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

Persistent Link:
http://hdl.handle.net/10150/610151
Title:
Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)
Author:
Ming, Ray; VanBuren, Robert; Liu, Yanling; Yang, Mei; Han, Yuepeng; Li, Lei-Ting; Zhang, Qiong; Kim, Min-Jeong; Schatz, Michael; Campbell, Michael; Li, Jingping; Bowers, John; Tang, Haibao; Lyons, Eric; Ferguson, Ann; Narzisi, Giuseppe; Nelson, David; Blaby-Haas, Crysten; Gschwend, Andrea; Jiao, Yuannian; Der, Joshua; Zeng, Fanchang; Han, Jennifer; Min, Xiang; Hudson, Karen; Singh, Ratnesh; Grennan, Aleel; Karpowicz, Steven; Watling, Jennifer; Ito, Kikukatsu
Affiliation:
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Road, Wuhan 430074, China; Department of Plant Biology, University of Illinois at Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL 61801, USA; College of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China; Institute of Biological Chemistry, Washington State University, Clark Hall, 100 Dairy Road, Pullman, WA 99164, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Eccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USA; Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA; Department of Crop and Soil Sciences, University of Georgia, 120 Carlton Street, Athens, GA 30602, USA; J Craig Venter Institute, 9704 Medical Center Drive, 20850 Rockville, MD, USA; School of Plant Sciences, iPlant Collaborative Bio5 Institute, University of Arizona, 1657 East Helen Street, Tucson, AZ 85745, USA; Department of Horticulture, Michigan State University, A288 Plant and Soil Sciences Building, 1066 Bogue Street, East Lansing, MI 48824, USA; Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USA; 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; Department of Biology and Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, 201 Life Sciences Building, University Park, PA 16802, USA; Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, 1 University Plaza, Youngstown, OH, 44555, USA; USDA-ARS, Purdue University, 915 West State Street, West Lafayette, IN 47907, USA; Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX 75252, USA; Department of Biology, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034, USA; School of Earth and Environmental Sciences, University of Adelaide, North Terrace, Adelaide, 5005, Australia; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japan; Institute for Conservation Biology, The University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia; Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 West Peabody Drive, Urbana, IL 61801, USA; Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA; Lawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, Emeryville, CA 94720, USA; Institute of Developmental Biology and Molecular Medicine & School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China; Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA; Hawaii Agriculture Research Center, 94-340 Kunia Road, Waipahu, HI 96797, USA; Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA; Fujian Normal University, Qishan Campus, Minhou, Fuzhou, 350117, China; Department of Biology and Molecular Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA; Institute of Tropical Biosciences and Biotechnology, China Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, Hainan 571101, China; Department of Plant and Microbial Biology, University of California, 1 Shields Avenue, Davis CA, 95161, USA; Department of Cell and Developmental Biology, University of Illinois, 1201 West Gregory Drive, Urbana IL, 61801, USA; The Genome Analysis Center, Monsanto, St Louis, MO 63167, USA; Global Change and Photosynthesis Research Unit, Agricultural Research Service, United States Department of Agriculture, 1206 West Gregory Drive, Urbana, IL, USA; 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; Department of Plant and Microbial Biology, University of California, 411 Koshland Hall, Berkeley, CA 94720, USA
Issue Date:
2013
Publisher:
BioMed Central
Citation:
Ming et al. Genome Biology 2013, 14:R41 http://genomebiology.com/2013/14/5/R41
Journal:
Genome Biology
Rights:
© 2013 Ming et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
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 101x and 5.2x. 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.
DOI:
10.1186/gb-2013-14-5-r41
Version:
Final published version
Additional Links:
http://genomebiology.com/2013/14/5/R41

