The genome and transcriptome of perennial ryegrass mitochondria

Abstract

BackgroundPerennial 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.ResultsIntact 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.ConclusionsThe 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.

The Potato Tuber Mitochondrial Proteome

“…In spite of the fact that all proteins encoded in mitochondrial DNA are subunits in the constitutively expressed respiratory complexes or appear to be essential housekeeping proteins, the finding of "only" 71 PPR proteins indicates that many RNA-related processes are inactive in POM. In mitochondria from perennial ryegrass (Lolium perenne) reproductive tissues, a transcript profile showed that the expression of several mitochondrially expressed ribosomal proteins was very low (Islam et al, 2013). This may mean that their expression, and the associated RNA-related processes including PPR proteins, are dependent on the tissue and/or environmental conditions.…”

De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

“…Comparison of the scaffolded assembly with published mitochondrial and chloroplast sequences for Lolium (Islam et al 2013 ;Diekmann et al 2008 ) identifi ed three scaffolds that were mitochondrial in origin and two that were chloroplast in origin. Removal of mitochondrial and chloroplast scaffolds resulted in a genomic assembly containing 424,745 scaffolds and with N50 of 25,193.…”

Plant Mitochondrial Omics: State-of-the-Art Knowledge

“…Fujii et al ( 2011 ) have very recently characterized the continuously expressed ORFs present in the intergenic region of mitochondrial genome of rice. Similarly, Islam et al ( 2013 ) have presented the mitochondrial genome and transcriptome sequence analyses of perennial ryegrass ( Lolium perenne L.), but still it lacks the detailed transcript mapping and promoter identifi cation. In contrast to plant mitochondrial transcriptome data, human mitochondrial transcriptome has been analyzed more comprehensively across different cell lines and tissues (Mercer et al 2011 ).…”