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Methods for the construction of parameter maps and whole tumour images are described in Supplementary Information.
Genetic studies of the persimmon are difficult to implement because of the hexaploid nature of the species and lack of linkage maps and whole genome sequences [i.e. only 14,189 EST sequences deposited in GenBank (accessed on 10/11/2013)].
More recently, the construction of physical maps and whole chromosome analyses demonstrated that 30 40 % of the gene complements in wheat and barley do not reside in the conserved syntenic gene order space (Choulet et al. 2010; Mayer et al. 2011; Wicker et al. 2011; Berkman et al. 2012).
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One of the major applications of genetic linkage map is to integrate physical maps and whole-genome assemblies.
Integration of physical maps and whole-genome sequence contigs allows the relationship to be established between the sequence-based contigs and the restriction fingerprint-based contigs, thereby reducing the levels of segmentation of the genome.
To date, two types of sequencing strategy have been adopted in order to fully sequence plant genomes: clone-by-clone sequencing based on physical maps and whole-genome shotgun sequencing.
The identification of actual causative locus will require the availability of intensive genetic information and genomic tools, such as dense, gene-rich linkage maps and whole-genome sequences, that are currently in development in salmonids (Davidson et al. 2010).
Power for both meiotic linkage mapping and whole genome association studies is optimized when independent breeding populations sharing a common ancestral mutation can be considered simultaneously.
Detailed chromosome information is provided by analysis of the RH map and whole genome sequences.
All SNP mapping and whole genome sequence data is available at wormbase.org.org
Gene order is determined using one of several approaches, including physical mapping, linkage mapping, and whole genome sequencing.
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