TY - JOUR

T1 - In situ and in silico Localization of Major Satellite DNAs in the Genome of the Red-Eared Slider (Trachemys scripta elegans, Emydidae, Testudines)

AU - Romanenko, Svetlana A.

AU - Prokopov, Dmitry Yu

AU - Marchenko, Sergey A.

AU - Kulak, Maria M.

AU - Ilina, Arina V.

AU - Serdyukova, Natalia A.

AU - Galkina, Svetlana A.

AU - Trifonov, Vladimir A.

N1 - The research was completed using equipment and materials of the large-scale research facilities \u201CCryobank of cell cultures\u201D Institute of Molecular and Cellular Biology SB RAS (Novosibirsk, Russia). The establishment of primary cell lines from T. scripta elegans was performed at the \u201CChromas\u201D research resource centre of Saint Petersburg State University (Saint Petersburg, Russia). Computational resources were provided by the ELIXIR-CZ project (LM2015047), part of the international ELIXIR infrastructure. This research was supported through computational resources provided by the Shared Services Center \u201CData Center of FEB RAS\u201D (Khabarovsk) [].

PY - 2025/3/11

Y1 - 2025/3/11

N2 - 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 recognized 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 localized 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 the 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 localized both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organization 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.

AB - 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 recognized 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 localized 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 the 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 localized both in situ and in silico on T. s. elegans chromosomes and in silico on chromosomal scaffolds. We revealed a complex structural organization 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.

KW - Cytogenomics

KW - FISH

KW - Repeats

KW - Reptilia

KW - Turtle

UR - https://www.mendeley.com/catalogue/7381a18c-8373-3ede-8a58-fc28cead2139/

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-105004285271&origin=inward&txGid=637e00a9ca13bc03833614c9fad64524

UR - https://pubmed.ncbi.nlm.nih.gov/40068658/

U2 - 10.1159/000544908

DO - 10.1159/000544908

M3 - Article

C2 - 40068658

SP - 1

EP - 13

JO - Cytogenetic and Genome Research

JF - Cytogenetic and Genome Research

SN - 1424-8581

ER -