Rana Debashis, van den Boogaart Tom, O'Neill Carmel M, Hynes Llewelyn, Bent Elisabeth, Macpherson Lee, Park Jee Young, Lim Yong Pyo, Bancroft Ian
Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK.
Plant J. 2004 Dec;40(5):725-33. doi: 10.1111/j.1365-313X.2004.02244.x.
The cultivated Brassica species are the group of crops most closely related to Arabidopsis thaliana (Arabidopsis). They represent models for the application in crops of genomic information gained in Arabidopsis and provide an opportunity for the investigation of polyploid genome formation and evolution. The scientific literature contains contradictory evidence for the dynamics of the evolution of polyploid genomes. We aimed at overcoming the inherent complexity of Brassica genomes and clarify the effects of polyploidy on the evolution of genome microstructure in specific segments of the genome. To do this, we have constructed bacterial artificial chromosome (BAC) libraries from genomic DNA of B. rapa subspecies trilocularis (JBr) and B. napus var Tapidor (JBnB) to supplement an existing BAC library from B. oleracea. These allowed us to analyse both recent polyploidization (under 10,000 years in B. napus) and more ancient polyploidization events (ca. 20 Myr for B. rapa and B. oleracea relative to Arabidopsis), with an analysis of the events occurring on an intermediate time scale (over the ca. 4 Myr since the divergence of the B. rapa and B. oleracea lineages). Using the Arabidopsis genome sequence and clones from the JBr library, we have analysed aspects of gene conservation and microsynteny between six regions of the genome of B. rapa with the homoeologous regions of the genomes of B. oleracea and Arabidopsis. Extensive divergence of gene content was observed between the B. rapa paralogous segments and their homoeologous segments within the genome of Arabidopsis. A pattern of interspersed gene loss was identified that is similar, but not identical, to that observed in B. oleracea. The conserved genes show highly conserved collinearity with their orthologues across genomes, but a small number of species-specific rearrangements were identified. Thus the evolution of genome microstructure is an ongoing process. Brassica napus is a recently formed polyploid resulting from the hybridization of B. rapa (containing the Brassica A genome) and B. oleracea (containing the Brassica C genome). Using clones from the JBnB library, we have analysed the microstructure of the corresponding segments of the B. napus genome. The results show that there has been little or no change to the microstructure of the analysed segments of the Brassica A and C genomes as a consequence of the hybridization event forming natural B. napus. The observations indicate that, upon polyploid formation, these segments of the genome did not undergo a burst of evolution discernible at the scale of microstructure.
栽培的芸苔属物种是与拟南芥关系最为密切的一类作物。它们是将拟南芥中获得的基因组信息应用于作物研究的模型，也为研究多倍体基因组的形成和进化提供了契机。科学文献中关于多倍体基因组进化动态存在相互矛盾的证据。我们旨在克服芸苔属基因组固有的复杂性，阐明多倍体对基因组特定区段微观结构进化的影响。为此，我们从白菜型油菜三型亚种（JBr）和甘蓝型油菜Tapidor变种（JBnB）的基因组DNA构建了细菌人工染色体（BAC）文库，以补充现有的甘蓝BAC文库。这些文库使我们能够分析近期的多倍体化事件（甘蓝型油菜中发生在10000年以内）和更古老的多倍体化事件（相对于拟南芥，白菜型油菜和甘蓝约2000万年前），并分析中间时间尺度上发生的事件（自白菜型油菜和甘蓝谱系分化以来约400万年间）。利用拟南芥基因组序列和JBr文库中的克隆，我们分析了白菜型油菜基因组六个区域与甘蓝和拟南芥基因组同源区域之间的基因保守性和微同源性。在白菜型油菜的旁系同源区段与其在拟南芥基因组中的同源区段之间观察到基因含量存在广泛差异。我们鉴定出一种穿插基因丢失模式，它与在甘蓝中观察到的模式相似但不完全相同。保守基因在不同基因组中与其直系同源基因表现出高度保守的共线性，但也鉴定出少数物种特异性重排。因此，基因组微观结构的进化是一个持续的过程。甘蓝型油菜是由白菜型油菜（含有芸苔A基因组）和甘蓝（含有芸苔C基因组）杂交形成的一个新近形成的多倍体。利用JBnB文库中的克隆，我们分析了甘蓝型油菜基因组相应区段的微观结构。结果表明，作为形成天然甘蓝型油菜的杂交事件的结果，芸苔A和C基因组分析区段的微观结构几乎没有变化或没有变化。这些观察结果表明，在多倍体形成时，基因组的这些区段在微观结构尺度上没有经历可辨别的进化爆发。
