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United States Department of Agriculture

Agricultural Research Service

Title: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).)

Author
item Ming, Ray
item Hou, Shaobin
item Feng, Yun
item Yu, Qingyi
item Dionne-laporte, Alexandre
item Saw, Jimmy
item Senin, Pavel
item Wang, Wei
item Ly, Benjamin
item Lewis, Kanako
item Salzberg, Steven
item Feng, Lu
item Jones, Meghan
item Skelton, Rachel
item Murray, Jan
item Chen, Cuixia
item Qian, Wubin
item Shen, Junguo
item Du, Peng
item Eustice, Moriah
item Tong, Eric
item Wang, Xiyin
item Lyons, Eric
item Paull, Robert
item Michael, Todd
item Wall, Kerr
item Rice, Danny
item Albert, Henrik
item Wang, Ming-li
item Zhu, Yun
item Schatz, Michael
item Nagarajan, Niranjan
item Agbayani, Ricelle
item Guan, Peizhu
item Blas, Andres
item Wai, Ching Man
item Ackerman, Christine
item Ren, Yan
item Liu, Chao
item Wang, Jianmei
item Wang, Jianping
item Na, Jong-kuk
item Shakirov, Eugene
item Haas, Brian
item Thimmapuram, Jyothi
item Nelson, David
item Tang, Haibao
item Bowers, John
item Gschwend, Andrea
item Delcher, Arthur
item Singh, Ratnesh
item Suzuki, Jon
item Tripathi, Savarni
item Neupane, Kabi
item Wei, Hairong
item Irikura, Beth
item Paidi, Maya
item Jiang, Ning
item Zhang, Wenli
item Presting, Gernot
item Windsor, Aaron
item Perez, Rafael Navajas
item Torres, Manuel
item Feltus, F. Alex
item Porter, Brad
item Li, Yingjun
item Burroughs, Max
item Luo, Ming-cheng
item Liu, Lei
item Mount, Stephen
item Christopher, David
item Moore, Paul
item Sugimura, Tak
item Jiang, Jiming
item Schuler, Mary
item Mitchell-olds, Thomas
item Shippen, Dorothy
item Depamphilis, Claude
item Palmer, Jeffrey
item Freeling, Michael
item Paterson, Andrew
item Gonsalves, Dennis
item Wang, Lei
item Alam, Maqsudul

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/22/2008
Publication Date: 4/24/2008
Citation: Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J., Senin, P., Wang, W., Ly, B.V., Lewis, K.L., Salzberg, S.L., Feng, L., Jones, M.R., Skelton, R.L., Murray, J.E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M., Tong, E., Wang, X., Lyons, E., Paull, R.E., Michael, T.P., Wall, K., Rice, D., Albert, H.H., Wang, M., Zhu, Y., Schatz, M., Nagarajan, N., Agbayani, R., Guan, P., Blas, A., Wai, C., Ackerman, C.M., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J., Shakirov, E.V., Haas, B., Thimmapuram, J., Nelson, D., Tang, H., Bowers, J.E., Gschwend, A.R., Delcher, A.L., Singh, R., Suzuki, J.Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Perez, R., Torres, M.J., Feltus, F., Porter, B., Li, Y., Burroughs, M., Luo, M., Liu, L., Mount, S.M., Christopher, D.A., Moore, P.H., Sugimura, T., Jiang, J., Schuler, M.A., Mitchell-Olds, T., Shippen, D., Depamphilis, C.W., Palmer, J.D., Freeling, M.R., Paterson, A.H., Gonsalves, D., Wang, L., Alam, M. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature. 452:991-996.

Interpretive Summary: DNA sequences contain an abundance of information ultimately useful for genetic improvement of plants and animals. To date, the genomes of only three higher plants have been sequenced and these have shown that although there is considerable genomic conservation among them, the differences are sufficiently great that it is necessary to have many more plants fully sequenced to enable efficient use of the data for crop improvement. A large team of scientists from 27 research organizations (including ARS in Hawaii, 23 university departments in the US, and two from Tianjin, China) report results from sequencing and annotating the genome of the tropical fruit crop papaya. This fourth plant sequenced is significant for it shows a genome smaller than the previous sequenced plants indicating a plasticity possibly related to the number of genome duplications in the evolution of the species and indicating its closer relationship to ancestral flowering plants. The sequence data will reveal information about some of the unique characteristics of this genetically transformed papaya line that have potential for a greater understanding of transgene integration and the mechanisms for its complex sexual system that includes both single sex and hermaphrodite plants.

Technical Abstract: We report a draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree crop. The papaya genome has more than two times the DNA but about 28% fewer genes than the genome of the related botanical model Arabidopsis. A lack of genome duplication, atypical of angiosperm genomes, appears to largely account for generally smaller papaya gene number in most functional groups, also suggesting that genes and genome may more closely resemble those of ancestral angiosperms than do others sequenced to date. Against a background of generally fewer genes than Arabidopsis, some papaya gene functional groups have undergone striking single-gene amplifications and/or evolved functional variations that suggest roles in the evolution of tree-like habit, such as deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Comparison of the four fully-sequenced clade members suggests a minimal angiosperm gene set of 13,621. Transgenesis of the sequenced genotype at three locations is closely associated with AT-rich chloroplast insertions into nuclear genome, and with Topo I recognition sites. Papaya offers numerous advantages as a system for fruit tree functional genomics, and its draft sequence will contribute to revealing the basis of its distinguishing morpho-physiological, medicinal, and nutritional properties.

Last Modified: 8/24/2016
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