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Research
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
- † Equal contributors
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
Genome Biology 2013, 14:R41 doi:10.1186/gb-2013-14-5-r41
Published: 10 May 2013Abstract
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.
