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

Journal Article


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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 on 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 sixteen 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.

Authors


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

Publication Date


  • 2013

Citation


  • Ming, R., Vanburen, R., Liu, Y., Yang, M., Han, Y., Li, L., Zhang, Q., Kim, M., Schatz, M. C., Campbell, M., Li, J., Bowers, J. E., Tang, H., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y., Der, J. P., Zeng, F., Han, J., Xiang, J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., Arro, J., Wai, C., Wafula, E., Spence, A., Han, Y., Xu, L., Zhang, J., Peery, R., Haus, M. J., Xiong, W., Walsh, J. A., Wu, J., Wang, M., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J., Gang, D. R., Jiang, N., Yandell, M., Depamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. & Shen-Miller, J. (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology: biology for the post-genomic era, 14 (5), R41-1-R41-11.

Scopus Eid


  • 2-s2.0-84877285242

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1550&context=smhpapers

Ro Metadata Url


  • http://ro.uow.edu.au/smhpapers/537

Has Global Citation Frequency


Start Page


  • R41-1

End Page


  • R41-11

Volume


  • 14

Issue


  • 5

Place Of Publication


  • United Kingdom

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 on 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 sixteen 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.

Authors


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

Publication Date


  • 2013

Citation


  • Ming, R., Vanburen, R., Liu, Y., Yang, M., Han, Y., Li, L., Zhang, Q., Kim, M., Schatz, M. C., Campbell, M., Li, J., Bowers, J. E., Tang, H., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y., Der, J. P., Zeng, F., Han, J., Xiang, J., Hudson, K. A., Singh, R., Grennan, A. K., Karpowicz, S. J., Watling, J. R., Ito, K., Robinson, S. A., Hudson, M. E., Yu, Q., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., Arro, J., Wai, C., Wafula, E., Spence, A., Han, Y., Xu, L., Zhang, J., Peery, R., Haus, M. J., Xiong, W., Walsh, J. A., Wu, J., Wang, M., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J., Gang, D. R., Jiang, N., Yandell, M., Depamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. & Shen-Miller, J. (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology: biology for the post-genomic era, 14 (5), R41-1-R41-11.

Scopus Eid


  • 2-s2.0-84877285242

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1550&context=smhpapers

Ro Metadata Url


  • http://ro.uow.edu.au/smhpapers/537

Has Global Citation Frequency


Start Page


  • R41-1

End Page


  • R41-11

Volume


  • 14

Issue


  • 5

Place Of Publication


  • United Kingdom