Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
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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.
Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L., ... Shen-Miller, J.
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Ming, Ray||VanBuren, Robert||Liu, Yanling||Yang, Mei||Han, Yuepeng||Li, Lei-Ting||Zhang, Qiong||Kim, Min-Jeong||Schatz, Michael C||Campbell, Michael||Li, Jingping||Bowers, John E||Tang, Haibao||Lyons, Eric||Ferguson, Ann A||Narzisi, Giuseppe||Nelson, David R||Blaby-Haas, Crysten E||Gschwend, Andrea R||Jiao, Yuannian||Der, Joshua P||Zeng, Fanchang||Han, Jennifer||Min, Xiang Jia||Hudson, Karen A||Singh, Ratnesh||Grennan, Aleel K||Karpowicz, Steven J||Watling, Jennifer R||Ito, Kikukatsu||Robinson, Sharon A||Hudson, Matthew E||Yu, Qingyi||Mockler, Todd C||Carroll, Andrew||Zheng, Yun||Sunkar, Ramanjulu||Jia, Ruizong||Chen, Nancy||Arro, Jie||Wai, Ching Man||Wafula, Eric||Spence, Ashley||Han, Yanni||Xu, Liming||Zhang, Jisen||Peery, Rhiannon||Haus, Miranda J||Xiong, Wenwei||Walsh, James A||Wu, Jun||Wang, Ming-Li||Zhu, Yun J||Paull, Robert E||Britt, Anne B||Du, Chunguang||Downie, Stephen R||Schuler, Mary A||Michael, Todd P||Long, Steve P||Ort, Donald R||Schopf, J William||Gang, David R||Jiang, Ning||Yandell, Mark||dePamphilis, Claude W||Merchant, Sabeeha S||Paterson, Andrew H||Buchanan, Bob B||Li, Shaohua||Shen-Miller, Jane
