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This article in TPG

  1. Vol. 2 No. 1, p. 93-101
    Received: Sept 6, 2008



Gene Content and Distribution in the Nuclear Genome of Fragaria vesca

  1. Ana Clara Pontaroli,
  2. Rebekah L. Rogers,
  3. Qian Zhang,
  4. Melanie E. Shields,
  5. Thomas M. Davis,
  6. Kevin M. Folta,
  7. Phillip SanMiguel and
  8. Jeffrey L. Bennetzen 
  1. A.C. Pontaroli, R.L. Rogers, and J.L. Bennetzen, Dep. of Genetics, Univ. of Georgia, Athens, GA 30602; Q. Zhang, M.E. Shields, and T.M. Davis, Dep. of Biological Sciences, Univ. of New Hampshire, Durham, NH 03824; K.M. Folta, Horticultural Sciences Dep., Univ. of Florida, Gainesville, FL 32611; P. SanMiguel, Dep. of Horticulture and Landscape Architecture, Purdue Univ., West Lafayette, IN 47907; A.C. Pontaroli, current address: Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA), CC 276 (7620) Balcarce, Buenos Aires, Argentina; R.L Rogers, current address: Dep. of Organismic and Evolutionary Biology, Harvard Univ., Cambridge, MA 02138. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. EU024823–EU024872.


Thirty fosmids were randomly selected from a library of Fragaria vesca subsp. americana (cv. Pawtuckaway) DNA. These fosmid clones were individually sheared, and ∼4- to 5-kb fragments were subcloned. Subclones on a single 384-well plate were sequenced bidirectionally for each fosmid. Assembly of these data yielded 12 fosmid inserts completely sequenced, 14 inserts as 2 to 3 contiguous sequences (contigs), and 4 inserts with 5 to 9 contigs. In most cases, a single unambiguous contig order and orientation was determined, so no further finishing was required to identify genes and their relative arrangement. One hundred fifty-eight genes were identified in the ∼1.0 Mb of nuclear genomic DNA that was assembled. Because these fosmids were randomly chosen, this allowed prediction of the genetic content of the entire ∼200 Mb F. vesca genome as about 30,500 protein-encoding genes, plus >4700 truncated gene fragments. The genes are mostly arranged in gene-rich regions, to a variable degree intermixed with transposable elements (TEs). The most abundant TEs in F. vesca were found to be long terminal repeat (LTR) retrotransposons, and these comprised about 13% of the DNA analyzed. Over 30 new repeat families were discovered, mostly TEs, and the total TE content of F. vesca is predicted to be at least 16%.

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