Abdelrahman, M., Burritt, D.J., Gupta, A., Tsujimoto, h., Tran, L.P. (2019b) Heat stress effects on source-sink relationships and metabolome dynamics in wheat. Experimental Botany 71: 543–554
Abdelrahman, M., El-Sayed, M., Sato, S., Hirakawa, H., Ito, S.I., Tanaka, K., et al. (2017c) RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PLoS One 12: e0181784.
Abdelrahman, M., Hirata, S., Sawada, Y., Hirai, M.Y., Sato, S., Hirakawa, H., et al. (2019a) Widely targeted metabolome and transcriptome landscapes of Allium fistulosum–A. cepa chromosome addition lines revealed a flavonoid hot spot on chromosome 5A. Scientific Reports 9: 3541.
Abdelrahman, M., Jogaiah, S., Burritt, D.J., Tran, L.P. (2018) Legume genetic resources and transcriptome dynamics under abiotic stress conditions. Plant Cell Environ. doi: 10.1111/pce.13123.
Abdelrahman, M., Mitoma, M., Ikeuchi, T., Mori, M., Murakami, K.,Ozakid, Y. (2018) Differential gene expression analysis and SNP/InDel marker discovery in resistant wild Asparagus kiusianus and susceptible A. officinalis in response to Phomopsis asparagi infection. Data in Brief 21: 2117–2121.
Abdelrahman, M., Sawada, Y., Nakabayashi, R., Sato, S., Hirakawa, H., El-Sayed, M., et al. (2015) Integrating transcriptome and target metabolome variability in doubled haploids of Allium cepa for abiotic stress protection. Molecular Breeding 35: 195.
Abdelrahman, M., Suzumura, N., Mitoma, M., Matsuo, S., Ikeuchi, T., Mori, M., et al. (2017b) Comparative de novo transcriptome profiles in Asparagus officinalis and A. kiusianus during the early stage of Phomopsis asparagi infection. Scientific Reports 7: 2608.
Ashkani, S., Rafii, M.Y., Shabanimofrad, M., Miah, G., Sahebi, M., Azizi, P., et al. (2015) Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop. Front Plant Science 6: 886.
Cheah, L-H., Horlock, C.M. (2007) Field-applied fungicides and postharvest treatments to control Asparagus diseases posing biosecurity threats to New Zealand. New Zealand. Plant Protection 60:94–98.
Chitrakar, B., Zhang, M., Adhikari, B. (2019) Asparagus (Asparagus officinalis): Processing effect on nutritional and phytochemical composition of spear and hard-stem byproducts. Trends Food Science Technology 93: 1–11.
Dawid, C., Hofmann, T. (2012) Identification of sensory-active phytochemicals in Asparagus (Asparagus officinalis L.). J Agriculture Food Chemistry 60: 11877–11888.
Di Maro, A., Pacifico, S., Fiorentino, A., Galasso, S., Gallicchio, M., Guida, V., et al. (2013) Raviscanina wild asparagus (Asparagus acutifolius L.): A nutritionally valuable crop with antioxidant and antiproliferative properties. Food Research International 53:180–188.
Die, J.V., Castro, P., Millán, T., Gil, J. (2018) Segmental and tandem duplications driving the recent NBS-LRR gene expansion in the Asparagus genome. Genes 9: 568.
Dong, T., Han, R., Yu, J., Zhu, M., Zhang, Y., Gong, Y., Li, Z. (2019) Anthocyanins accumulation and molecular analysis of correlated genes by metabolome and transcriptome in green and purple asparaguses (Asparagus officinalis, L.). Food Chemistry 217: 18–28.
Ferreyra, M.L.F., Rius, S.P., Casati, P. (2012) Flavonoids: biosynthesis, biological functions, and biotechnological applications. Frontiers Plant Science 3: 222.
Garrett, A.K., Andersen, K.F., Asche, F., Bowden, R.L., Forbes, G.A., Kulakow, P.A., et al. (2017) Resistance genes in global crop breeding networks. Phytopathology 107: 1268- 1278.
Harkess, A., Zhou, J., Xu, C., Bowers, J.E., Van der Hulst, R., Ayyampalayam, S., et al. (2017) Origin and evolution of a young Y chromosome. Nature Communications 8:1279.
Hayes, P.Y., Jahidin, A.H., Lehmann, R., Penman, K., Kitching, W., De Voss, J.J. (2008) Steroidal saponins from the roots of Asparagus racemosus. Phytochemistry 69: 796-804.
He, C., Hsiang, T., Wolyn, D.J. (2001) Activation of defense responses to Fusarium infection in Asparagus densiflorus. European J Plant Pathology 107: 473–483.
Hussain, M., Debnath, B., Qasim, M., Bamisile, B.S., Islam, W., Hameed, M.S., et al. (2019) Role of saponins in plant defense against specialist herbivores. Molecules 24: 2067.
