Department of Plant Biology, Michigan State University.
Ecology, Evolutionary Biology, and Behavior Program, Michigan State University.
Genome Biol Evol. 2018 Oct 1;10(10):2596-2613. doi: 10.1093/gbe/evy193.
Gene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, using the Solanaceae family as a model and Pfam domain families as a proxy for gene families, we investigated variation in gene family sizes across species and the likely factors contributing to the variation. We found that genes in highly variable families have high turnover rates and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high- and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggest that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.
基因复制和丢失导致了物种间基因内容的差异和表型分化。然而，密切相关的植物物种之间的基因内容变化程度以及导致这种变化的因素仍不清楚。在这里，我们以茄科植物作为模型，以 Pfam 结构域家族作为基因家族的代表，研究了物种间基因家族大小的变化以及可能导致这种变化的因素。我们发现，在高度可变的家族中，基因的周转率很高，并且往往与茄科植物之间已经分化的过程有关，而在低变异性家族中的基因则往往具有管家作用。此外，高变异性和低变异性基因家族中的基因分别倾向于通过串联和全基因组复制而复制。这一发现以及不同复制机制的基因所经历的不同选择压力的观察结果表明，复制机制会影响基因家族的周转率。我们曾试图用假基因数量作为基因丢失的替代指标，但发现大量的假基因实际上是假基因复制的产物，这与大多数植物假基因是曾经功能复制的残余物的预期相反。我们的研究结果揭示了基因家族大小、基因功能、复制机制和进化率之间的复杂关系。茄科植物中谱系特异性基因家族扩张的模式为更好地理解这个在经济上重要的家族中表型多样性的遗传基础提供了基础。
