Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
Genome. 2010 Nov;53(11):929-38. doi: 10.1139/G10-053.
The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142,399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus; including microarray hybridization and 3' anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3' capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags.
甘蓝型油菜基因组的结构特点与其进化起源有关。油菜基因组是由两个密切相关的二倍体芸薹属物种杂交形成的，这两个物种都起源于一个六倍体祖先。在其近亲和远亲的历史中，广泛的全基因组重复事件导致油菜的异源四倍体基因组维持了大多数基因的多个拷贝，这预示着一个高度复杂和冗余的转录组，可能会混淆任何表达分析。对 142399 个甘蓝型油菜表达序列标签的严格组装，允许开发出一套分化良好的参考转录本，这些转录本被用作评估现有工具在鉴定和区分油菜转录本方面的功效的基础；包括微阵列杂交和 3'锚定序列标签捕获。微阵列平台无法区分来自两个亲本或密切同源物的转录本，尽管观察到的差异表达似乎偏向于独特的转录本。3'捕获的使用增强了在油菜转录组中明确识别同源物的能力，但受到标签长度的限制。通过应用经济高效的下一代测序技术，可以全面编目多倍体物种的基因表达，这些技术将捕获数百万个长序列标签。
