Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.
School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK.
Genes (Basel). 2019 Aug 28;10(9):648. doi: 10.3390/genes10090648.
The formation of new genes by combining parts of existing genes is an important evolutionary process. Remodelled genes, which we call composites, have been investigated in many species, however, their distribution across all of life is still unknown. We set out to examine the extent to which genomes from cells and mobile genetic elements contain composite genes. We identify composite genes as those that show partial homology to at least two unrelated component genes. In order to identify composite and component genes, we constructed sequence similarity networks (SSNs) of more than one million genes from all three domains of life, as well as viruses and plasmids. We identified non-transitive triplets of nodes in this network and explored the homology relationships in these triplets to see if the middle nodes were indeed composite genes. In total, we identified 221,043 (18.57%) composites genes, which were distributed across all genomic and functional categories. In particular, the presence of composite genes is statistically more likely in eukaryotes than prokaryotes.
通过组合现有基因的部分来形成新基因是一个重要的进化过程。我们已经在许多物种中研究了经过改造的基因，即所谓的嵌合体，但它们在所有生命形式中的分布仍然未知。我们着手研究细胞和移动遗传元件的基因组中包含嵌合体基因的程度。我们将显示至少与两个不相关的组成基因部分同源的基因定义为嵌合体基因。为了识别嵌合体和组成基因，我们构建了来自生命的三个域（细菌、古菌和真核生物）以及病毒和质粒的超过一百万个基因的序列相似性网络 (SSN)。我们在这个网络中识别了非传递的三节点对，并探索了这些三节点对中的同源关系，以确定中间节点是否确实是嵌合体基因。总共，我们鉴定了 221,043 个（18.57%）嵌合体基因，它们分布在所有基因组和功能类别中。特别是，嵌合体基因在真核生物中比原核生物更常见。
