BioNano genome mapping improves the flax reference genome
You FM, Li P, Luo M-C, Duguid SD, Rashid K, Booker HM, Deyholos M, Cloutier S (2016) BioNano genome mapping improves the flax reference genome. 7th International Crop Science Congress, Beijing, August 14-19, 2016 (Oral talk)
Flax (Linum usitatissimum, n=15) is a self-pollinated annual species in Linaceae family and was domesticated ~7,000 years ago for its seed oil and its stem fibers. The flax genome is ~370Mb in size. The genome of cv. CDC Bethune was previously sequenced using the whole genome shotgun strategy (WGS) and Illumina sequencing platform and assembled previously with 3,852 scaffolds larger than 1kb covering a total of 300Mb. A number of genomic resources were developed to order an orient the scaffolds by chromosomes. These include a physical map generated from 43K BAC clones assembled into 419 FPC contigs, 54Mb of BAC-end sequences, three genetic maps with >100 K SNPs and 770 SSRs and the sequencing of 407 flax accessions which yielded 1.7M SNPs. Using these resources, a total of 768 scaffolds were refined and assigned to 15 linkage groups. To further improve the assembly, an optical mao of cv. CDC Bethune using BioNano technology were developed. A total of 82Gb of raw DNA molecules were obtained representing more than 200× genome equivalent with N50 of 249Kb. These raw molecules were assembled into 251 contigs with an improved N50 of 2.15 Mb and a total size of 317Mb. The flax optical map was useful for detection of mis-assembly and scaffolding errors, ordering and orientating of scaffolds, and estimating of gaps. A total of 286Mb of scaffold sequences were anchored to the 317 Mb BioNano map, covering 97% of all predicted genes of the WGS assembly, The draft pseudomolecules contained ~330 Mb of sequences (including gaps) with linkage groups varying in sizes from 13.8 to 25.1 Mb.
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