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

  • Author(s): 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
  • 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
  • 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
  • William Schopf, J
  • Gang, David R
  • Jiang, Ning
  • Yandell, Mark
  • dePamphilis, Claude W
  • Merchant, Sabeeha S
  • Paterson, Andrew H
  • Buchanan, Bob B
  • Li, Shaohua
  • Shen-Miller, Jane
  • et al.
Abstract

Abstract 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.

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