TOPAAS, a tomato and potato assembly assistance system for selection and finishing of bacterial artificial chromosomes

Plant Physiology
Sander A PetersRené M Klein-Lankhorst

Abstract

We have developed the software package Tomato and Potato Assembly Assistance System (TOPAAS), which automates the assembly and scaffolding of contig sequences for low-coverage sequencing projects. The order of contigs predicted by TOPAAS is based on read pair information; alignments between genomic, expressed sequence tags, and bacterial artificial chromosome (BAC) end sequences; and annotated genes. The contig scaffold is used by TOPAAS for automated design of nonredundant sequence gap-flanking PCR primers. We show that TOPAAS builds reliable scaffolds for tomato (Solanum lycopersicum) and potato (Solanum tuberosum) BAC contigs that were assembled from shotgun sequences covering the target at 6- to 8-fold coverage. More than 90% of the gaps are closed by sequence PCR, based on the predicted ordering information. TOPAAS also assists the selection of large genomic insert clones from BAC libraries for walking. For this, tomato BACs are screened by automated BLAST analysis and in parallel, high-density nonselective amplified fragment length polymorphism fingerprinting is used for constructing a high-resolution BAC physical map. BLAST and amplified fragment length polymorphism analysis are then used together to determine the precis...Continue Reading

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Citations

Jun 5, 2007·Nature Protocols·Marnik VuylstekeMichiel J T van Eijk
Jul 23, 2008·The Plant Journal : for Cell and Molecular Biology·Dóra SzinayRené M Klein Lankhorst
Mar 5, 2008·International Journal of Plant Genomics·Amalia BaroneLuigi Frusciante
Mar 26, 2009·Critical Reviews in Biotechnology·Vikrant GuptaArun K Sharma
May 4, 2013·Breeding Science·Koh AokiAtsushi Toyoda
Feb 12, 2009·The Plant Journal : for Cell and Molecular Biology·Sander A PetersRoeland C H J van Ham

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