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United States Department of Agriculture

Agricultural Research Service

Title: Analysis of Papaya Bac End Sequences Reveals First Insights into the Organization of a Tree-Fruit Genome

item Jeffrey Lai, Chun Wan - UNIV HAWAII, MANOA
item Yu, Quingyi - HARC
item Hou, Shaobin - UNIV HAWAII, MANOA
item Skelton, Rachel - HARC
item Jones, Meghan - HARC
item Lewis, Kanako - UNIV HAWAII, MANOA
item Murray, Jan - HARC
item Eustice, Moriah - HARC
item Agbayani, Richelle - HARC
item Guan, Peizhu - HARC
item Moore, Paul
item Ming, Ray - UNIV ILLINIOS
item Presting, Gernot - UNIV HAWAII, MANOA

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: October 6, 2005
Publication Date: January 12, 2006
Citation: Jeffrey Lai, C., Yu, Q., Hou, S., Skelton, R.L., Jones, M.L., Lewis, K., Murray, J., Eustice, M., Agbayani, R., Guan, P., Moore, P.H., Ming, R., Presting, G. 2006. Analysis Of Papaya BAC End Sequences Reveals First Insights Into The Organization Of A Tree-Fruit Genome. Plant and Animal Genome XIV International Conference Proceedings. P491, Pg. 224.

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. Here we present the sequence analysis of 4.7% of the papaya genome based on 50,661 BAC end sequences (BESs) representing 17,483,563 high quality bases generated from 26,017 individual papaya BAC clones. A total of 7,456 microsatellites of at least 12 bases length were discovered in 5,452 BESs, and primer pairs were generated for 2,575 of these SSRs. Sixteen percent of BESs contained plant repeat elements, the vast majority of which were class I retrotransposons (83.3%). Approximately 19.1% of the low-copy BESs had homology to Arabidopsis thaliana cDNA. A total of 53, 167, and 11 BAC end sequence pairs could be mapped to co-linear regions in the Arabidopsis thaliana, Populus trichocarpa and Oryza sativa genomes, respectively. Surprisingly, a higher degree of co-linearity was found with the more distantly related poplar than with the Arabidopsis genome. Several novel papaya-specific repeats were identified. Detailed analysis are available in a searchable web database at (http:/

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