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

Ray Ming, Robert VanBuren, Yanling Liu, Mei Yang, Yuepeng Han, Lei Ting Li, Qiong Zhang, Min Jeong Kim, Michael C. Schatz, Michael Campbell, Jingping Li, John E. Bowers, Haibao Tang, Eric Lyons, Ann A. Ferguson, Giuseppe Narzisi, David R. Nelson, Crysten E. Blaby-Haas, Andrea R. Gschwend, Yuannian JiaoJoshua P. Der, Fanchang Zeng, Jennifer Han, Xiang Jia Min, Karen A. Hudson, Ratnesh Singh, Aleel K. Grennan, Steven J. Karpowicz, Jennifer R. Watling, Kikukatsu Ito, Sharon A. Robinson, Matthew E. Hudson, Qingyi Yu, Todd C. Mockler, Andrew Carroll, Yun Zheng, Ramanjulu Sunkar, Ruizong Jia, Nancy Chen, Jie Arro, Ching Man Wai, Eric Wafula, Ashley Spence, Yanni Han, Liming Xu, Jisen Zhang, Rhiannon Peery, Miranda J. Haus, Wenwei Xiong, James A. Walsh, Jun Wu, Ming Li Wang, Yun J. Zhu, Robert E. Paull, Anne B. Britt, Chunguang Du, Stephen R. Downie, Mary A. Schuler, Todd P. Michael, Steve P. Long, Donald R. Ort, J. William Schopf, David R. Gang, Ning Jiang, Mark Yandell, Claude W. dePamphilis, Sabeeha S. Merchant, Andrew H. Paterson, Bob B. Buchanan, Shaohua Li, Jane Shen-Miller

Research output: Contribution to journalArticle

145 Citations (Scopus)

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.

Original languageEnglish
Article numberR41
JournalGenome Biology
Volume14
Issue number5
DOIs
StatePublished - 10 May 2013

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Nelumbo
Nelumbo nucifera
Lotus
genome
Genome
Vitis
Seeds
cleaning
Nucleotides
grapes
Genome Size
Food
nucleotides
Rhizome
Paint
Meristem
seed
Mutation Rate
Starvation
root meristems

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Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L. T., ... Shen-Miller, J. (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14(5), [R41]. https://doi.org/10.1186/gb-2013-14-5-r41
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 Jia ; 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 Man ; 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. / Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). In: Genome Biology. 2013 ; Vol. 14, No. 5.
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title = "Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)",
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.",
author = "Ray Ming and Robert VanBuren and Yanling Liu and Mei Yang and Yuepeng Han and Li, {Lei Ting} and Qiong Zhang and Kim, {Min Jeong} and Schatz, {Michael C.} and Michael Campbell and Jingping Li and Bowers, {John E.} and Haibao Tang and Eric Lyons and Ferguson, {Ann A.} and Giuseppe Narzisi and Nelson, {David R.} and Blaby-Haas, {Crysten E.} and Gschwend, {Andrea R.} and Yuannian Jiao and Der, {Joshua P.} and Fanchang Zeng and Jennifer Han and Min, {Xiang Jia} and Hudson, {Karen A.} and Ratnesh Singh and Grennan, {Aleel K.} and Karpowicz, {Steven J.} and Watling, {Jennifer R.} and Kikukatsu Ito and Robinson, {Sharon A.} and Hudson, {Matthew E.} and Qingyi Yu and Mockler, {Todd C.} and Andrew Carroll and Yun Zheng and Ramanjulu Sunkar and Ruizong Jia and Nancy Chen and Jie Arro and Wai, {Ching Man} and Eric Wafula and Ashley Spence and Yanni Han and Liming Xu and Jisen Zhang and Rhiannon Peery and Haus, {Miranda J.} and Wenwei Xiong and Walsh, {James A.} and Jun Wu and Wang, {Ming Li} and Zhu, {Yun J.} and Paull, {Robert E.} and Britt, {Anne B.} and Chunguang Du and Downie, {Stephen R.} and Schuler, {Mary A.} and Michael, {Todd P.} and Long, {Steve P.} and Ort, {Donald R.} and {William Schopf}, J. and Gang, {David R.} and Ning Jiang and Mark Yandell and dePamphilis, {Claude W.} and Merchant, {Sabeeha S.} and Paterson, {Andrew H.} and Buchanan, {Bob B.} and Shaohua Li and Jane Shen-Miller",
year = "2013",
month = "5",
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Ming, R, VanBuren, R, Liu, Y, Yang, M, Han, Y, Li, LT, Zhang, Q, Kim, MJ, Schatz, MC, Campbell, M, Li, J, Bowers, JE, Tang, H, Lyons, E, Ferguson, AA, Narzisi, G, Nelson, DR, Blaby-Haas, CE, Gschwend, AR, Jiao, Y, Der, JP, Zeng, F, Han, J, Min, XJ, Hudson, KA, Singh, R, Grennan, AK, Karpowicz, SJ, Watling, JR, Ito, K, Robinson, SA, Hudson, ME, Yu, Q, Mockler, TC, Carroll, A, Zheng, Y, Sunkar, R, Jia, R, Chen, N, Arro, J, Wai, CM, Wafula, E, Spence, A, Han, Y, Xu, L, Zhang, J, Peery, R, Haus, MJ, Xiong, W, Walsh, JA, Wu, J, Wang, ML, Zhu, YJ, Paull, RE, Britt, AB, Du, C, Downie, SR, Schuler, MA, Michael, TP, Long, SP, Ort, DR, William Schopf, J, Gang, DR, Jiang, N, Yandell, M, dePamphilis, CW, Merchant, SS, Paterson, AH, Buchanan, BB, Li, S & Shen-Miller, J 2013, 'Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)', Genome Biology, vol. 14, no. 5, R41. https://doi.org/10.1186/gb-2013-14-5-r41

