Taking advantage of reference-guided assembly in a slowly-evolving lineage: application to Testudo graeca

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. Of chelonians, terrestrial tortoises 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 genus Testudo with one of the most iconic tortoise species in the Mediterranean basin: T. graeca. Results We used high quality, paired-end Illumina sequences to build a reference-guided assembly with the chromosome level assembly 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 25998 protein-coding genes, and a 41.2% fraction was determined as repetitive in our assembled genome. Demographic history reconstruction based on the genome revealed two events (population decline and recovery) consistent with previously suggested phylogeographic patterns for the species. This outlines the value of genomes like this 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 Testudo graeca annotated genome paves the way to delve deeper into the species' evolutionary history and provides a valuable resource to increase making direct conservation efforts on their threatened populations.