Ito, T., Konno, I., Kubota, S., Ochiai, T., Sonoda, T., Hayashi, Y., et al. (2011) Production and characterization of interspecific hybrids between Asparagus kiusianus Makino and A. officinalis L. Euphytica 182: 285–294.
Iwato, M., Kosaza, M., Takeuchi, Y., Matsumoto, M., Inada, M., Ozaki, Y., et al. (2014) Stem blight resistance of Asparagus kiusianus and its hybrid with A. officinalis. Advances Horticultural Science 28: 202–207.
Jaramillo-Carmona, S., Rodriguez-Arcos, R, Jiménez-Araujo, A., López, S., Gil, J., Moreno, R., Guillén-Bejarano, R. (2017) Saponin profile of wild Asparagus species. Food Science 82: 638–646.
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L. (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14: R36.
Kubota, S., Konno, I., Kanno, K. (2012) Molecular phylogeny of the genus Asparagus (Asparagaceae) explains interspecific crossability between the garden asparagus (A. officinalis) and other Asparagus species. Theoretical Applied Genetics 124:345–354.
Langmead, B., Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9: 357–359.
Lei, Z., Zhou, C., Ji, X., Wei, G., Huang, Y., Yu, W., et al. (2018) Transcriptome analysis reveals genes involved in flavonoid biosynthesis and accumulation in Dendrobium catenatum from different locations. Scientific Reports 8: 6373.
Li, B., Dewey, C.N. (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12:323.
Lu, Y., Chen, Q., Bu, Y., Luo, R., Hao, S., Zhang, J., et al. (2017) Flavonoid accumulation plays an important role in the rust resistance of malus plant leaves. Frontiers Plant Science 8: 1286.
Matsuda, F., Nakabayashi, R., Yang, Z., Okazaki, Y., Yonemaru, J-I., Ebana, K., et al. (2015) Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. Plant J 81: 13-23.
Monteiro, F., Sebastiana, M., Pais, M., Figueiredo, A. (2013) Reference gene selection and validation for the early responses to downy mildew infection in susceptible and resistant Vitis vinifera cultivars. PLoS ONE 8:e72998.
Mostafa, A., Sudisha, J., El-Sayed, M., Ito, S., Ikeda, T., Yamauchi, N., et al. (2013) Aginoside saponin, a potent antifungal compound, and secondary metabolite analyses from Allium nigrum L. Phytochem Lett 6: 274–280.
Murphy, A.M., Otto, B., Brearley, C.A., Carr, J.P., Hanke, D.E. (2008) A role for inositol hexakisphosphate in the maintenance of basal resistance to plant pathogens. Plant J 56: 638–652.
Nakamura, Y., Afendi, F.M., Parvin, A.K., Ono, N., Tanaka, K., Hirai Morita, A., et al. (2014) KNApSAcK Metabolite Activity Database for retrieving the relationships between metabolites and biological activities. Plant Cell Physiology 55:e7.
Negi, J.S., Singh, P., Joshi, G.P., Rawat, M.S., Bisht, V.K. (2010) Chemical constituents of Asparagus. Pharmacogn Rev 4: 215–220.
Nowogórska, A., Patykowski, J. (2015) Selected reactive oxygen species and antioxidant enzymes in common bean after Pseudomonas syringae pv. phaseolicola and Botrytis cinerea infection. Acta Physiologiae Plantarum 37:1725.
Olsen, K.M., Hehn, A., Jugdé, H., Slimestad, R., Larbat, R., Bourgaud, F. (2010) Identification and characterisation of CYP75A31, a new flavonoid 3'5'-hydroxylase, isolated from Solanum lycopersicum. BMC Plant Biology 10: 21.
Powell, J.J., Carere, J., Sablok, G., Fitzgerald, T.L., Stiller, J., Colgrave, M.L., et al. (2017) Transcriptome analysis of Brachypodium during fungal pathogen infection reveals both shared and distinct defense responses with wheat. Scientific Reports 7:17212.
Ramírez, V., López, A., Mauch-Mani, B., José Gil, M., Vera, P. (2013) An extracellular subtilase switch for immune priming in Arabidopsis. PLOS Pathogens 12: e1006003.
Robinson, M.D., McCarthy, D.J., Smyth, G.K. (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139– 140.
Robinson, M.D., Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11: R25.
Roos, J., Hopkins, R., Kvarnheden, A., Dixelius, C. (2011) The impact of global warming on plant diseases and insect vectors in Sweden. European J Plant Pathology 129: 9–19.
Sakaguchi, Y., Mine, Y., Okubo, H. and Ozaki, Y. (2008). Anthocyanin variation in Asparagus species and its inheritance Acta Horticulturae 776: 285–290.
Sharma, U., Saini, R., Bobita, Kumar, N., Singh, B. (2009). Steroidal saponins from Asparagus racemosus. Chemical Pharmaceutical Bulletin 57: 890–893.
