Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/10/2013
Publication Date: 5/10/2013
Citation: Ming, R., VanBuren, R., Liu, Y., Yang, M., Han, Y., Li, L.T., Zhang, Q., Kim, M.J., 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., 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., Mockler, T.C., Carroll, A., Zheng, Y., Sunkar, R., Jia, R., Chen, N., Arro, J., Wai, C.M., Wafula, E., Spence, A., Han, Y., Xu, L., Zhang, J., Peery, R., Haus, M., Xiong, W., Walsh, J.A., Wu, J., Wang, M.L., 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.W., 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. 14(5):R41. DOI:10.1186/gb-2013-14-5-r41. Interpretive Summary: Sacred lotus (Nelumbo nucifera) is a land plant that has adapted to an aquatic lifestyle. It has exceptionally long-lived seeds that have been shown to germinate after 1000 years. Because it is distantly related to a number of plants species of agronomic interest, the complete sequence of the sacred lotus genome is useful for the study of plant genes. In particular, the genes involved in producing the waxy leaf coating which waterproofs leaf surfaces, genes involved in development of the submerged roots, and in the metabolism of the seed are of interest to plant biologists. This manuscript describes the complete genome sequence of sacred lotus in the context of other plant genome sequences.
Technical Abstract: Sacred lotus, a basal eudicot of agricultural, medicinal, cultural, and religious importance, is particularly noted for its 1,300-year seed longevity, and for its outstanding water repellency, the "lotus effect”. The genome sequence of the Sacred lotus variety 'China Antique' lacks the paleo-triplication found in all other eudicots sequenced to date, although having a lineage-specific duplication about 57.5 million years ago. Sacred lotus has evolved remarkably slowly, experiencing less nucleotide mutation and retaining a higher percentage of duplicated genes than most other angiosperms, making it a better resource than the current standard (grape) for reconstructing the pan-eudicot genome and for accelerating comparative analysis between eudicots and monocots. We identified lotus-specific genes governing processes related to seed longevity, amplifications of gene number in the cuticular wax, cutin, and suberin biosynthesis pathways that may have contributed to the evolution of leaf surface structures relevant to the lotus effect, gene duplication events that are involved in thermogenesis and adaption to aquatic life-styles. The lotus genome also contains a great number of hAT (Ac/Ds-like) repeats (nearly 7% of the genome) whose amplifications have not yet been reported in other sequenced plant genomes.