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Abstract <p>Amphibians are recognized as biological indicators of ecosystem health due to their sensitivity to environmental changes, and therefore genomic studies aimed at their conservation are becoming increasingly important. The genome assembly of the endemic Tavas Frog, <i>Rana tavasensis</i> has been obtained using the Oxford Nanopore Technologies (ONT) platform were assembled de novo using the Flye assembler. Where the completeness of the initial assembly was insufficient, scaffold refinement was performed using the RagTag tool via the reference genome of <i>Rana temporaria</i>, one of the closest species. Assembly quality was assessed using various structural metrics, and genome integrity was verified using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Large-scale structural variants detected in the genome were linked to gene annotations; variant-containing genes were functionally analysed using Gene Ontology (GO) terms. These analyses revealed significant differences from the reference species, particularly in biological processes related to immunity, development, and stress response. Furthermore, analyses performed using RepeatMasker identified numerous repeat classes, including Long Interspersed Nuclear Elements (LINE), Short Interspersed Nuclear Elements (SINE), Long Terminal Repeats (LTR), and DNA transposons, and their distribution within the genome was visualized. The number of variants were highest in the <i>MHC2</i> (86.7 ± 15.9), <i>MHY</i> (79.4 ± 42.8) and <i>HOX</i> (53.45 ± 7.95) genes that were related to immune, muscular and developmental systems, respectively. This genomic resource is important for the understanding of the evolutionary and functional genomic characteristics of the species using the evaluations of structural variant analysis, functional annotations, and repeat sequences.</p>

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The Genome Sequence of the Endemic Tavas Frog, Rana tavasensis Baran & Atatür, 1986 from Denizli, Türkiye

  • 期刊论文

  • 发表日期：

    2026年6月15日

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  • A. Kaska,
  • S. A. Ulubeli,
  • S. Düşen,
  • Y. Kaska

摘要

Abstract

Amphibians are recognized as biological indicators of ecosystem health due to their sensitivity to environmental changes, and therefore genomic studies aimed at their conservation are becoming increasingly important. The genome assembly of the endemic Tavas Frog, Rana tavasensis has been obtained using the Oxford Nanopore Technologies (ONT) platform were assembled de novo using the Flye assembler. Where the completeness of the initial assembly was insufficient, scaffold refinement was performed using the RagTag tool via the reference genome of Rana temporaria, one of the closest species. Assembly quality was assessed using various structural metrics, and genome integrity was verified using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Large-scale structural variants detected in the genome were linked to gene annotations; variant-containing genes were functionally analysed using Gene Ontology (GO) terms. These analyses revealed significant differences from the reference species, particularly in biological processes related to immunity, development, and stress response. Furthermore, analyses performed using RepeatMasker identified numerous repeat classes, including Long Interspersed Nuclear Elements (LINE), Short Interspersed Nuclear Elements (SINE), Long Terminal Repeats (LTR), and DNA transposons, and their distribution within the genome was visualized. The number of variants were highest in the MHC2 (86.7 ± 15.9), MHY (79.4 ± 42.8) and HOX (53.45 ± 7.95) genes that were related to immune, muscular and developmental systems, respectively. This genomic resource is important for the understanding of the evolutionary and functional genomic characteristics of the species using the evaluations of structural variant analysis, functional annotations, and repeat sequences.