Theoretical and practical advances in genome halving
Theoretical and practical advances in genome halving
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发表时间：
2004
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通讯作者：
F. Collyn;L. Guy;M. Marceau;M. Simonet;Claude-Alain H. Roten
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作者：
F. Collyn;L. Guy;M. Marceau;M. Simonet;Claude-Alain H. Roten
动机：生物体的整个基因组复制是一件罕见但壮观的事件，使多种新基因功能迅速出现。随着时间的推移，染色体上重复基因的平行连接可能会被相互易位打乱，而基因的染色体内顺序可能会通过倒置和转位而被打乱。一些重复的基因可能会进化到无法辨认的程度或被删除。因此，在现代基因组中唯一可检测到的古代复制事件的特征可能是包含平行平行基因的各种染色体片段的存在，每个片段在基因组中恰好出现两次。在复制前重建祖先基因组的连锁结构的问题被称为基因组减半与无序染色体。结果：在这篇文章中，我们得到了基因组减半距离的一个新的上界，它比最已知的距离紧，并且一个新的下界几乎总是比最已知的距离紧。我们还定义了基因组直径减半的概念，并得到了它的上下界。我们对基因组减半距离的更严格的限制产生了一种重建祖先复制基因组的新算法。我们基于这一新算法创建了一个软件包GenomeHalving，并在酵母基因组上进行了测试，确定了将酵母基因组减半的易位序列，该序列比之前猜测的可能的长度要短。
Motivation: Duplication of an organism’s entire genome is a rare but spectacular event, enabling the rapid emergence of multiple new gene functions. Over time, the parallel linkage of duplicated genes across chromosomes may be disrupted by reciprocal translocations, while the intra-chromosomal order of genes may be shuffled by inversions and transpositions. Some duplicate genes may evolve unrecognizably or be deleted. As a consequence, the only detectable signature of an ancient duplication event in a modern genome may be the presence of various chromosomal segments containing parallel paralogous genes, with each segment appearing exactly twice in the genome. The problem of reconstructing the linkage structure of an ancestral genome before duplication is known as genome halving with unordered chromosomes. Results: In this paper, we derive a new upper bound on the genome halving distance that is tighter than the best known, and a new lower bound that is almost always tighter than the best known. We also define the notion of genome halving diameter, and obtain both upper and lower bounds for it. Our tighter bounds on genome halving distance yield a new algorithm for reconstructing an ancestral duplicated genome. We create a software package GenomeHalving based on this new algorithm and test it on the yeast genome, identifying a sequence of translocations for halving the yeast genome that is shorter than previously conjectured possible.