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Title: ANALYSIS OF PAPAYA BAC END SEQUENCES REVEALS FIRST INSIGHTS INTO THE ORGANIZATION OF A FRUIT TREE GENOME

Author
item LAI, CWJ - UNIV HAWAII
item YU, Q - HARC
item HOU, S - UNIV HAWAII
item SKELTON, R - HARC
item JONES, MR - HARC
item LEWIS, KLT - UNIV HAWAII
item MURRAY, J - UNIV ILLINOIS
item EUSTICE, M - HARC
item GUAN, P - HARC
item AGBAYANI, R - HARC
item Moore, Paul
item MING, R - UNIV ILLINOIS
item PRESTING, GG - UNIV HAWAII

Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2006
Publication Date: 5/16/2006
Citation: Lai, C., Yu, Q., Hou, S., Skelton, R., Jones, M., Lewis, K., Murray, J., Eustice, M., Guan, P., Agbayani, R., Moore, P.H., Ming, R., Presting, G. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Molecular Genetics and Genomics. 276:1-12.

Interpretive Summary: Bacterial Artificial Chromosome (BAC) libraries have become important tools in crop genomics to construct physical maps, map genes of agricultural importance, perform comparative genomics between crop species, and analyze genome structure. An ARS research unit in Hawaii was previously involved in the production and characterization of a BAC library of the tropical fruit crop papaya. Now we report results from a collaborative effort among a team of scientists from the University of Hawaii, the Hawaii Agriculture Research Center, the University of Illinois, and ARS to analyze the DNA sequences of more than 50,000 papaya BAC ends. The BAC end sequences revealed a plant genome containing all of the major repeat classes of DNA, a protein coding content very similar to that of Arabidopsis, a large number of useful microsatellites, and a surprising amount of co-linearity with the genome of poplar, the model tree for DNA sequence analysis. The papaya BAC end sequences will provide a valuable resource for future physical mapping and accelerate the construction of a new generation of genetic maps to assist in crop improvement.

Technical Abstract: Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We present the analysis of 4.7% of the papaya genome based on BAC end sequences (BESs) representing 17 million high quality bases. Microsatellites discovered in 5,452 BESs and flanking primer sequences are available to papaya breeding programs at http://genomics.hawaii.edu/papaya/BES. Sixteen percent of BESs contained plant repeat elements, the vast majority (83.3%) of which were class I retrotransposons. Several novel papaya-specific repeats were identified. Approximately 19.1% of the low-copy BESs had homology to Arabidopsis cDNA. Increasing numbers of completely sequenced plant genomes and BES projects enable novel approaches to comparative plant genomics. Paired BESs of Carica, Arabidopsis, Populus, Brassica and Lycopersicon were mapped onto the completed genomes of Arabidopsis and Populus. The degree of microsynteny observed was highest among closely related organisms, but surprisingly papaya revealed a higher degree of apparent synteny with the more distantly related poplar than the closely related Arabidopsis. This supports recent observations of frequent genome rearrangements in the Arabidopsis lineage and suggests that the poplar genome sequence may be more useful for elucidating the papaya and other rosid genomes. These insights will play a critical role in selecting species and sequencing strategies that will optimally represent crop genomes in sequence databases.