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首页> 外文期刊>BMC Genomics >Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis
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Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis

机译：序列水平分析揭示了甘蓝节段重排引起的基因组进化复杂性

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Background The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level. Results We developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity discontinuities anticipated on the basis of previous studies. Our analyses revealed numerous instances of newly detected collinearity blocks. For B. rapa linkage group A8, we were able to develop a model for the derivation of the chromosome from the ancestral karyotype. We were also able to identify a rearrangement event in the ancestor of B. rapa that was not shared with the ancestor of A. thaliana, and is represented in triplicate in the B. rapa genome. In addition to inter-chromosomal rearrangements, we identified and analysed 32 BACs containing the end points of segmental inversion events. Conclusion Our results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions of genes in B. rapa based on the locations of orthologues in A. thaliana can be misleading. Our results will be of relevance to a wide range of plants that have polyploid genomes, many of which are being considered according to a paradigm of comprising conserved synteny blocks with respect to sequenced, related genomes.
机译：背景技术与拟南芥有关的芸苔属物种包括一组重要的农作物，代表了研究多倍体进化结果的极好的系统。以前的研究已经提出了一个祖先核型的结构和通过三联和节段重排进行的双歧杆菌基因组进化的模型，但是这些尚未在序列水平上得到验证。结果我们开发了计算工具来分析B. rapa BAC末端序列的公共集合，以鉴定出代表B. rapa和拟南芥基因组之间共线性不连续性的候选对象。对于每个推定的不连续性，对其中一个BAC进行测序，并与拟南芥的基因组进行共线性分析。鉴定其他BAC克隆并进行测序，作为对R. rapa四个染色体进行测序的不断努力的一部分。令人惊讶的是，在19个染色体间重排中，很少有对应于先前研究基础上预期的共线性不连续性的集合。我们的分析揭示了许多新检测到的共线性块的实例。对于B. rapa连锁群A8，我们能够开发一个模型来从祖先的核型衍生出染色体。我们还能够鉴定出不与拟南芥祖先共享的，在拟南芥祖先中发生的重排事件，并在该基因中以一式三份表示。除了染色体间的重排，我们还鉴定并分析了32个BAC，它们包含分段倒置事件的终点。结论我们的结果表明，先前对拟南芥，芸苔属和祖先核型基因组之间的共线性进行的研究尽管非常有用，但却代表了它们真正关系的过度简化。大量隐密共线基因组片段的存在和片段倒置的频繁发生，意味着根据拟南芥中直向同源物的位置推断双歧杆菌中基因的位置可能会产生误导。我们的结果将与具有多倍体基因组的广泛植物相关，其中许多植物是根据包含与序列相关的基因组保守的同义区块的范例来考虑的。

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