tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana

• Published in: BMC plant biology 2023-12, Vol.23 (1), p.623-623, Article 623
• Main Authors: Szymanski, Maciej, Maurya, Anand, Kopec, Piotr, Karlowski, Wojciech M
• Format: Article
• Language: English
• Subjects: Arabidopsis - genetics; Arabidopsis thaliana; Base Sequence; Chromosome 5; Chromosomes; Divergence; Ecotypes; Gene clusters; Gene expression; Genes; Genetic aspects; Genetic research; Genetic variation; Genome; Genomes; Genomic analysis; Helitron; Heterogeneity; Multigene Family; Phylogenetics; Proteins; RNA polymerase; RNA, Transfer - genetics; Synteny; Transfer RNA; Transposable elements; tRNA; tRNA Cys; tRNA gene clusters
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-023-04632-x

Although most of the genes encoding tRNAs in plants are dispersed throughout the genome, a fraction of them form tRNA gene clusters. In Arabidopsis thaliana, the smallest of tRNA clusters on chromosome 5 consists of four tRNA-Cys-GCA genes placed within repeating units of 0.4 kbp. A systematic analysis of the genomic sequences of syntenic regions from various ecotypes of A. thaliana showed that the general structure of the cluster, consisting of a tRNA-Cys pseudogene followed by repeating units containing tRNA-Cys genes, is well conserved. However, there is significant heterogeneity in the number of repeating units between different ecotypes. A unique feature of this cluster is the presence of putative transposable elements (Helitron). In addition, two further tRNA-Cys gene mini-clusters (gene pairs) in A. thaliana were identified. RNA-seq-based evaluation of expression of tRNA-Cys-GCA genes showed a positive signal for 11 out of 13 unique transcripts. An analysis of the conservation of the tRNA-Cys clusters from A. thaliana with the corresponding regions from four other Arabidopsis species suggests a sequence of events that led to the divergence of these regions.