Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

Ming, R, VanBuren, R, Liu, Y, Yang, M, Han, Y, Li, LT, Zhang, Q, Kim, MJ, Schatz, MC, Campbell, M, Li, J, Bowers, JE, Tang, H, Lyons, E, Ferguson, AA, Narzisi, G, Nelson, DR, Blaby-Haas, CE, Gschwend, AR, Jiao, Y, Der, JP, Zeng, F, Han, J, Min, XJ, Hudson, KA, Singh, R, Grennan, AK, Karpowicz, SJ, Watling, JR, Ito, K, Robinson, SA, Hudson, ME, Yu, Q, Mockler, TC, Carroll, A, Zheng, Y, Sunkar, R, Jia, R, Chen, N, Arro, J, Wai, CM, Wafula, E, Spence, A, Han, Y, Xu, L, Zhang, J, Peery, R, Haus, MJ, Xiong, W, Walsh, JA, Wu, J, Wang, ML, Zhu, YJ, Paull, RE, Britt, AB, Du, C, Downie, SR, Schuler, MA, Michael, TP, Long, SP, Ort, DR, William Schopf, J, Gang, DR, Jiang, N, Yandell, M, dePamphilis, CW, Merchant, SS, Paterson, AH, Buchanan, BB, Li, S and Shen-Miller, J (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14 (5). ISSN 1474-760X

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Abstract

© 2013 Ming et al. Background: Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. Results: The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. Conclusions: The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.