Ming, R., VanBuren, R., Liu, Y. L., Yang, M., Han, Y. P., Li, L. T., Zhang, Q., Kim, M. J., Schatz, M. C., Campbell, M., Li, J. P., Bowers, J. E., Tang, H. B., Lyons, E., Ferguson, A. A., Narzisi, G., Nelson, D. R., Blaby-Haas, C. E., Gschwend, A. R., Jiao, Y. N., Der, J. P., Zeng, F. C., Han, J., Min, X. 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. Y., Mockler, T. C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R. Z., Chen, N., Arro, J., Wai, C. M., Wafula, E., Spence, A., Han, Y. N., Xu, L. M., Zhang, J. S., Peery, R., Haus, M. J., Xiong, W. W., Walsh, J. A., Wu, J., Wang, M. L., Zhu, Y. J., Paull, R. E., Britt, A. B., Du, C. G., Downie, S. R., Schuler, M. A., Michael, T. P., Long, S. P., Ort, D. R., Schopf, J. W., Gang, D. R., Jiang, N., Yandell, M., dePamphilis, C. W., Merchant, S. S., Paterson, A. H., Buchanan, B. B., Li, S. H., Shen-Miller, J. (2013) Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology, 14 (5). ISSN 1465-6906
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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 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.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | early diversification divergence times core eudicots sequence gene paleohexaploidy evolution fruits plants rates |
| Subjects: | bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes Investigative techniques and equipment > assays > next generation sequencing Investigative techniques and equipment > assays > whole genome sequencing |
| CSHL Authors: | |
| Communities: | CSHL labs > Schatz lab |
| Depositing User: | Matt Covey |
| Date: | 2013 |
| Date Deposited: | 11 Nov 2013 21:17 |
| Last Modified: | 19 Jul 2021 14:26 |
| PMCID: | PMC4053705 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/28859 |
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