Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.
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ABSTRACT:
SUBMITTER: Santuari L
PROVIDER: S-EPMC2847716 | biostudies-literature | 2010
REPOSITORIES: biostudies-literature
Publications
Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays.
Santuari Luca L Pradervand Sylvain S Amiguet-Vercher Amelia-Maria AM Thomas Jerôme J Dorcey Eavan E Harshman Keith K Xenarios Ioannis I Juenger Thomas E TE Hardtke Christian S CS
Genome biology 20100112 1
Identification of small polymorphisms from next generation sequencing short read data is relatively easy, but detection of larger deletions is less straightforward. Here, we analyzed four divergent Arabidopsis accessions and found that intersection of absent short read coverage with weak tiling array hybridization signal reliably flags deletions. Interestingly, individual deletions were frequently observed in two or more of the accessions examined, suggesting that variation in gene content partl ...[more]
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