Insights into papaya genome organization based on BAC end sequence analysis

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2006
Authors
Lai, Chun Wan Jeffrey
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Abstract
Papaya is a major tree-fruit plant grown mainly in tropical and subtropical regions. A BAC library was end sequenced and the resulting 50,661 BAC-end sequences were analyzed bioinformatically. A total of 7,456 SSRs were identified among 5,452 BESs. Sixteen percent of BESs contain plant repeat homologies. BESs lacking plant repeats revealed 6,769 (19.1%) Arabidopsis cDNA homologies. BESs without plant repeat and Arabidopsis cDNA homology contained 1,124 (3.2%) RefSeq and 644 (1.8%) non-redundant protein sequence homologies. Low-copy papaya BES pairs (9,038) were compared to Arabidopsis, poplar, and rice genome sequences. A total of 53 BES pairs were mapped to Arabidopsis, 167 to poplar and 11 to rice. Low rate of co-mapping papaya BES pairs to Arabidopsis confirms the recent genome rearrangement in Arabidopsis. Poplar exhibited highest level of co-linearity with papaya and can be a reference genome for papaya genomic studies.
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Thesis (M.S.)--University of Hawaii at Manoa, 2006.
Includes bibliographical references (leaves 69-79).
ix, 79 leaves, bound ill. 29 cm
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Papaya -- Genome mapping
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Theses for the degree of Master of Science (University of Hawaii at Manoa). Molecular Biosciences and Bioengineering; no. 4090
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