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

R. Ming,R. VanBuren,Yanling Liu,Mei Yang,Yuepeng Han,Leiting Li,Qiong Zhang,Min-Jeong Kim,M. Schatz,Michael Campbell,Jingping Li,J. Bowers,Haibao Tang,E. Lyons,Ann A. Ferguson,G. Narzisi,D. Nelson,Crysten E. Blaby-Haas,Andrea R Gschwend,Yuannian Jiao,J. Der,Fanchang Zeng,Jennifer O. Han,X. Min,K. Hudson,Ratnesh K Singh,A. K. Grennan,Steven J. Karpowicz,J. Watling,Kikukatsu Ito,S. Robinson,M. Hudson,Qingyi Yu,T. Mockler,Andrew Carroll,Yun Zheng,R. Sunkar,Ruizong Jia,N. Chen,J. Arro,C. M. Wai,E. Wafula,Ashley K. Spence,Yan-Chuang Han,Liming Xu,Jisen Zhang,R. Peery,Miranda J. Haus,Wenwei Xiong,J. A. Walsh,Jun Wu,Ming-li Wang,Yun Zhu,R. Paull,A. Britt,Chunguang Du,S. R. Downie,M. Schuler,T. Michael,S. Long,D. Ort,J. William Schopf,D. Gang,Ning Jiang,M. Yandell,C. dePamphilis,S. Merchant,A. Paterson,B. Buchanan,Shaohua Li,J. Shen-Miller

Published 2013 in Genome Biology

ABSTRACT

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. 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. 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.

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