Full metadata record

DC FieldValue Language
dc.contributor.authorMing, Rayen
dc.contributor.authorVanBuren, Roberten
dc.contributor.authorLiu, Yanlingen
dc.contributor.authorYang, Meien
dc.contributor.authorHan, Yuepengen
dc.contributor.authorLi, Lei-Tingen
dc.contributor.authorZhang, Qiongen
dc.contributor.authorKim, Min-Jeongen
dc.contributor.authorSchatz, Michaelen
dc.contributor.authorCampbell, Michaelen
dc.contributor.authorLi, Jingpingen
dc.contributor.authorBowers, Johnen
dc.contributor.authorTang, Haibaoen
dc.contributor.authorLyons, Ericen
dc.contributor.authorFerguson, Annen
dc.contributor.authorNarzisi, Giuseppeen
dc.contributor.authorNelson, Daviden
dc.contributor.authorBlaby-Haas, Crystenen
dc.contributor.authorGschwend, Andreaen
dc.contributor.authorJiao, Yuannianen
dc.contributor.authorDer, Joshuaen
dc.contributor.authorZeng, Fanchangen
dc.contributor.authorHan, Jenniferen
dc.contributor.authorMin, Xiangen
dc.contributor.authorHudson, Karenen
dc.contributor.authorSingh, Ratneshen
dc.contributor.authorGrennan, Aleelen
dc.contributor.authorKarpowicz, Stevenen
dc.contributor.authorWatling, Jenniferen
dc.contributor.authorIto, Kikukatsuen
dc.date.accessioned2016-05-20T08:59:43Z-
dc.date.available2016-05-20T08:59:43Z-
dc.date.issued2013en
dc.identifier.citationMing et al. Genome Biology 2013, 14:R41 http://genomebiology.com/2013/14/5/R41en
dc.identifier.doi10.1186/gb-2013-14-5-r41en
dc.identifier.urihttp://hdl.handle.net/10150/610151-
dc.description.abstractBACKGROUND: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 101x and 5.2x. 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 expressionen
dc.description.abstractthese 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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://genomebiology.com/2013/14/5/R41en
dc.rights© 2013 Ming et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleGenome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)en
dc.typeArticleen
dc.contributor.departmentKey Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Lumo Road, Wuhan 430074, Chinaen
dc.contributor.departmentDepartment of Plant Biology, University of Illinois at Urbana-Champaign, 1201 West Gregory Drive, Urbana, IL 61801, USAen
dc.contributor.departmentCollege of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, Chinaen
dc.contributor.departmentInstitute of Biological Chemistry, Washington State University, Clark Hall, 100 Dairy Road, Pullman, WA 99164, USAen
dc.contributor.departmentSimons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USAen
dc.contributor.departmentEccles Institute of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT 84112, USAen
dc.contributor.departmentPlant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USAen
dc.contributor.departmentDepartment of Crop and Soil Sciences, University of Georgia, 120 Carlton Street, Athens, GA 30602, USAen
dc.contributor.departmentJ Craig Venter Institute, 9704 Medical Center Drive, 20850 Rockville, MD, USAen
dc.contributor.departmentSchool of Plant Sciences, iPlant Collaborative Bio5 Institute, University of Arizona, 1657 East Helen Street, Tucson, AZ 85745, USAen
dc.contributor.departmentDepartment of Horticulture, Michigan State University, A288 Plant and Soil Sciences Building, 1066 Bogue Street, East Lansing, MI 48824, USAen
dc.contributor.departmentDepartment of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue Suite G01, Memphis, TN 38163, USAen
dc.contributor.departmentDepartment of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, 607 Charles E Young Drive East, CA 90095, USAen
dc.contributor.departmentDepartment of Biology and Intercollege Graduate Program in Plant Biology, The Pennsylvania State University, 201 Life Sciences Building, University Park, PA 16802, USAen
dc.contributor.departmentCenter for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, 1 University Plaza, Youngstown, OH, 44555, USAen
dc.contributor.departmentUSDA-ARS, Purdue University, 915 West State Street, West Lafayette, IN 47907, USAen
dc.contributor.departmentTexas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX 75252, USAen
dc.contributor.departmentDepartment of Biology, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034, USAen
dc.contributor.departmentSchool of Earth and Environmental Sciences, University of Adelaide, North Terrace, Adelaide, 5005, Australiaen
dc.contributor.departmentCryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, Iwate 020-8550, Japanen
dc.contributor.departmentInstitute for Conservation Biology, The University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australiaen
dc.contributor.departmentDepartment of Crop Sciences, University of Illinois at Urbana-Champaign, 1101 West Peabody Drive, Urbana, IL 61801, USAen
dc.contributor.departmentDonald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USAen
dc.contributor.departmentLawrence Berkeley National Laboratory, 1 Cyclotron Road Berkeley, Emeryville, CA 94720, USAen
dc.contributor.departmentInstitute of Developmental Biology and Molecular Medicine & School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, Chinaen
dc.contributor.departmentDepartment of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USAen
dc.contributor.departmentHawaii Agriculture Research Center, 94-340 Kunia Road, Waipahu, HI 96797, USAen
dc.contributor.departmentDepartment of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USAen
dc.contributor.departmentFujian Normal University, Qishan Campus, Minhou, Fuzhou, 350117, Chinaen
dc.contributor.departmentDepartment of Biology and Molecular Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USAen
dc.contributor.departmentInstitute of Tropical Biosciences and Biotechnology, China Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou, Hainan 571101, Chinaen
dc.contributor.departmentDepartment of Plant and Microbial Biology, University of California, 1 Shields Avenue, Davis CA, 95161, USAen
dc.contributor.departmentDepartment of Cell and Developmental Biology, University of Illinois, 1201 West Gregory Drive, Urbana IL, 61801, USAen
dc.contributor.departmentThe Genome Analysis Center, Monsanto, St Louis, MO 63167, USAen
dc.contributor.departmentGlobal Change and Photosynthesis Research Unit, Agricultural Research Service, United States Department of Agriculture, 1206 West Gregory Drive, Urbana, IL, USAen
dc.contributor.departmentIGPP 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, USAen
dc.contributor.departmentDepartment of Plant and Microbial Biology, University of California, 411 Koshland Hall, Berkeley, CA 94720, USAen
dc.identifier.journalGenome Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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