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Long read sequencing technology to solve complex genomic regions assembly in plants
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Background: Numerous completed or on-going whole genome sequencing projects have highlighted the factthat obtaining a high quality genome sequence is necessary to address comparative genomics questions such as structural variations among genotypes and gain or loss of specific function. Despite the spectacular progress thathas been made in sequencing technologies, obtaining accurate and reliable data is still a challenge, both at the whole genome scale and when targeting specific genomic regions. These problems are even more noticeable for complex plant genomes. Most plant genomes are known to be particularly challenging due to their size, high density of repetitive elements and various levels of ploidy. To overcome these problems, we have developed a strategy to reduce genome complexity by using the large insert BAC libraries combined with next generation sequencing technologies.Results: We compared two different technologies (Roche-454 and Pacific Biosciences PacBio RS II) tosequence pools of BAC clones in order to obtain the best quality sequence. We targeted nine BAC clones fromdifferent species (maize, wheat, strawberry, barley, sugarcane and sunflower) known to be complex in terms ofsequence assembly. We sequenced the pools of the nine BAC clones with both technologies. We comparedassembly results and highlighted differences due to the sequencing technologies used.Conclusions: We demonstrated that the long reads obtained with the PacBio RS II technology serve to obtaina better and more reliable assembly, notably by preventing errors due to duplicated or repetitive sequences in thesame region.
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