Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA.
Department of Plant and Microbial Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN, 55108, USA.
Plant J. 2018 Jan;93(1):131-141. doi: 10.1111/tpj.13765. Epub 2017 Dec 2.
Maize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non-shared gene loss events between individuals following a whole-genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole-genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variably fractionated syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable than syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.
玉米是一个具有丰富的存在/缺失变异和拷贝数变异的多倍体古种。存在/缺失变异产生的一种机制是差异分馏。分馏是指在二倍体化过程中，一对重复基因从玉米的一个亚基因组中丢失。差异分馏是指在全基因组复制事件之后，个体之间非共享的基因丢失事件。我们使用两个自交系 B73 和 PH207 的全基因组从头组装来研究由差异分馏引起的基因组同线性部分的存在/缺失变异的流行情况。在这两个基因组之间，同线性基因高度保守，只有不到 1%的同线性基因受到差异分馏的影响。所鉴定的少数可变分馏同线性基因不太可能导致功能表型变异，因为在注释基因集中这些基因大量缺失。在对 60 个不同自交系的进一步比较中，非同线性基因的变异性是同线性基因的六倍，这表明在其他基因组组装之间进行比较不太可能导致同线性基因之间发现大规模的存在/缺失变异。
