ArticlePloS one2024
Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca.
Article in PloS one, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- The tiger who came to T2T: Telomere-to-Telomere genome assembly of the Sumatran tiger (Panthera tigris sumatrae) using nanopore simplex reads.BMC genomics · 2026Article
- Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity.Ecology and evolution · 2025Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundObtaining de novo chromosome-level genome assemblies greatly enhances conservation and evolutionary biology studies. For many research teams, long-read sequencing technologies (that produce highly contiguous assemblies) remain unaffordable or unpractical. For the groups that display high synteny conservation, these limitations can be overcome by a reference-guided assembly using a close relative genome. Among chelonians, tortoises (Testudinidae) are considered one of the most endangered taxa, which calls for more genomic resources. Here we make the most of high synteny conservation in chelonians to produce the first chromosome-level genome assembly of the genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: Testudo graeca.
resultsWe used high-quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome-level reference of Gopherus evgoodei. We reconstructed a 2.29 Gb haploid genome with a scaffold N50 of 107.598 Mb and 5.37% gaps. We sequenced 25,998 protein-coding genes, and identified 41.2% of the assembly as repeats. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) that were consistent with previously suggested phylogeographic patterns for the species. This outlines the value of such reference-guided assemblies for phylogeographic studies.
conclusionsOur results highlight the value of using close relatives to produce de novo draft assemblies in species where such resources are unavailable. Our annotated genome of T. graeca paves the way to delve deeper into the species' evolutionary history and provides a valuable resource to enhance direct conservation efforts on their threatened populations.
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