Open Access Highly Accessed Research article

The genome and transcriptome of perennial ryegrass mitochondria

Md Shofiqul Islam1, Bruno Studer2, Stephen L Byrne1, Jacqueline D Farrell1, Frank Panitz3, Christian Bendixen3, Ian Max Møller1 and Torben Asp1*

Author Affiliations

1 Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Forsøgsvej 1, Slagelse, DK 4200, Denmark

2 Department of Environmental Systems Science, Forage Crop Genetics, ETH Zurich, Zurich, CH 8092, Switzerland

3 Department of Molecular Biology and Genetics, Science and Technology, Aarhus University, Blichers Allé 20, Tjele, DK 8830, Denmark

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BMC Genomics 2013, 14:202  doi:10.1186/1471-2164-14-202

Published: 23 March 2013

Abstract

Background

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.

Results

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.

Conclusions

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.

Keywords:
De novo assembly; Mitochondrial gene expression; Mitochondrial genome; Next-generation sequencing; Perennial ryegrass (Lolium perenne L.)