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Gene content and distribution in the nuclear genome of Fragaria vesca

Abstract
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, [ver mas...]
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%. [Cerrar]
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Author
Pontaroli, Ana Clara;   Rogers, Rebekah L.;   Qian, Zhang;   Shields, Melanie E.;   Davis, Thomas M.;   Folta, Kevin M.;   SanMiguel, Phillip;   Bennetzen, Jeffrey L.;  
Fuente
Plant Genome 2 (1) : 93-101 (2009)
Date
2009-03
Editorial
Crop Science Society of America
ISSN
1940-3372
URI
https://dl.sciencesocieties.org/publications/tpg/articles/2/1/93
http://hdl.handle.net/20.500.12123/5465
DOI
https://doi.org/10.3835/plantgenome2008.09.0007
Formato
pdf
Tipo de documento
artículo
Palabras Claves
Fragaria vesca; Fresa; Genomas; Genomes; ADN; DNA; Secuencia Nucleotídica; Nucleotide Sequence; Frutilla de los bosques; Woodland Strawberry;
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Excepto donde se diga explicitamente, este item se publica bajo la siguiente descripción: Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Unported (CC BY-NC-SA 2.5)
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