Coate Jeremy E, Farmer Andrew D, Schiefelbein John W, Doyle Jeff J
Department of Biology, Reed College, Portland, OR, United States.
National Center for Genome Resources, Santa Fe, NM, United States.
Front Genet. 2020 Nov 3;11:596150. doi: 10.3389/fgene.2020.596150. eCollection 2020.
Gene duplication is a key evolutionary phenomenon, prevalent in all organisms but particularly so in plants, where whole genome duplication (WGD; polyploidy) is a major force in genome evolution. Much effort has been expended in attempting to understand the evolution of duplicate genes, addressing such questions as why some paralog pairs rapidly return to single copy status whereas, in other pairs, both paralogs are retained and may diverge in expression pattern or function. The effect of a gene - its site of expression and thus the initial locus of its function - occurs at the level of a cell comprising a single cell type at a given state of the cell's development. Using single cell transcriptomic data we categorized patterns of expression for 11,470 duplicate gene pairs across 36 cell clusters comprising nine cell types and their developmental states. Among these 11,470 pairs, 10,187 (88.8%) had at least one copy expressed in at least one of the 36 cell clusters. Pairs produced by WGD more often had both paralogs expressed in root cells than did pairs produced by small scale duplications. Three quarters of gene pairs expressed in the 36 cell clusters (7,608/10,187) showed extreme expression bias in at least one cluster, including 352 cases of reciprocal bias, a pattern consistent with expression subfunctionalization. More than twice as many pairs showed reciprocal expression bias between cell states than between cell types or between roots and leaves. A group of 33 gene pairs with reciprocal expression bias showed evidence of concerted divergence of gene networks in stele vs. epidermis. Pairs with both paralogs expressed without bias were less likely to have paralogs with divergent mutant phenotypes; such bias-free pairs showed evidence of preservation by maintenance of dosage balance. Overall, we found considerable evidence of shifts in gene expression following duplication, including in >80% of pairs encoding 7,653 genes expressed ubiquitously in all root cell types and states for which we inferred the polarity of change.
基因复制是一种关键的进化现象，在所有生物中都普遍存在，在植物中尤为如此，其中全基因组复制（WGD；多倍体）是基因组进化的主要驱动力。人们在试图理解复制基因的进化方面付出了很多努力，解决了诸如为什么一些旁系同源基因对会迅速恢复到单拷贝状态，而在其他基因对中，两个旁系同源基因都被保留并且可能在表达模式或功能上发生分歧等问题。基因的作用——其表达位点以及因此其功能的初始位点——发生在由处于细胞发育给定状态的单一细胞类型组成的细胞水平上。我们使用单细胞转录组数据对跨越36个细胞簇（包括9种细胞类型及其发育状态）的11470对复制基因的表达模式进行了分类。在这11470对基因中，10187对（88.8%）至少有一个拷贝在36个细胞簇中的至少一个中表达。由WGD产生的基因对比由小规模复制产生的基因对更常出现两个旁系同源基因都在根细胞中表达的情况。在36个细胞簇中表达的基因对中有四分之三（7608/10187）在至少一个簇中表现出极端的表达偏向，包括352例相互偏向的情况，这种模式与表达亚功能化一致。在细胞状态之间表现出相互表达偏向的基因对比在细胞类型之间或根与叶之间多两倍以上。一组具有相互表达偏向的33对基因显示出在中柱与表皮中基因网络协同分化的证据。两个旁系同源基因都无偏向性表达的基因对其旁系同源基因具有不同突变表型的可能性较小；这种无偏向性的基因对显示出通过维持剂量平衡而得以保留的证据。总体而言，我们发现了大量复制后基因表达发生变化的证据，包括在编码7653个在所有根细胞类型和状态中普遍表达的基因的基因对中，超过80%的基因对我们推断了变化的极性。
