BMC Genomics. 2013 Mar 23;14:202. doi: 10.1186/1471-2164-14-202.
Perennial ryegrass (Lolium perenne L.) is one of the most important forage and turf grass species of temperate regions worldwide. Its mitochondrial genome is inherited maternally and contains genes that can influence traits of agricultural importance. Moreover, the DNA sequence of mitochondrial genomes has been established and compared for a large number of species in order to characterize evolutionary relationships. Therefore, it is crucial to understand the organization of the mitochondrial genome and how it varies between and within species. Here, we report the first de novo assembly and annotation of the complete mitochondrial genome from perennial ryegrass.
Intact mitochondria from perennial ryegrass leaves were isolated and used for mtDNA extraction. The mitochondrial genome was sequenced to a 167-fold coverage using the Roche 454 GS-FLX Titanium platform, and assembled into a circular master molecule of 678,580 bp. A total of 34 proteins, 14 tRNAs and 3 rRNAs are encoded by the mitochondrial genome, giving a total gene space of 48,723 bp (7.2%). Moreover, we identified 149 open reading frames larger than 300 bp and covering 67,410 bp (9.93%), 250 SSRs, 29 tandem repeats, 5 pairs of large repeats, and 96 pairs of short inverted repeats. The genes encoding subunits of the respiratory complexes - nad1 to nad9, cob, cox1 to cox3 and atp1 to atp9 - all showed high expression levels both in absolute numbers and after normalization.
The circular master molecule of the mitochondrial genome from perennial ryegrass presented here constitutes an important tool for future attempts to compare mitochondrial genomes within and between grass species. Our results also demonstrate that mitochondria of perennial ryegrass contain genes crucial for energy production that are well conserved in the mitochondrial genome of monocotyledonous species. The expression analysis gave us first insights into the transcriptome of these mitochondrial genes in perennial ryegrass.
黑麦草（Lolium perenne L.）是世界温带地区最重要的饲料和草坪草之一。其线粒体基因组通过母系遗传，包含可影响农业重要性状的基因。此外，为了描述进化关系，已经建立并比较了大量物种的线粒体基因组的 DNA 序列。因此，了解线粒体基因组的组织及其在物种间和种内的变化至关重要。在这里，我们报道了首例多年生黑麦草完整线粒体基因组的从头组装和注释。
从多年生黑麦草草叶中分离出完整的线粒体并用于 mtDNA 提取。使用罗氏 454 GS-FLX Titanium 平台对线粒体基因组进行测序，达到 167 倍覆盖率，并组装成一个 678,580bp 的圆形主分子。线粒体基因组共编码 34 种蛋白质、14 种 tRNA 和 3 种 rRNA，基因空间总计 48,723bp（7.2%）。此外，我们鉴定出 149 个大于 300bp 的开放阅读框，覆盖 67,410bp（9.93%），250 个 SSRs、29 个串联重复序列、5 对大重复序列和 96 对短反向重复序列。编码呼吸复合物亚基的基因 - nad1 到 nad9、 cob、cox1 到 cox3 和 atp1 到 atp9 - 无论是绝对值还是归一化后，表达水平都很高。
本文呈现的多年生黑麦草线粒体基因组的圆形主分子构成了未来在禾本科物种内和种间比较线粒体基因组的重要工具。我们的结果还表明，多年生黑麦草的线粒体包含对能量产生至关重要的基因，这些基因在单子叶植物的线粒体基因组中得到很好的保守。表达分析使我们首次深入了解多年生黑麦草这些线粒体基因的转录组。
