Gene content and distribution in the nuclear genome of Fragaria vesca

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%.

Bibliographic Details

Main Authors:	Pontaroli, Ana Clara, Rogers, Rebekah L., Qian, Zhang, Shields, Melanie E., Davis, Thomas M., Folta, Kevin M., SanMiguel, Phillip, Bennetzen, Jeffrey L.
Format:	info:ar-repo/semantics/artículo biblioteca
Language:	eng
Published:	Crop Science Society of America 2009-03
Subjects:	Fragaria vesca, Fresa, Genomas, ADN, Secuencia Nucleotídica, Genomes, DNA, Nucleotide Sequence, Frutilla de los bosques, Woodland Strawberry,
Online Access:	https://dl.sciencesocieties.org/publications/tpg/articles/2/1/93 http://hdl.handle.net/20.500.12123/5465 https://doi.org/10.3835/plantgenome2008.09.0007
Tags:	Add Tag No Tags, Be the first to tag this record!