The reproducibility of an inferred tree and the diploidization of gene segregation after genome duplication
The reproducibility of an inferred tree and the diploidization of gene segregation after genome duplication
复制标题
推断树的再现性和基因组复制后基因分离的二倍化
DOI：
10.1093/gbe/evz272
复制
发表时间：
2020
影响因子：
3.3
通讯作者：
Nei Masatoshi
中科院分区：
文献类型：
--
作者：
Katsura Yukako;Nei Masatoshi
我们以前介绍了一个数值量称为稳定性（Ps）的推断树，并表明，树是可靠的这种稳定性以及树的可靠性，这通常是计算为自助概率（Pb），必须是高的。然而，如果在一个物种中发生基因组复制，则该基因组的基因家族也复制，并且仅由于这个原因，在复制基因家族的树中，某些Ps值可能很高。此外，如果这些基因家族是可识别的，则复制基因家族的拓扑结构可以与原始基因家族的拓扑结构相似。然而，在基因组复制后，基因家族通常部分缺失或部分复制，并且复制的基因家族可能不显示与原始家族相同的拓扑结构。因此，有必要计算重复的和原始基因家族的拓扑结构的相似性。在本文中，我们引入了另一个量称为再现性（Pr）的两个基因家族的相似性进行衡量。为了说明如何计算Pr值，我们首先计算每个MHC II类α和β链基因家族的Pb和Ps值，它们显然是由基因组复制产生的。然后计算MHC II类α和β链基因家族的Pr值。α和β链基因家族的Pr值现在很低，这表明基因组复制后发生了基因分离的二倍体化。目前，高等动物，定义为具有复杂表型特征的动物，通常具有较高的基因组大小，并且这种基因组大小的增加似乎是由基因组复制和基因组复制后基因分离的二倍体化引起的。
We previously introduced a numerical quantity called the stability (Ps) of an inferred tree and showed that for the tree to be reliable this stability as well as the reliability of the tree, which is usually computed as the bootstrap probability (Pb), must be high. However, if genome duplication occurs in a species, a gene family of the genome also duplicates, and for this reason alone some Ps values can be high in a tree of the duplicated gene families. In addition, the topology of the duplicated gene family can be similar to that of the original gene family if such gene families are identifiable. After genome duplication, however, the gene families are often partially deleted or partially duplicated, and the duplicated gene family may not show the same topology as that of the original family. It is therefore necessary to compute the similarity of the topologies of the duplicated and the original gene families. In this paper, we introduce another quantity called the reproducibility (Pr) for measuring the similarity of the two gene families. To show how to compute the Pr values, we first compute the Pb and Ps values for each of the MHC class II α and β chain gene families, which were apparently generated by genome duplication. We then compute the Pr values for the MHC class II α and β chain gene families. The Pr values for the α and β chain gene families are now low, and this suggests that the diploidization of gene segregation has occurred after the genome duplication. Currently higher animals, defined as animals with complex phenotypic characters, generally have a higher genome size, and this increase in genome size appears to have been caused by genome duplication and diploidization of gene segregation after genome duplication.