In situ and in silico localization of major satellite DNAs in the genome of the red-eared slider (Trachemys scripta elegans, Emydidae, Testudines).

Abstract

Introduction: Satellite DNA is an important component of the eukaryotic genome. Some satellite DNAs plays an important role in various biological processes. The red-eared slider (Trachemys scripta elegans, 2n=50, C=1.43 pg) belongs to the American freshwater turtle family and is recognised as one of the world's most invasive species. In the T. s. elegans chromosome-level genome assembly, which has been recently published, satellite DNAs comprise only 0.1%. From the repetitive repertoire of the T. elegans genome, only ribosomal DNA genes and telomeric repeats have been localised on the species' chromosomes.

Methods: Using publicly available short-read sequencing data, we conducted de novo identification of the most abundant satellite DNAs in T. s. elegans using TAREAN pipeline. We combined bioinformatics (using blastn) and chromosome mapping by fluorescence in situ hybridization to describe the distribution of major tandem repetitive DNAs. The diversity and distribution of satDNA in the assembled genome of T. s. elegans were explored using the SatXplor pipeline.

Results: Six major satellite sequences occupying approximately 0.8% of the genome were identified in the genome data, all of which were successfully localised both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organisation of these sequences: monomers may be moderately or highly variable and they may contain regions homologous to retrotransposons. Cytogenetic mapping showed the accumulation of satellite DNAs in the pericentromeric regions of most chromosomes and in the distal regions of the short arms of submetacentric chromosomes. Comparisons between cytogenetic maps and genome assembly data revealed discrepancies in the number and chromosomal locations of the identified satellite DNA clusters.

Conclusion: The red-eared slider genome has a greater proportion of satellite DNA than was previously reported. These satellites demonstrate no specificity for either macrochromosomes or microchromosomes. Differences between in situ and in silico results indicate the challenges of repetitive sequence assembly, as well as discrepancies between chromosome numbering in the current chromosome-level genome assembly and the physical chromosome map.