Section of Integrative Biology, University of Texas, Austin, TX 78712, USA.
J Mol Evol. 2010 Feb;70(2):149-66. doi: 10.1007/s00239-009-9317-3. Epub 2010 Jan 21.
Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.
质体基因组的草科(禾本科)是不寻常的在其组织和序列进化的速度。最近在可用性的草质体基因组序列的激增,但没有进行全面的比较分析基因组进化,包括在 Poales 任何相关的家庭。我们报告的叶天南质体基因组,迄今首次非草科植物测序,并介绍了比较基因组组织和序列进化在 Poales。我们的研究结果证实,草质体基因组表现出加速的基因组重排和核苷酸取代。禾本科植物有多个结构重排,包括三个反转,三个基因损失(accD、ycf1、ycf2),在两个基因的内含子损失(clpP、rpoC1),和扩张的反向重复(IR)进入大、小单拷贝区。这些重排仅限于禾本科植物,和 IR 扩张到小单拷贝区与家庭的系统发育相关。比较 73 蛋白编码基因的 47 被子植物包括九个禾本科属确认导致禾本科植物的分支具有显著加速变化的速度相对于其他单子叶植物和被子植物。此外,在草科植物的序列进化的速度较低,表明家族多样化过程中的减速。总的来说,有一个强烈的相关性加速的基因组重排和核苷酸取代的禾本科植物,这一现象最近已经指出在整个被子植物。的原因的相关性是未知的,但错误的 DNA 修复已经在其他系统,包括细菌和动物的线粒体基因组。