Locating rearrangement events in a phylogeny based on highly fragmented assemblies.
Locating rearrangement events in a phylogeny based on highly fragmented assemblies.
复制标题
DOI：
10.1186/s12864-015-2294-6
复制
发表时间：
2016-01-11
期刊：
影响因子：
4.4
通讯作者：
Sankoff D
中科院分区：
文献类型：
--
作者：
Zheng C;Sankoff D
基因组重排操作的推断需要完整的基因组组装作为输入数据，因为重排可能涉及任意大比例的一条或多条染色体。大多数基因组序列项目，尤其是那些不存在物理图谱的非模式生物体的项目，会产生非常碎片化的组装，因此重新排列的片段可能无法识别，因为它的两个端点位于不同的支架上。然而，断点很容易识别，只要它们不与支架末端重合即可。对于系统发育背景，在将片段组装与多个完整组装进行比较时，可以得出对断点的某些组合约束。我们询问我们可以在多大程度上使用片段化基因组和多个完整基因组之间的断点数据来恢复系统发育中的所有排列。我们通过染色体倒位来模拟基因组进化，将其中一个基因组片段化成大量支架来代表组装的不完整性。我们确定了该基因组与其余基因组之间的所有断点。我们设计了一种算法，在尝试确定重排事件发生在系统发育的哪个分支上时考虑这些断点。我们对恢复率对支架大小和重排率的依赖性进行了分析，并表明进行重排模拟的真实树在估计推断的真实事件数量方面往往是最简约的。令人有些惊讶的是，仅在片段化基因组和其他基因组之间确定的断点足以恢复模拟产生的大部分重排。即使在与片段化基因组谱系脱节的系统发育部分中，这一点也成立。
The inference of genome rearrangement operations requires complete genome assemblies as input data, since a rearrangement can involve an arbitrarily large proportion of one or more chromosomes. Most genome sequence projects, especially those on non-model organisms for which no physical map exists, produce very fragmented assembles, so that a rearranged fragment may be impossible to identify because its two endpoints are on different scaffolds. However, breakpoints are easily identified, as long as they do not coincide with scaffold ends. For the phylogenetic context, in comparing a fragmented assembly with a number of complete assemblies, certain combinatorial constraints on breakpoints can be derived. We ask to what extent we can use breakpoint data between a fragmented genome and a number of complete genomes to recover all the arrangements in a phylogeny. We simulate genomic evolution via chromosomal inversion, fragmenting one of the genomes into a large number of scaffolds to represent the incompleteness of assembly. We identify all the breakpoints between this genome and the remainder. We devise an algorithm which takes these breakpoints into account in trying to determine on which branch of the phylogeny a rearrangement event occurred. We present an analysis of the dependence of recovery rates on scaffold size and rearrangement rate, and show that the true tree, the one on which the rearrangement simulation was performed, tends to be most parsimonious in estimating the number of true events inferred. It is somewhat surprising that the breakpoints identified just between the fragmented genome and each of the others suffice to recover most of the rearrangements produced by the simulations. This holds even in parts of the phylogeny disjoint from the lineage of the fragmented genome.