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Fig. 2 | Genome Biology

Fig. 2

From: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

Fig. 2

a Alignment of MAGIC/CSxRenan genetic map (left axis, Additional file 2b) against IWGSC RefSeq v1.0 chromosome 7A (right axis). On the right axis, ticks denote the boundaries of the 18 super-scaffolds defined in this manuscript. The table summarizes the assembly information integrated in each super-scaffold (see also Additional files 4b and 5). Some cross-overs in the alignment of the MAGIC and IWGSC genetic maps reflect ambiguities that can arise as a result of the high and distributed repetitive sequence content of the wheat genome combined with the fact that the MAGIC map is based on a multiple cross between 8 modern varieties and the physical map is Chinese Spring. In some cases the map suggested no linkage between markers located in a physical contig. If re-examination of the physical contig indicated a ‘weak link’ in the physical contig assembly (example shown in Additional file 8: Figure S3), then the assembly was split into ‘a’ and ‘b’ contigs. If the physical contig evidence was unambiguous, the markers were set aside for reconsideration in light of more evidence being obtained. b An example of a locally finished sequence (BAC pool 7AS-11826; 655 Kb) showing integration of multiple data types: paired-end Illumina data from BACs (top, green); three independent mate-pair libraries; Minimum tiling path (MTP) BAC start and end points, based on mapping junction with vector; Bionano optical map alignments. Note that coverage of BAC pool data varies depending on double and triple coverage of BACs in MTP. Sequence is contiguous with no gaps. The assembled sequence joined two Bionano maps. This 655 Kb contig included the P450 gene, TaCYP78A3, shown to be associated with variation in grain size [48]

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