Abstract
BackgroundDetermining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method.ResultsThe strategy was tested on a draft genome of the fungal pathogen Venturia inaequalis, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome Fragaria vesca. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for V. inaequalis and F. vesca, respectively, to genetic linkage maps.ConclusionsWe demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.
Highlights
Determining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects
The framework linkage map developed for this progeny [17], which covers a total of 804 cM, was divided into 54 bins using eight individuals following the method described previously [11]
Using a foundation genetic map, we have developed the possibility of anchoring and ordering genome sequence contigs rapidly, and cost-effectively, without the need of prior extensive genetic knowledge of the organism studied
Summary
Determining the position and order of contigs and scaffolds from a genome assembly within an organism’s genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method. From the short overlapping sequence fragments obtained, it is possible to generate draft genome sequences using various algorithms developed for de novo sequence assembly [5,6,7]. Despite improvements in the software used in the assembly of small DNA sequences, it is very difficult to build a fully assembled genome using short read sequence data. For relatively small genomes with limited numbers of sequence repeats, gaps between genomic sequences can be bridged by polymerase chain reaction or cloning strategies
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