Accepted_test

This study investigates large tandem repeats (TRs) in the genome of the grass frog (Rana temporaria) using bioinformatics and experimental methods. TRs play crucial roles in chromosomal functions but remain understudied, especially in non-mammalian species. The research utilizes Illumina reads from a low-coverage genome sequence and the aRanTem1.1 genome assembly to identify and map TRs. The extracTR tool and TAREAN were employed to analyze k-mers and identify TRs, which were then confirmed through fluorescence in situ hybridization (FISH).

Results revealed six abundant TRs with two k-mer families uniquely identified by extracTR. The FISH probes targeting these TRs showed intense hybridization signals mainly at the centromeres of the frog's chromosomes, with additional signals on chromosome arms. Using the aRanTem1.1 reference genome, 768 TR arrays over 10,000 bp were identified, grouped into 76 families or singletons. TRs showed varied monomer lengths and GC content, and their chromosome specificity was mapped, highlighting discrepancies between in situ and in silico data. Notably, TRs of the Rtem219A family contained 5S rRNA sequences, suggesting their evolutionary dynamism and potential spread across the genome.

The study underscores the complexity of assembling and annotating repetitive DNA sequences, particularly TRs, due to their prevalence in challenging genomic regions. It also highlights the effectiveness of combining bioinformatics tools and experimental validation to advance our understanding of genomic architecture and evolution in amphibians.