Low‐coverage reduced representation sequencing reveals subtle within‐island genetic structure in Aldabra giant tortoises

Genomic insights into the conservation status of the Idle Crayfish Austropotamobius bihariensis Pârvulescu, 2019: low genetic diversity in the endemic crayfish species of the Apuseni Mountains

BACKGROUND

Biodiversity in freshwater ecosystems is declining due to an increased anthropogenic footprint. Freshwater crayfish are keystone species in freshwater ecosystems and play a crucial role in shaping the structure and function of their habitats. The Idle Crayfish Austropotamobius bihariensis is a native European species with a narrow distribution range, endemic to the Apuseni Mountains (Romania). Although its area is small, the populations are anthropogenically fragmented. In this context, the assessment of its conservation status is timely.

RESULTS

Using a reduced representation sequencing approach, we identified 4875 genomic SNPs from individuals belonging to 13 populations across the species distribution range. Subsequent population genomic analyses highlighted low heterozygosity levels, low number of private alleles and small effective population size. Our structuring analyses revealed that the genomic similarity of the populations is conserved within the river basins.

CONCLUSION

Genomic SNPs represented excellent tools to gain insights into intraspecific genomic diversity and population structure of the Idle Crayfish. Our study highlighted that the analysed populations are at risk due to their limited genetic diversity, which makes them extremely vulnerable to environmental alterations. Thus, our results emphasize the need for conservation measures and can be used as a baseline to establish species management programs.

Chromosome-level genome assembly for the Aldabra giant tortoise enables insights into the genetic health of a threatened population

Background

The Aldabra giant tortoise (Aldabrachelys gigantea) is one of only two giant tortoise species left in the world. The species is endemic to Aldabra Atoll in Seychelles and is listed as Vulnerable on the International Union for Conservation of Nature Red List (v2.3) due to its limited distribution and threats posed by climate change. Genomic resources for A. gigantea are lacking, hampering conservation efforts for both wild and ex situpopulations. A high-quality genome would also open avenues to investigate the genetic basis of the species’ exceptionally long life span.

Findings

We produced the first chromosome-level de novo genome assembly of A. gigantea using PacBio High-Fidelity sequencing and high-throughput chromosome conformation capture. We produced a 2.37-Gbp assembly with a scaffold N50 of 148.6 Mbp and a resolution into 26 chromosomes. RNA sequencing–assisted gene model prediction identified 23,953 protein-coding genes and 1.1 Gbp of repetitive sequences. Synteny analyses among turtle genomes revealed high levels of chromosomal collinearity even among distantly related taxa. To assess the utility of the high-quality assembly for species conservation, we performed a low-coverage resequencing of 30 individuals from wild populations and two zoo individuals. Our genome-wide population structure analyses detected genetic population structure in the wild and identified the most likely origin of the zoo-housed individuals. We further identified putatively deleterious mutations to be monitored.

Conclusions

We establish a high-quality chromosome-level reference genome for A. gigantea and one of the most complete turtle genomes available. We show that low-coverage whole-genome resequencing, for which alignment to the reference genome is a necessity, is a powerful tool to assess the population structure of the wild population and reveal the geographic origins of ex situ individuals relevant for genetic diversity management and rewilding efforts.