABA catabolism. N. Phytol. 201, 1192–1204 (2014).
41. Fan, M. et al. The bHLH Transcription Factor HBI1 Mediates the Trade-Off between Growth and Pathogen-Associated Molecular Pattern-Triggered Immunity in Arabidopsis. Plant. Cell. 26, 828–841 (2014).
42. Phukan, U. J., Jeena, G. S. & Shukla, R. K. WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants. Front. plant. science. 7, 760 (2016).
43. Peng, Y. et al. OsWRKY62 is a negative regulator of basal and Xa21-mediated defense against Xanthomonas oryzae pv. oryzae in rice. Mol. Plant. 1, 446–458 (2008).
44. Chen, J. et al. Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Responses. Plant. Cell. 29, 1425–1439 (2017).
45. Shuai, B., Reynaga-Pena, C. G. & Springer, P. S. The LATERAL ORGAN BOUNDARIES gene defines a novel, plant-specific gene family. Plant. Physiology. 129, 747–761 (2002).
46. Li, C. et al. OsLBD37 and OsLBD38, two class II type LBD proteins, are involved in the regulation of heading date by controlling the expression of Ehd1 in rice. Biochemical And. Biophysical Res. Communications. 486, 720–725 (2017).
47. Fan, M., Xu, C., Xu, K. & Hu, Y. LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration. Cell Research. 22, 1169–1180 (2012).
48. Liu, J. et al. WOX11 and 12 Are Involved in the First-Step Cell Fate Transition during de Novo Root Organogenesis in Arabidopsis. Plant. Cell. 26, 1081–1093 (2014).
49. Lu, Q. et al. Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth. Plant. Biotechnol. J. 16, 124–136 (2018).
50. Lavenus, J. et al. Lateral root development in Arabidopsis: fifty shades of auxin. Trends Plant. Science. 18, 455–463 (2013).
51. Gil, J. F. et al. Massive up-regulation of LBD transcription factors and EXPANSINs highlights the regulatory programs of rhizomania disease. Mol. Plant. Pathology. 19, 2333–2348 (2018).
52. Kim, Y.-K. et al. ATHB23, an Arabidopsis class I homeodomain-leucine zipper gene, is expressed in the adaxial region of young leaves. Plant. Cell Reports. 26, 1179–1185 (2007).
53. Henriksson, E. et al. Homeodomain leucine zipper class I genes in Arabidopsis. Expression patterns and phylogenetic relationships. Plant. Physiology. 139, 509–518 (2005).
54. Barrero, J. M. et al. Gene expression profiling identifies two regulatory genes controlling dormancy and ABA sensitivity in Arabidopsis seeds. Plant. Journal. 61, 611–622 (2010).
55. Yang, H. J. et al. The OsEBP-89 gene of rice encodes a putative EREBP transcription factor and is temporally expressed in developing endosperm and intercalary meristem. Plant. Mol. Biology. 50, 379–391 (2002).
56. Sakuma, Y. et al. Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant. Cell. 18, 1292–1309 (2006).
57. Zhang, Z. & Huang, R. Enhanced tolerance to freezing in tobacco and tomato overexpressing transcription factor TERF2/LeERF2 is modulated by ethylene biosynthesis. Plant. Mol. Biology. 73, 241–249 (2010).
58. Peng, X. et al. Improved drought and salt tolerance of Arabidopsis thaliana by transgenic expression of a novel DREB gene from Leymus chinensis. Plant. Cell Reports. 30, 1493–1502 (2011).
59. Yi, S. Y. et al. The pepper transcription factor CaPF1 confers pathogen and freezing Tolerance in Arabidopsis. Plant. Physiology. 136, 2862–2874 (2004).
60. Zhang, G. et al. Overexpression of the soybean GmERF3 gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco. J. Of. Exp. Botany. 60, 3781–3796 (2009).
61. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30, 2114–2120 (2014).
62. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. biotechnology. 29, 644–652 (2011).
63. Krajaejun, T., Reamtong, O., Lohnoo, T., Yingyong, W. & Thammasudjarit, R. Assessment of temperature-dependent proteomes of Pythium insidiosum by using the SWISS-PROT database. Med. Mycology. 57, 918–921 (2019).
64. Finn, R. D. et al. The Pfam protein families database. Nucleic Acids Res. suppl_1 (2009).
65. Huerta-Cepas, J. et al. Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).
66. Kanehisa, M., Sato, Y., Furumichi, M., Morishima, K. & Tanabe, M. New approach for understanding genome variations in KEGG. Nucleic Acids Res. 47, D590–D595 (2019).
67. Huntley, R., Dimmer, E., Barrell, D., Binns, D., & Apweiler, R. The Gene Ontology Annotation (GOA) Database. Nature Precedings. (2009).
68. Alexa, A., Rahnenfuhrer, J. & Lengauer, T. Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics. 22, 1600–1607 (2006).
69. Xie, C. et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39, W316–W322 (2011).
70. Jin, J. P. et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 45, D1040–D1045 (2017).
71. Kalra, S. et al. De Novo Transcriptome Sequencing Reveals Important Molecular Networks and Metabolic Pathways of the Plant, Chlorophytum borivilianum. Plos One. 8 (2013).