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). / 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 Jia; 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 Man; 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.

In: Genome Biology, Vol. 14, No. 5, R41, 10.05.2013.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.)

AU - Ming, Ray

AU - VanBuren, Robert

AU - Liu, Yanling

AU - Yang, Mei

AU - Han, Yuepeng

AU - Li, Lei Ting

AU - Zhang, Qiong

AU - Kim, Min Jeong

AU - Schatz, Michael C.

AU - Campbell, Michael

AU - Li, Jingping

AU - Bowers, John E.

AU - Tang, Haibao

AU - Lyons, Eric

AU - Ferguson, Ann A.

AU - Narzisi, Giuseppe

AU - Nelson, David R.

AU - Blaby-Haas, Crysten E.

AU - Gschwend, Andrea R.

AU - Jiao, Yuannian

AU - Der, Joshua P.

AU - Zeng, Fanchang

AU - Han, Jennifer

AU - Min, Xiang Jia

AU - Hudson, Karen A.

AU - Singh, Ratnesh

AU - Grennan, Aleel K.

AU - Karpowicz, Steven J.

AU - Watling, Jennifer R.

AU - Ito, Kikukatsu

AU - Robinson, Sharon A.

AU - Hudson, Matthew E.

AU - Yu, Qingyi

AU - Mockler, Todd C.

AU - Carroll, Andrew

AU - Zheng, Yun

AU - Sunkar, Ramanjulu

AU - Jia, Ruizong

AU - Chen, Nancy

AU - Arro, Jie

AU - Wai, Ching Man

AU - Wafula, Eric

AU - Spence, Ashley

AU - Han, Yanni

AU - Xu, Liming

AU - Zhang, Jisen

AU - Peery, Rhiannon

AU - Haus, Miranda J.

AU - Xiong, Wenwei

AU - Walsh, James A.

AU - Wu, Jun

AU - Wang, Ming Li

AU - Zhu, Yun J.

AU - Paull, Robert E.

AU - Britt, Anne B.

AU - Du, Chunguang

AU - Downie, Stephen R.

AU - Schuler, Mary A.

AU - Michael, Todd P.

AU - Long, Steve P.

AU - Ort, Donald R.

AU - William Schopf, J.

AU - Gang, David R.

AU - Jiang, Ning

AU - Yandell, Mark

AU - dePamphilis, Claude W.

AU - Merchant, Sabeeha S.

AU - Paterson, Andrew H.

AU - Buchanan, Bob B.

AU - Li, Shaohua

AU - Shen-Miller, Jane

PY - 2013/5/10

Y1 - 2013/5/10

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84877285242&partnerID=8YFLogxK

U2 - 10.1186/gb-2013-14-5-r41

DO - 10.1186/gb-2013-14-5-r41

M3 - Article

C2 - 23663246

AN - SCOPUS:84877285242

VL - 14

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 5

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ER -

Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT et al. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology. 2013 May 10;14(5). R41. https://doi.org/10.1186/gb-2013-14-5-r41