Benjamini, Y. and Hochberg, Y. (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. 57:289-300.
Birschwilks, M., Sauer, N., Scheel, D., and Neumann, S. (2007). Arabidopsis thaliana is a susceptible host plant for the holoparasite Cuscuta spec. Planta. 226:1231-41.
Carlsbecker, A., and Helariutta, Y. (2005). Phloem and xylem specification: pieces of the puzzle emerge. Current Opinion in Plant Biology. 8:512-517. doi: 10.1016/j.pbi. 2005.07.001
Chen, D., Shao, Q., Yin, L., and Zheng, B. (2019). Polyamine Function in Plants: Metabolism, Regulation on Development, and Roles in Abiotic Stress Responses. Frontiers in Plant Science. 9:1945. doi: 10.3389/fpls.2018.01945.
Dawson, J.H., Musselman, L.J., Wolswinkel, P., and Dörr, I. (1994). Biology and control of Cuscuta. Reviews of Weed Science 6:265-317.
De Rybel, B., Möller, B., Yoshida, S., Grabowicz, I., Barbier, de Reuille, P., Boeren, S., Smith, R.S., Borst, J.W., and Weijers, D. (2013). A bHLH complex controls embryonic vascular tissue establishment and indeterminate growth in Arabidopsis. Developmental Cell. 24:426-37. doi: 10.1016/j.devcel.2012.12.013.
Demura, T., Tashiro, G., Horiguchi, G., Kishimoto, N., Kubo, M., Matsuka, N., MInami, A., Nagata-Hiwatashi, M., Nakamura, K., Okamura, Y., Sassa, N., Suzuki, S., Yazaki, J., Kikuchi, S., and Fukuda, H. (2002). Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation of mesophyll cells into xylem cells. Proceeding of the National Academy of Sciences of the United States of America. 99:15794-9.
Endo, H., Yamaguchi, M., Tamura, T., Nakano, Y., Nishikubo, N., Yoneda, A., Kato, K., Kubo, M,. Kajita, S., Katayama, Y., Ohtani, M., and Demura, T. (2015). Multiple classes of transcription factors regulate the expression of VASCULAR-RELATED NAC- DOMAIN7, a master switch of xylem vessel differentiation. Plant and Cell Physiology. 56:242-54. doi: 10.1093/pcp/pcu134.
Fukuda, H. (2004). Signaling that control plant vascular cell differentiation. Molecular Cell Biology. 5:379-91. doi: 10.1038/nrm1364
Fukuda, H. (2016). Signaling, transcriptional regulation, and asynchronous pattern formation governing plant xylem development. Proceeding of Japan Academy. Series B, Physical and biological sciences. 92:98-107. doi: 10.2183/pjab.92.98.
Futschik, M.E., and Carlisle, B. (2005). Noise-robust soft clustering of gene expression time-course data. Journal of Bioinformatics and Computational Biology. 3:965-88.
Heide-Jørgensen, H.S. (2008). Parasitic flowering plants. Leiden: Brill
Hong, L., Shen, H., Chen, H., Hu, X., Xu, X., Ye, W., and Wang, Z. (2011). The Morphology and Anatomy of the Holoparasitic Angiosperm Cuscuta campestris. Pakistan Journal of Botany 43:1853-1859
Ikeue, D., Schudoma, C., Zhang, W., Ogata, Y., Sakamoto, T., Kurata, T., Furahashi, T., Kragler, F., and Aoki, K. (2015). A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads. Plant Methods 11:34. doi: 10.1186/s13007-015-0066-6.
Johnson, N.L., Kotz, S., and Kemp, A.W. (1992). UnivariatDeiscrete Distribution (Second Edition). New York: John Wiley and Sons.
Katoh, K., and Standley D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution. 30:772-80. doi: 10.1093/molbev/mst010.
Kim, D., Langmead, B., and Salzberg, S.L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 12:357-60. doi: 10.1038/nmeth.3317.
Kondo, Y., Nurani, A.M., Saito, C., Ichihashi, Y., Saito, M., Yamazaki, K., Mitsuda, N., Ohme-Takagi, M., and Fukuda, H. (2016). Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-Like Cells. The Plant Cell. 28:1250-62. doi: 10.1105/tpc.16.00027.
Kubo, M., Udagawa, M., Nishikubo, N., Horiguchi, G., Yamaguchi, M., Ito, J., Mimura, T., Fukuda, H., and Demura, T. (2005). Transcription switches for protoxylem and Metaxylem vessel formation. Gene and Development. 19: 1855-1860.
Kumar, S., Stecher, G., and Tamura, K. (2016). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 33:1870-4. doi: 10.1093/molbev/msw054.
Lamesch, P., Berardini, T.Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D.L., Garcia-Hernandez, M., Karthikeyan, A.S., Lee, C.H., Nelson, W.D., Ploetz, L., Singh, S., Wensel, A., and Huala, E. (2012). The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research. 40:D1202-10. doi: 10.1093/nar/gkr1090.
Lane, H.C., and Kasperbauer, M.J. (1965). Photomorphogenic Responses of Dodder Seedlings. Plant Physiology. 40: 109-16
Lee, K.B. (2009). Structure and Development of the Endophyte in the Parasitic Angiosperm Cuscuta japonica. Journal of Plant Biology 52:355-363. doi: 10.1007/ s12374-009-9046-6.
Lymperopoulos, P., Msanne, J., and Rabara, R. (2018). Phytochrome and Phytohormones: Working in Tandem for Plant Growth and Development. Frontiers in Plant Science. 9:1037. doi: 10.3389/fpls.2018.01037.
