|Wai, Ching Man|
|Perez, Rafael Navajas|
|Feltus, F. Alex|
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.