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DNA Research Advance Access originally published online on May 4, 2009
DNA Research 2009 16(3):165-176; doi:10.1093/dnares/dsp008
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© The Author 2009. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Complete Chloroplast Genome Sequence of a Major Allogamous Forage Species, Perennial Ryegrass (Lolium perenne L.)

Kerstin Diekmann1,2,*, Trevor R. Hodkinson2, Kenneth H. Wolfe3, Rob van den Bekerom1,4, Philip J. Dix4 and Susanne Barth1

1 Teagasc Crops Research Centre, Oak Park, Carlow, Ireland
2 School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
3 Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
4 Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland

Received 10 February 2009 ; accepted 12 April 2009.

Lolium perenne L. (perennial ryegrass) is globally one of the most important forage and grassland crops. We sequenced the chloroplast (cp) genome of Lolium perenne cultivar Cashel. The L. perenne cp genome is 135 282 bp with a typical quadripartite structure. It contains genes for 76 unique proteins, 30 tRNAs and four rRNAs. As in other grasses, the genes accD, ycf1 and ycf2 are absent. The genome is of average size within its subfamily Pooideae and of medium size within the Poaceae. Genome size differences are mainly due to length variations in non-coding regions. However, considerable length differences of 1–27 codons in comparison of L. perenne to other Poaceae and 1–68 codons among all Poaceae were also detected. Within the cp genome of this outcrossing cultivar, 10 insertion/deletion polymorphisms and 40 single nucleotide polymorphisms were detected. Two of the polymorphisms involve tiny inversions within hairpin structures. By comparing the genome sequence with RT–PCR products of transcripts for 33 genes, 31 mRNA editing sites were identified, five of them unique to Lolium. The cp genome sequence of L. perenne is available under Accession number AM777385 [GenBank] at the European Molecular Biology Laboratory, National Center for Biotechnology Information and DNA DataBank of Japan.

Key words: chloroplast genome; Lolium perenne; Poaceae; chloroplast DNA variation; RNA editing

* To whom correspondence should be addressed. Tel. +353 59-9170-243. Fax. +353 59-9142-423. E-mail: kerstin.diekmann{at}teagasc.ie


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