McCarthy, R.L., Znong, R., and Ye, Z.H. (2009). MYB83 is a direct target of SND1 and acts redundantly with MYB46 in the regulation of secondary cell wall biosynthesis in Arabidopsis. Plant and Cell Physiology. 50:1950-64. doi: 10.1093/pcp/pcp139.
Nagar, R., Singh, M., and Sanwal, G.G. (1984). Cell Wall Degrading Enzymes in Cuscuta reflexa and Its Host. Journal of Experimental Biology 35:1104-1112. doi: 10.1093/jxb/35.8.1104.
Ohashi-Ito, K., Demura, T., and Fukuda, H. (2002). Promotion of Transcript Accumulation of Novel Zinnia Immature Xylem-Specific HD-Zip III Homeobox Genes by Brassinosteroids. Plant and Cell Physiology. 43:1146-53.
Ohashi-Ito, K., Saegusa, M., Iwamoto, K., Oda, Y., Katayama, H., Kojima, M., Sakakibara, H., and Fukuda, H. (2014). A bHLH complex activates vascular cell division via cytokinin action in root apical meristem. Current Biology. 24:2053-8. doi: 10.1016/j.cub.2014.07.050.
Okamura, M., Nakayama, M., Umemoto, N., Cano, E.A., Hase, Y., Nishizaki, Y., Sasaki, N., and Ozemi, Y. (2013). Crossbreeding of a metallic color carnation and diversification of the peculiar coloration by ion-beam irradiation. Euphytica. 191:45-56. doi: 10.1007/s10681-012-0859-x
Olsen, S., Striberny, B., Hollmann, J., Schwocke, R.,Popper, Z., and Krause, K. (2016). Getting ready for host invasion: elevated expression and action of xyloglucan endotransglucosylases/hydrolases in developing haustoria of the holoparasitic angiosperm Cuscuta. Journal of Experimental Botany 67:695-708. doi: 10.1093/jxb/ erv482.
Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T., and Salzberg, S.L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnology. 33:290-5. doi: 10.1038/nbt.3122.
Ranjan, A., Ichihashi, Y., Farhi, M., Zumstein, K., Townsley, B., David-Schwartz, R., and Sinha. N.R. (2014). De novo assembly and characterization of the transcriptome of the parasitic weed dodder identifies genes associated with plant parasitism. Plant Physiology 166:1186-1199. doi: 10.1104/pp.113.234864.
Scarpella, E., Marcos, D., Friml, J., and Berleth, T. (2006). Control of leaf vascular patterning by polar auxin transport. Genes and development. 20:1015-27.
Schlereth, A., Möller, B., Liu, W., Kientz, M., Flipse, J., Rademacher, E.H., Schmid, M., Jürgens, G., and Weijers, D. (2010). MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Nature. 464:913-6. doi: 10.1038/nature08836.
Shimizu, K., Hozumi, A., and Aoki, K. (2018). Organization of Vascular Cells in the Haustorium of the Parasitic Flowering Plant Cuscuta japonica. Plant and Cell Physiology. 59:715-723. doi: 10.1093/pcp/pcx197.
Sun, J., Nishiyama, T., Shimizu, K., and Kadota, K. (2013). TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics. 14:219. doi: 10.1186/1471-2105-14-219.
Tada, Y., Sugai, M., and Furuhashi, K. (1996). Haustoria of Cusucuta japonica, a holoparasitic flowering plant, are induced by a cooperative effect of far-red light and tactile stimuli. Plant Cell Physiology 37:1049-1053. doi: 10.1093/ oxfordjournals.pcp.a029052.
Tan, T.T., Endo, H., Sano, R., Kurata, T., Yamaguchi, M., Ohtani, M., and Demura, T. (2018). Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation. Plant Physiology. 176:773-789. doi: 10.1104/pp.17.00461.
Taylor, N.G., Howells, R.M., Huttly, A.K., Vickers, K., and Turner, S.R. (2003). Interactions among three distinct CesA proteins essential for cellulose synthesis. Proceeding of the National Academy of Sciences of the United States of America. 100:1450-5.
Taylor, N.G., Laurie, S., and Turner, S.R. (2000). Multiple cellulose synthase catalytic subunits are required for cellulose synthesis in Arabidopsis. The Plant Cell. 12:2529-2540.
Tsukaya, H., Ohshima, T., Naito, S., Chino, M., and Komeda, Y. (1991). Sugar- dependent Expression of the CHS-A Gene for Chalcone Synthase from Petunia in Transgenic Arabidopsis. Plant Physiology 97:1414-21.
Vogel, A., Schwacke, R., Denton, A.K., Usadel, B., Hollman, J., Fischer, K., Bolger, A., Schmidt, M.H., Bolger, M.E., Gundlach, H., Mayer, K.F.X., Weiss-Schneeweiss, H., Temsch, E.M., and Krause, K. (2018). Footprints of parasitism in the genome of the parasitic flowering plant Cuscuta campestris. Nature Communications 9:2515. doi: 10.1038/s41467-018-04344-z.
Westwood, J.H., Yoder, J.I., Timko, M.P., and dePamphills, C.W. (2010). The evolution of parasitism in plants. Trends Plant Science. 15:227-35. doi: 10.1016/j.tplants. 2010.01.004.
Yamaguchi, H., Hase, Y., Tanaka, A., Shikazono, N., Degi, K., Shimizu, A., and Morishita, T. (2009). Mutagenic effects of ion-beam irradiation on rice. Breeding Science. 59:169-77. doi: 10.1270/jsbbs.59.169.
Zhong, R., Richardson, E.A., and Ye, Z.H. (2007). The MYB46 transcription factor is a direct target of SND1 and regulates secondary wall biosynthesis in Arabidopsis. The Plant Cell. 19:2776-92.