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ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #215430
Title: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Author
item MING, RAY - HARC
item HOU, SHAOBIN - UNIV OF HI
item FENG, YUN - NANKAI UNIV
item YU, QINGYI - HARC
item DIONNE-LAPORTE, ALEXANDRE - UNIV OF HI
item SAW, JIMMY - UNIV OF HI
item SENIN, PAVEL - UNIV OF HI
item WANG, WEI - NANKAI UNIV
item LY, BENJAMIN - UNIV OF HI
item LEWIS, KANAKO - UNIV OF HI
item SALZBERG, STEVEN - UNIV OF MARYLAND
item FENG, LU - NANKAI UNIV
item JONES, MEGHAN - HARC
item SKELTON, RACHEL - HARC
item MURRAY, JAN - HARC
item CHEN, CUIXIA - UNIV OF ILL URBANA-CHAMP
item QIAN, WUBIN - NANKAI UNIV
item SHEN, JUNGUO - TIANJIN RSCH CNTR
item DU, PENG - TIANJIN RSCH CNTR
item EUSTICE, MORIAH - HARC
item TONG, ERIC - HARC
item WANG, XIYIN - UNIV OF GEORGIA
item LYONS, ERIC - UC BERKELEY
item PAULL, ROBERT - UNIV OF HI
item MICHAEL, TODD - RUTGERS
item WALL, KERR - PENNSYLVANIA STATE UNIV
item RICE, DANNY - INDIANA UNIV
item Albert, Henrik
item WANG, MING-LI - HARC
item ZHU, YUN - HARC
item SCHATZ, MICHAEL - UNIVERSITY OF MARYLAND
item NAGARAJAN, NIRANJAN - UNIVERSITY OF MARYLAND
item AGBAYANI, RICELLE - HARC
item GUAN, PEIZHU - HARC
item BLAS, ANDRES - HARC
item WAI, CHING MAN - HARC
item ACKERMAN, CHRISTINE - HARC
item REN, YAN - NANKAI UNIV
item LIU, CHAO - NANKAI UNIV
item WANG, JIANMEI - NANKAI UNIV
item WANG, JIANPING - UNIV OF ILL URBANA-CHAMP
item NA, JONG-KUK - UNIV OF ILL URBANA-CHAMP
item SHAKIROV, EUGENE - TEXAS A&M UNIV
item HAAS, BRIAN - THE INST FOR GENOMIC RSCH
item THIMMAPURAM, JYOTHI - UNIV OF ILL URBANA-CHAMP
item NELSON, DAVID - UNIV OF TENNESSEE
item TANG, HAIBAO - UNIV OF ILL URBANA-CHAMP
item BOWERS, JOHN - UNIV OF GEORGIA
item GSCHWEND, ANDREA - UNIV OF ILL URBANA-CHAMP
item DELCHER, ARTHUR - UNIV OF MARYLAND
item SINGH, RATNESH - HARC
item SUZUKI, JON - UNIV OF HI
item TRIPATHI, SAVARNI - UNIV OF HI
item NEUPANE, KABI - LEEWARD COMM COLLEGE
item WEI, HAIRONG - WICELL RESEARCH INST
item IRIKURA, BETH - UNIV OF HI
item PAIDI, MAYA - HARC
item JIANG, NING - MICHIGAN STATE UNIV
item ZHANG, WENLI - UNIV OF WISCONSIN
item PRESTING, GERNOT - UNIV OF HI
item WINDSOR, AARON - DUKE UNIV
item PEREZ, RAFAEL NAVAJAS - UNIV OF GEORGIA
item TORRES, MANUEL - UNIV OF GEORGIA
item FELTUS, F. ALEX - UNIV OF GEORGIA
item PORTER, BRAD - UNIV OF HI
item LI, YINGJUN - UNIV OF ILL URBANA-CHAMP
item BURROUGHS, MAX - UNIV OF MARYLAND
item LUO, MING-CHENG - UC DAVIS
item LIU, LEI - UNIV OF ILL URBANA-CHAMP
item MOUNT, STEPHEN - UNIV OF MARYLAND
item CHRISTOPHER, DAVID - UNIV OF HI
item Moore, Paul
item SUGIMURA, TAK - MAUI HI PERF COMP CNTR
item JIANG, JIMING - UNIV OF WISCONSIN
item SCHULER, MARY - UNIV OF ILL URBANA-CHAMP
item MITCHELL-OLDS, THOMAS - DUKE UNIV
item SHIPPEN, DOROTHY - TEXAS A&M UNIV
item DEPAMPHILIS, CLAUDE - PENNSYLVANIA STATE UNIV
item PALMER, JEFFREY - INDIANA UNIV
item FREELING, MICHAEL - UC BERKELEY
item PATERSON, ANDREW - UNIV OF GEORGIA
item Gonsalves, Dennis
item WANG, LEI - TIANJIN RESEARCH CNTR
item ALAM, MAQSUDUL - UNIV OF HI

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.