A global picture of tRNA genes in plant genomes

Morgane Michaud, Valérie Cognat, Anne-Marie Duchêne and Laurence Maréchal-Drouard

The Plant Journal, special issue "The Plant Genomes: An evolutionary view on structure and function" scheduled for publication early 2011

Abstract :

While transfer RNA (tRNA) has a fundamental role in cell life, little is known about tRNA gene organization and expression on a genome-side scale in eukaryotes, particularly in plants. Here, we survey the content and distribution of tRNA genes throughout five flowering plants and one green alga. Transfer RNA gene content is homogenous in plants and is mostly correlated with genome size. The number of tRNA pseudogenes and of organellar-like tRNA genes present in nuclear genomes greatly varies from one plant species to the other. These pseudogenes or organellar-like genes seem to be generated or inserted randomly during evolution. In higher plants, intron-containing tRNA genes are rare and correspond to genes coding for tRNATyr and tRNAMete. By contrast, in green algae, more than half of the tRNA genes contain an intron, likely supporting a divergent way of acquisition and of splicing process, as compared to land plants. Numerous tRNAs are co-transcribed in Chlamydomonas whereas they are mostly transcribed as single unit in flowering plants. The only exception is the presence of tRNAGly-snoRNA or tRNAMete-snoRNA cotranscripts in dicots and monocots respectively. The internal or external motifs required for efficient transcription of tRNA genes by the RNA polymerase III are well conserved among angiosperms. Interestingly, we report the existence of a new family of tRNA-related SINEs in Populus trichocarpa nuclear genome. Finally, as mitochondria and chloroplasts contain a genetic information, a rapid survey of the tRNA gene population in the two organelles is also showed.

Supplementary data : Plant genomic tRNA database

Based on whole genome sequencing projects, on the software tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE/) and on the few experimental data available, we survey in this contribution the genomic content and distribution of tRNA genes and tRNA-related SINE genes throughout five flowering plants (Arabidopsis thaliana, Medicago truncatula, Populus trichocarpa, Oriza sativa and Brachypodium distachyon) and one green alga (Chlamydomonas reinhardtii). We first curated manually the lists of tDNAs extracted from each genome. Pseudogenes as well as organellar-like tDNAs were tentatively correctly annotated. When available, plastidial or mitochondrial genome sequences are available, tRNA genes are included in the database. Inevitably, a few errors probably exist and some tRNA genes are still missing.
For detailed description of information in tables see tRNAscan-SE and information provided in the article.

Arabidopsis thaliana
Brachypodium distachyon
Chlamydomonas reinhardtii
Medicago truncatula
Oryza sativa japonica
Populus trichocarpa

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