Algorithms and analyses for the evolution of plant chromosomes and gene orders

我们研究结构基因组进化的基因顺序，集中在显花植物。一个焦点是通过反复的全基因组加倍和重复基因的丢失来扩展和收缩单基因家族的分支过程模型，以及通过假基因化或DNA切除在同线背景下这种丢失的性质。另一个重点是在整个染色体内的基因顺序水平上基于遗传学的祖先基因组重建。 全基因组加倍、三倍或更大程度的复制在几乎所有开花植物的谱系中都得到了证实，在一些植物的祖先中重复出现两次、三次或更多次。当这一事件发生在植物基因组进化中时，它启动了一个更渐进的补偿过程，称为分离，即重复基因的丢失。我们利用分支过程模型的经常性的全基因组复制和分馏，其中的参数估计的分馏率。在最初的开发中，我们测试了锦葵科和茄科的分析。我们计划实施一个全面的管道，继续发展我们的方法，并调查大量的植物家族进行比较研究。 在分馏的研究中增加同线维，探讨分馏的机理。通过检测在一系列连续的基因被删除后还有多少序列保留下来，我们发现这个残基保持在一个恒定的低水平，与有多少基因丢失无关--如果有任何缺失序列的遗迹的话，也很少--“假基因”。在这种情况下，这些必须是罕见的或极其短暂的。我们已经在10个基因组中验证了这一点，但计划研究更广泛的基因组复制事件样本，包括最近在农业背景下的样本。 我们还将观察表观缺失是基因移出或移入同线环境的人为产物的频率。我们计划的一个关键部分是构建一个管道“RACCROCHE”，用于祖先基因组的基于遗传学的推断。 该方法的策略是积累大量的广义基因邻接，而不仅仅是直接邻居，从所有现存的染色体，受到系统发育过滤器在每个祖先节点的同源性，作为输入的最大权重匹配算法。后者输出每个包含多达几百个基因的“重叠群”。然后将这些重叠群的所有对与每个现存基因组中的每个染色体进行匹配，以编制共现得分和成对顺序。然后将得分矩阵聚类以将叠连群的集合划分成不相交的有序集合，其自然地可解释为与同源性的特定节点相关联的祖先基因组的染色体。我们已经对整个单子叶植物分支和几个蔷薇目的数据进行了测试。

We study structural genome evolution in terms of gene order, concentrating on the flowering plants. One focus ison branching process models for the expansion and contraction of single gene families through recurrent whole genome doubling and loss of duplicate genes, as well as the nature of this loss in syntenic context via pseudogenization or DNA excision. The other focus is on phylogeny-based ancestral genome reconstruction at the level of gene order within whole chromosomes. Whole-genome doubling, tripling or replicating to a greater degree is attested in almost all lineages of the flowering plants, recurring in the ancestry of some plants two, three or more times. When this event occurs in plant genome evolution, it sets in operation a more gradual compensatory process called fractionation, the loss of duplicate genes. We make use of branching process models of recurrent whole genome duplication and fractionation, where the parameters to be estimated are fractionation rates. In the initial development, we tested the analyses on the Malvaceae and the Solanaceae. We plan to implement a full-fledged pipeline with continued developments of our method, and survey a large number of plant families for a comparative study. Adding a syntenic dimension to the study of fractionation, we explore the mechanism of fractionation. By examining how much sequence remains after a contiguous series of genes is deleted, we find that this residue remains at a constant low level independent of how many genes are lost-there are few if any relics of the missing sequence -"pseudogenes". These must be rare or extremely transient in this context. We have already verified this in ten genomes, but plan to look at  a much wider sample of genome replication events, including very recent ones in the agricultural context.  We will also look to see how frequently apparent deletion is an artifact of gene movement out of, or into, syntenic contexts. A key part of our program is to construct a pipeline 'RACCROCHE" for the phylogeny-based inference of ancestral genomes.   The strategy of this method is to accumulate a large number of generalized gene adjacencies, not just immediate neighbours, from all the extant chromosomes, subject to a phylogenetic filter at each ancestral node of the phylogeny, as input to a maximum weight matching algorithm. The latter outputs "contigs" containing up to several hundred genes each. All pairs of these contigs are then matched against each of the chromosomes in each of the extant genomes to compile a co-occurrence score and a pairwise order. The matrix of scores is then clustered to partition the set of contigs into disjoint, ordered sets,which are naturally interpretable as the chromosomes of the ancestral genome associated with the particular node of the phylogeny. We have done tests on data from the entire monocot clade and from several rosid orders.