Gene Content and Distribution in the Nuclear Genome of Fragaria vesca
- Ana Clara Pontaroli,
- Rebekah L. Rogers,
- Qian Zhang,
- Melanie E. Shields,
- Thomas M. Davis,
- Kevin M. Folta,
- Phillip SanMiguel and
- Jeffrey L. Bennetzen
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%.Please view the pdf by using the Full Text (PDF) link under 'View' to the left.
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