Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, New Jersey, USA.
Mol Biol Evol. 2012 Feb;29(2):861-71. doi: 10.1093/molbev/msr261. Epub 2011 Oct 14.
A salient feature of genomes of higher organisms is the birth and death of gene copies. An example is the alpha prolamin genes, which encode seed storage proteins in grasses (Poaceae) and represent a medium-size gene family. To better understand the mechanism, extent, and pace of gene amplification, we compared prolamin gene copies in the genomes of two different tribes in the Panicoideae, the Paniceae and the Andropogoneae. We identified alpha prolamin (setarin) gene copies in the diploid foxtail millet (Paniceae) genome (490 Mb) and compared them with orthologous regions in diploid sorghum (730 Mb) and ancient allotetraploid maize (2,300 Mb) (Andropogoneae). Because sequenced genomes of other subfamilies of Poaceae like rice (389 Mb) (Ehrhartoideae) and Brachypodium (272 Mb) (Pooideae) do not have alpha prolamin genes, their collinear regions can serve as "empty" reference sites. A pattern emerged, where genes were copied and inserted into other chromosomal locations followed by additional tandem duplications (clusters). We observed both recent (species-specific) insertion events and older ones that are shared by these tribes. Many older copies were deleted by unequal crossing over of flanking sequences or damaged by truncations. However, some remain intact with active and inactive alleles. These results indicate that genomes reflect only a snapshot of the gene content of a species and are far less static than conventional genetics has suggested. Nucleotide substitution rates for active alpha prolamins genes were twice as high as for low copy number beta, gamma, and delta prolamin genes, suggesting that gene amplification accelerates the pace of divergence.
高等生物基因组的一个显著特征是基因拷贝的诞生和死亡。一个例子是α醇溶蛋白基因，它编码禾本科（Poaceae）种子中的贮藏蛋白，代表一个中等大小的基因家族。为了更好地理解基因扩增的机制、程度和速度，我们比较了 Panicoideae 中的两个不同部落——Paniceae 和 Andropogoneae——的醇溶蛋白基因拷贝。我们在二倍体谷子（Paniceae）基因组（490Mb）中鉴定了α醇溶蛋白（setarin）基因拷贝，并将其与二倍体高粱（730Mb）和古老的异源四倍体玉米（2300Mb）（Andropogoneae）的同源区进行了比较。由于禾本科其他亚科如水稻（389Mb）（Ehrhartoideae）和短柄草（272Mb）（Pooideae）的测序基因组没有α醇溶蛋白基因，它们的共线性区域可以作为“空”参考位点。出现了一种模式，即基因被复制并插入到其他染色体位置，然后进行额外的串联重复（簇）。我们观察到了最近（物种特异性）的插入事件和这些部落共有的较老的插入事件。许多较老的拷贝通过侧翼序列的不等交换或截断而被删除。然而，一些仍然完整，具有活性和非活性等位基因。这些结果表明，基因组仅反映了物种基因组成的一个快照，远不如传统遗传学所暗示的那样静态。活性α醇溶蛋白基因的核苷酸取代率是低拷贝数β、γ和δ醇溶蛋白基因的两倍，这表明基因扩增加速了分化的速度。
