tRNA-Cys gene clusters exhibit high variability in Arabidopsis thaliana

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 analy...

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Published inBMC plant biology Vol. 23; no. 1; p. 623
Main Authors Szymanski, Maciej, Maurya, Anand, Kopec, Piotr, Karlowski, Wojciech M
Format Journal Article
LanguageEnglish
Published England BioMed Central Ltd 07.12.2023
BioMed Central
BMC
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
Poland
tRNA gene clusters
Helitron
tRNA
Transposable elements
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Summary: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.
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content type line 23
ISSN:1471-2229
1471-2229
DOI:10.1186/s12870-023-04632-x