Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada.
BMC Genomics. 2011 May 9;12:217. doi: 10.1186/1471-2164-12-217.
Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome.
The physical map consists of 416 contigs spanning 368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding.
The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.
亚麻（Linum usitatissimum L.）是一种重要的油用植物，富含ω-3 脂肪酸，具有良好的健康益处，可用作工业原料。亚麻籽还含有木脂素，可降低某些类型癌症的风险。其韧皮纤维具有广泛的工业应用。然而，用于分子育种的基因组工具却不存在。因此，启动了一个名为 Total Utilization Flax GENomics (TUFGEN) 的项目。我们在这里报告了亚麻的第一个全基因组物理图谱，并生成和分析了来自 43776 个克隆的 BAC 末端序列 (BES)，为基因组提供了初步见解。
物理图谱由 416 个重叠群组成，跨度约 368 Mb，由 32025 个指纹组装而成，大致代表了估计的单倍体基因组（370-675 Mb）的 54.5%到 99.4%。根据指纹图估算的重叠群的 N50 大小约为 1494 kb。最长的重叠群约为 5562 kb，由 437 个克隆组成。有 96 个重叠群包含超过 100 个克隆。约 54.6 Mb，占基因组的 8-14.8%，来自 80337 个 BES。注释表明，基因组的很大一部分由核糖体 DNA 组成（约 13.8%），其次是已知的转座子（6.1%）。此外，约 7.4%的序列被鉴定为含有新的重复元件。与亚麻 ESTs 和 NCBI-ESTs 的同源性搜索表明，约 5.6%的转录组是亚麻特有的。共鉴定了 4064 个推定的基因组 SSRs，并正在开发为新型标记物，用于分子育种。
用 BAC 克隆构建的亚麻全基因组物理图谱为获取具有经济重要性的目标基因座提供了一个框架，可用于标记开发和定位克隆。BES 的分析为亚麻基因组的独特性提供了线索。与其他植物基因组相比，rDNA 的比例非常高，而已知转座子的比例较低。从 BES 中鉴定的 SSRs将在饱和现有连锁图谱和锚定物理图谱和遗传图谱方面具有重要价值。BAC 克隆的物理图谱和配对末端读数也将作为构建和验证全基因组鸟枪法组装的支架。
