During evolution, the increasing proportion of complex genes and young genes in the genome substantially contributes to the increasing of genome/organism complexity1-4. As for an individual organism, it is the process of embryonic development that makes the genome complexity be represented as the phenotypic complexity at organismal level. Our study focus on the basic question: how are the complex and young genes utilized during embryonic development to form the organismal complexity?
We found that complex genes, such as long genes, genes with multiple cis-regulatory modules5, genes encoding long proteins or multi-domain proteins1,3, tend to be utilized preferentially at each embryonic developmental stage, with the strongest strength of over-representation at mid-late stages. This trend is mainly due to complex genes with middle-age, which originated approximately during Cambrian Bio-radiation. On the other hand, young genes tend to be expressed at specific developmental stages. And it's obvious that young genes tend to be expressed in the early stage of the differentiation of embryonic stem cells (ESCs) into nerve cells. These main results are robust across protostomia and deuterostomia regardless of different technologies used to produce the data. These results indicate that complex genes and young genes contribute to the organismal complexity at two different levels: Complex genes contribute to the complexity of individual proteome at certain states, whereas young genes contribute to the diversity of proteomes at different spatial-temporal states.
This study also provided a new view for the relationship between evolutionary and developmental processes, which is a fundamental question in evolutionary developmental biology. Our results support "funnel-like model" in a new view, and can answer why there are different Evo-Devo-relation models, which gives new insights into Von-Bear theory.