Genome-Wide Discovery of Single-Nucleotide Polymorphisms and Their Application in Population Genetic Studies in the Endangered Japanese Eel (Anguilla japonica)

Bing-Jian Liu,Yu-Long Li,Jin-Xian Liu,Bai-Dong Zhang

doi:10.3389/fmars.2019.00782

Abstract

The Japanese eel (Anguilla japonica) is a commercially important aquatic species in East Asia. The number of the Japanese eels has been dramatically declining over the last four decades and it is now listed as an endangered species (ICUN 2014). To manage and conserve this endangered species, it is necessary to assess population genetic diversity, genetic structure, and identify regions of the genome which are under selection. Here, we generated a catalogue of novel SNP markers for the Japanese eel using restriction-site-associated DNA (RAD) sequencing of 24 individuals from two geographic locations. The 73,557 identified SNPs were widely distributed across the draft genome of the Japanese eel. No genetic differentiation between the two populations was detected based on all loci or neutral loci. However, highly significant genetic differentiation was detected based on loci which appeared to be under selection. BLAST2GO annotations of the outlier SNPs yielded hits for 61 (72%) of 85 significant BLASTX matches. KEGG pathway analysis identified some of the putative targets of local selection, including genes in several important pathways such as calcium signaling pathway, intestinal immune network for IgA production and others. This SNP catalogue will provide a valuable resource for future population genetic and genomic studies and allows for targeting speciﬁc genes and genomic regions under selection in the Japanese eel genome.

Highlights

Recent advances in next-generation sequencing (NGS) technologies have greatly improved the speed of genome sequencing, facilitating the application of genomic approaches in many research areas, including ecology, conservation, fisheries genetics, and so on (Hudson, 2008; Harismendy et al, 2009; Allendorf et al, 2010; Ekblom and Galindo, 2011; Dudgeon et al, 2012)
We compared the number of single-nucleotide polymorphism (SNP) generated from single-end and pairedend data, and we found that paired-end sequencing resulted in more high-quality SNPs
Despite microsatellites presenting higher diversity per locus, the large number of unlinked SNPs may overcome their relatively low mutation rates (10−8–10−9 per generation), and panels of several 1000 SNPs are likely to be more informative than the 10–20 microsatellite loci used in standard population genetic studies (Helyar et al, 2011; Seeb et al, 2011)

Summary

Introduction

Recent advances in next-generation sequencing (NGS) technologies have greatly improved the speed of genome sequencing, facilitating the application of genomic approaches in many research areas, including ecology, conservation, fisheries genetics, and so on (Hudson, 2008; Harismendy et al, 2009; Allendorf et al, 2010; Ekblom and Galindo, 2011; Dudgeon et al, 2012). One promising approach is restriction site-associated DNA (RAD) sequencing, which reduces genome complexity by sequencing the same loci across the genomes of numerous individuals, enabling comparisons between individuals, and reducing sequencing cost. This approach consists of employing specific restriction enzymes to cleave double-stranded genomic DNA into random fragments and amplifying and sequencing the regions flanking the restriction enzyme cut sites through specific adapters and NGS platforms, such as Illumina. As sequencing cost continues to drop, these methods will have numerous applications in a genetic analysis of complex genomes

Methods

Results

Conclusion