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Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca.
Mira-Jover, Andrea; Graciá, Eva; Giménez, Andrés; Fritz, Uwe; Rodríguez-Caro, Roberto Carlos; Bourgeois, Yann.
Afiliación
  • Mira-Jover A; Ecology Area, University Institute for Agro-food and Agro-environmental Research and Innovation (CIAGRO), Miguel Hernández University, Elche, Carretera de Beniel, Orihuela (Alicante), Spain.
  • Graciá E; Ecology Area, University Institute for Agro-food and Agro-environmental Research and Innovation (CIAGRO), Miguel Hernández University, Elche, Carretera de Beniel, Orihuela (Alicante), Spain.
  • Giménez A; Ecology Area, University Institute for Agro-food and Agro-environmental Research and Innovation (CIAGRO), Miguel Hernández University, Elche, Carretera de Beniel, Orihuela (Alicante), Spain.
  • Fritz U; Museum of Zoology, Senckenberg Dresden, Dresden, Germany.
  • Rodríguez-Caro RC; Departamento de Ecología, Universidad de Alicante, San Vicent del Raspeig, Spain.
  • Bourgeois Y; DIADE, University of Montpellier, Montpellier, France.
PLoS One ; 19(8): e0303408, 2024.
Article en En | MEDLINE | ID: mdl-39121089
ABSTRACT

BACKGROUND:

Obtaining 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.

RESULTS:

We 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.

CONCLUSIONS:

Our 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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Tortugas / Genoma Límite: Animals Idioma: En Revista: PLoS One Asunto de la revista: CIENCIA / MEDICINA Año: 2024 Tipo del documento: Article País de afiliación: España Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Tortugas / Genoma Límite: Animals Idioma: En Revista: PLoS One Asunto de la revista: CIENCIA / MEDICINA Año: 2024 Tipo del documento: Article País de afiliación: España Pais de publicación: Estados Unidos