Singh, G., Tiwari, M., Singh, S.P., Singh, S., Trivedi, P.K., Misra, P. (2016) Silencing of sterol glycosyltransferases modulates the withanolide biosynthesis and leads to compromised basal immunity of Withania somnifera. Scientific Reports 6: 25562.
Shen, Y., Xu, C-L., Xuan, W-D., Li, H-L., Liu, R-H., Xu, X-K., Chen H-S. (2011) A new furostanol saponin from Asparagus cochinchinensis. Archives Pharmacal Research 34: 1587–1591.
Sonoda, T., Uragami, A., Itoh, K., Kohmura, H., Ohwada, M., Kaji, K. (2001) Evaluation of Asparagus species and comparison between sexes in A. officinalis cultivars for resistance to stem blight. J Japanese Society Horticultural Science 70:244–250.
Sonoda, T., Uragami, A., Kaji, K. (1997) Evaluation of Asparagus officinalis cultivars for resistance to stem blight by using a novel inoculation method. Horticultural Science 32:1085–1086.
Srivastava, P.L., Shukla, S., Kalunke, R.M. (2018) Comprehensive metabolic and transcriptomic profiling of various tissues provide insights for saponin biosynthesis in the medicinally important Asparagus racemosus. Scientific Reports 8: 9098.
Taggar, G.K., Gill, R.S., Gupta, A.K., Sandhu, J.S. (2012) Fluctuations in peroxidase and catalase activities of resistant and susceptible black gram (Vigna mungo (L.) Hepper) genotypes elicited by Bemisia tabaci (Gennadius) feeding. Plant Signaling Behavior 7: 1321–1329.
Takahashi, H., Yoshida, C., Takeda, T. (2019) Sugar composition in Asparagus spears and its relationship to soil chemical properties. Journal Applied Glycoscience 66: 47–50.
Takeuchi, Y., Kakizoe, E., Yoritomi, R., Iwato, M., Kanno, A., Ikeuchi, T., et al. (2017) Features in stem blight resistance confirmed in interspecific hybrids of Asparagus officinalis L. and Asparagus kiusianus Makino. Horticult J 87: 200–205.
Thao, L.D., Dung, N.T. (2019) First report of Phomopsis asparagi causing stem blight on asparagus in Vietnam. New Disease Reports 39: 7.
Tossi, V.E., Regalado, J.J., Iannicelli, J., Laino, L.E., Burrieza, H.P., Escandón, A.S., et al. (2019) Beyond Arabidopsis: Differential UV-B response mediated by UVR8 in diverse species. Frontiers Plant Science 10: 780.
Tsugawa, H., Nakabayashi, R., Mori, T., Yamada, Y., Takahashi, M., Rai, A., et al. (2019) A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms. Nature Methods 16: 295–298.
Vázquez-Castilla, S., Jaramillo-Carmona, S., Fuentes-Alventosa, J.M., Jiménez-Araujo, A., Rodriguez-Arcos, R., Cermeño-Sacristán, P., et al. (2013) Optimization of a method for the profiling and quantification of saponins in different green asparagus genotypes. J Agriculture Food Chemistry 61: 6250-6258.Xiao, J.F., Zhou, B., Ressom, H.W. (2012) Metabolite identification and quantitation in LC-MS/MS-based metabolomics. Trends Analytical Chemistry 32: 1–14.
Yang, Y-Q., Lan, B., Jian, Y-L., Chang, D-D., Zhang, S-L., Li, X-M. (2016) Infection process and pathogenic mechanism of Phomopsis asparagi, the Asparagus stem blight pathogen. Phytoparasitica 44:11–18.
Yano, R., Takagi, K., Takada, Y., Mukaiyama, K., Tsukamoto, C., Sayama, T., et al. (2016) Metabolic switching of astringent and beneficial triterpenoid saponins in soybean is achieved by a loss-of-function mutation in cytochrome P450 72A69. Plant J 89: 527-539.
Yi, T.G., Yeoung, Y.R., Choi, I.Y., Park, N.I. (2019) Transcriptome analysis of Asparagus officinalis reveals genes involved in the biosynthesis of rutin and protodioscin. PLoS One 14: e0219973.
Zaw, M., Naing, T.A.A., Matsumoto, M., (2017) First report of stem blight of asparagus caused by Phomopsis asparagi in Myanmar. New Disease Reports 35: 17.
Zhang, H-J., Sydara, K., Tan, G., Ma, C., Southavong, B., Soejarto, D.D., et al. (2004) Bioactive Constituents from Asparagus cochinchinensis. J Natural Product 67: 194-200.
Zhang, N., Sun, Q., Li, H., Li, X., Cao, Y., Zhang, H., et al. (2016) Melatonin improved anthocyanin accumulation by regulating gene expressions and resulted in high reactive oxygen species scavenging capacity in cabbage. Frontiers Plant Science 7: 197.