1KSA- Nanopore sequencing and draft genome assembly of Chrysoblephus laticeps
Understanding the genomic architecture of species of conservation concern is essential for fostering effective conservation initiatives. Current biodiversity assessment approaches increasingly incorporate genetic metrics to evaluate the status of species and populations of conservation interest. However, due to the limited availability of conspecific genomes for most non-model species, previous studies have often depended on heterospecific genomes. This approach has been shown to significantly impact the precision of genetic metrics, resulting in inaccurate measurements and insights. However, it is currently unknown what the impact of using non-species-specific genomes is for the determination of genetic indicators in vulnerable marine fishes, such as red roman (Chrysoblephus laticeps). Red roman is a southern African endemic species, which, due to overexploitation, is currently considered Near Threatened on the International Union for Conservation of Nature (IUCN) Red List. Recent studies have shown significant life history and physiological differences between exploited and protected populations. Here, we present the first high-quality scaffold-level genome assembly and annotations for the red roman, using a combination of Oxford Nanopore and Illumina sequencing, and compared key genetic indicators (diversity, population structure and effective population size) obtained from reads mapped to the genomes of other Sparidae species, with well-established genomic resources. The final assembly had 1 263 scaffolds, a total length of 758 Mb, with a scaffold N50 of 5.89 Mb and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 99.30%. As expected, comparative analyses with genomes of different sparid species revealed enhanced read alignment, genotyping accuracy, and Single Nucleotide Polymorphism (SNP) retention after filtering. Furthermore, there were significant overall differences across the genomes for the measures of observed heterozygosity (HO), nucleotide diversity (p), Tajima's D, FST, and estimates of effective population size (Ne), with different genomes presenting different (and sometimes contrasting) genetic indicators metrics and, consequently, demographic histories for red roman. Our study not only significantly improved genomic resources for genomic conservation analyses in C. laticeps, but most importantly highlighted the importance of species-specific reference genomes for accurate evolutionary and conservation inference in highly variable marine fishes.
Understanding the genomic architecture of species of conservation concern is essential for fostering effective conservation initiatives. Current biodiversity assessment approaches increasingly incorporate genetic metrics to evaluate the status of species and populations of conservation interest. However, due to the limited availability of conspecific genomes for most non-model species, previous studies have often depended on heterospecific genomes. This approach has been shown to significantly impact the precision of genetic metrics, resulting in inaccurate measurements and insights. However, it is currently unknown what the impact of using non-species-specific genomes is for the determination of genetic indicators in vulnerable marine fishes, such as red roman (Chrysoblephus laticeps). Red roman is a southern African endemic species, which, due to overexploitation, is currently considered Near Threatened on the International Union for Conservation of Nature (IUCN) Red List. Recent studies have shown significant life history and physiological differences between exploited and protected populations. Here, we present the first high-quality scaffold-level genome assembly and annotations for the red roman, using a combination of Oxford Nanopore and Illumina sequencing, and compared key genetic indicators (diversity, population structure and effective population size) obtained from reads mapped to the genomes of other Sparidae species, with well-established genomic resources. The final assembly had 1 263 scaffolds, a total length of 758 Mb, with a scaffold N50 of 5.89 Mb and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 99.30%. As expected, comparative analyses with genomes of different sparid species revealed enhanced read alignment, genotyping accuracy, and Single Nucleotide Polymorphism (SNP) retention after filtering. Furthermore, there were significant overall differences across the genomes for the measures of observed heterozygosity (HO), nucleotide diversity (p), Tajima's D, FST, and estimates of effective population size (Ne), with different genomes presenting different (and sometimes contrasting) genetic indicators metrics and, consequently, demographic histories for red roman. Our study not only significantly improved genomic resources for genomic conservation analyses in C. laticeps, but most importantly highlighted the importance of species-specific reference genomes for accurate evolutionary and conservation inference in highly variable marine fishes.
University of Pretoria