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

Ray Ming12*, Robert VanBuren2, Yanling Liu1, Mei Yang1, Yuepeng Han1, Lei-Ting Li23, Qiong Zhang12, Min-Jeong Kim4, Michael C Schatz5, Michael Campbell6, Jingping Li7, John E Bowers8, Haibao Tang9, Eric Lyons10, Ann A Ferguson11, Giuseppe Narzisi5, David R Nelson12, Crysten E Blaby-Haas13, Andrea R Gschwend2, Yuannian Jiao147, Joshua P Der14, Fanchang Zeng2, Jennifer Han2, Xiang Jia Min15, Karen A Hudson16, Ratnesh Singh17, Aleel K Grennan2, Steven J Karpowicz18, Jennifer R Watling19, Kikukatsu Ito20, Sharon A Robinson21, Matthew E Hudson22, Qingyi Yu17, Todd C Mockler23, Andrew Carroll24, Yun Zheng25, Ramanjulu Sunkar26, Ruizong Jia27, Nancy Chen28, Jie Arro2, Ching Man Wai2, Eric Wafula14, Ashley Spence2, Yanni Han1, Liming Xu1, Jisen Zhang29, Rhiannon Peery2, Miranda J Haus2, Wenwei Xiong30, James A Walsh2, Jun Wu3, Ming-Li Wang27, Yun J Zhu2731, Robert E Paull28, Anne B Britt32, Chunguang Du30, Stephen R Downie2, Mary A Schuler233, Todd P Michael34, Steve P Long2, Donald R Ort235, J William Schopf36, David R Gang4, Ning Jiang11, Mark Yandell6, Claude W dePamphilis14, Sabeeha S Merchant13, Andrew H Paterson7, Bob B Buchanan37, Shaohua Li1* and Jane Shen-Miller36*

Author Affiliations

1 Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Road, Wuhan 430074, China

2 Department of Plant Biology, University of Illinois at Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL 61801, USA

3 College of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China

4 Institute of Biological Chemistry, Washington State University, Clark Hall, 100 Dairy Road, Pullman, WA 99164, USA

5 Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA

6 Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA

7 Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA

8 Department of Crop and Soil Sciences, University of Georgia, 120 Carlton Street, Athens, GA 30602, USA

9 J Craig Venter Institute, 9704 Medical Center Drive, 20850 Rockville, MD, USA

10 School of Plant Sciences, iPlant Collaborative Bio5 Institute, University of Arizona, 1657 East Helen Street, Tucson, AZ 85745, USA

11 Department of Horticulture, Michigan State University, A288 Plant and Soil Sciences Building, 1066 Bogue Street, East Lansing, MI 48824, USA

12 Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USA

13 Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, 607 Charles E Young Drive East, CA 90095, USA

14 Department of Biology and Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, 201 Life Sciences Building, University Park, PA 16802, USA

15 Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, 1 University Plaza, Youngstown, OH, 44555, USA

16 USDA-ARS, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA

17 Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX 75252, USA

18 Department of Biology, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034, USA

19 School of Earth and Environmental Sciences, University of Adelaide, North Terrace, Adelaide, 5005, Australia

20 Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan

21 Institute for Conservation Biology, The University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia

22 Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 West Peabody Drive, Urbana, IL 61801, USA

23 Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA

24 Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, Emeryville, CA 94720, USA

25 Institute of Developmental Biology and Molecular Medicine & School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China

26 Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA

27 Hawaii Agriculture Research Center, 94-340 Kunia Road, Waipahu, HI 96797, USA

28 Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA

29 Fujian Normal University, Qishan Campus, Minhou, Fuzhou, 350117, China

30 Department of Biology and Molecular Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA

31 Institute of Tropical Biosciences and Biotechnology, China Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, Hainan 571101, China

32 Department of Plant and Microbial Biology, University of California, 1 Shields Avenue, Davis CA, 95161, USA

33 Department of Cell and Developmental Biology, University of Illinois, 1201 West Gregory Drive, Urbana IL, 61801, USA

34 The Genome Analysis Center, Monsanto, St Louis, MO 63167, USA

35 Global Change and Photosynthesis Research Unit, Agricultural Research Service, United States Department of Agriculture, 1206 West Gregory Drive, Urbana, IL, USA

36 IGPP Center for the Study of Evolution and Origin of Life, Geology Building, Room 5676, University of California, Los Angeles, 595 Charles E Young Drive East, Los Angeles, CA 90095-1567, USA

37 Department of Plant and Microbial Biology, University of California, 411 Koshland Hall, Berkeley, CA 94720, USA

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Genome Biology 2013, 14:R41  doi:10.1186/gb-2013-14-5-r41

Published: 10 May 2013

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.