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Title: Analysis Of Papaya BAC End Sequences: Insights Into The Organization Of A Tree Fruit Genome

Author
item LAI, C - UNIVERSITY OF HAWAII
item YU, Q - HARC
item HOU, S - UNIVERSITY OF HAWAII
item SKELTON, R - HARC
item JONES, M - HARC
item LEWIS, K - UNIVERSITY OF HAWAII
item MURRAY, J - HARC
item EUSTICE, M - HARC
item AGBAYANI, R - HARC
item EGUAN, P - HARC
item Moore, Paul
item MING, R - UNIVERSITY OF ILL
item PRESTING, G - UNIVERSITY OF HAWAII

Submitted to: Plant and Animal Genome Conference
Publication Type: Proceedings
Publication Acceptance Date: 10/4/2006
Publication Date: 1/24/2006
Citation: Lai, C.W., Yu, Q., Hou, S., Skelton, R.L., Jones, M.R., Lewis, K.L., Murray, J., Eustice, M., Agbayani, R., Eguan, P., Moore, P.H., Ming, R., Presting, G. 2007 Analysis Of Papaya BAC End Sequences: Insights Into The Organization Of A Tree Fruit Genome. Plant and Animal Genome Conference XV.

Interpretive Summary:

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 www.genomics.hawaii.edu. Sixteen percent of BESs contain plant repeat elements, the vast majority (83.3%) of which are class I retrotransposons. Several novel papaya-specific repeats were identified. Approximately 19.1% of the BESs have homology to Arabidopsis cDNA. Paired BESs of Carica, Arabidopsis, Populus, Brassica and Lycopersicon were mapped onto the completed genomes of Arabidopsis and Populus. In general the level of microsynteny was highest between closely related organisms. However, papaya revealed a higher degree of apparent synteny with the more distantly related Populus than with the more closely related Arabidopsis. This, as well as significant colinearity observed between peach and Populus genome sequences, support recent observations of frequent genome rearrangements in the Arabidopsis lineage and suggest that the Populus genome sequence will be useful for elucidating the papaya and other rosid genomes. Understanding the degree of colinearity between genomes should help in the selection of species and sequencing strategies that will optimally represent crop genomes in sequence databases.