substantial deletion overlap among divergent arabidopsis genomes revealed by intersection of short reads and tiling arrays大量删除不同的拟南芥基因组之间的重叠了十字路口的短读和瓷砖数组.pdf

Santuari et al. Genome Biology 2010, 11:R4 /2010/11/1/R4 M E T H O D Open Access Method Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays 1 2,3 1 3 1 Luca Santuari , Sylvain Pradervand , Amelia-Maria Amiguet-Vercher , Jerôme Thomas , Eavan Dorcey , 3 2 4 1 Keith Harshman , Ioannis Xenarios , Thomas E Juenger and Christian S Hardtke* ArabidopsisA new approach to detedemonstrated ongentgenomes combines short read sequenc-ing and tilling array data. Its utility isgenomic variationArabidopsisct deletions in diver-strains. Abstract 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 partly reflects a common history of deletion events. Background eventually enable precise mapping of larger deletions. Ultra-high throughput sequencing (UHTS) has become However, to date bioinformatic tools to exploit such data affordable to re-sequence genomes of model organisms,