A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication

Abstract

BackgroundRecent advancements in next-generation sequencing technology have enabled cost-effective sequencing of whole or partial genomes, permitting the discovery and characterization of molecular polymorphisms. Double-digest restriction-site associated DNA sequencing (ddRAD-seq) is a powerful and inexpensive approach to developing numerous single nucleotide polymorphism (SNP) markers and constructing a high-density genetic map. To enrich genomic resources for Japanese eel (Anguilla japonica), we constructed a ddRAD-based genetic map using an Ion Torrent Personal Genome Machine and anchored scaffolds of the current genome assembly to 19 linkage groups of the Japanese eel. Furthermore, we compared the Japanese eel genome with genomes of model fishes to infer the history of genome evolution after the teleost-specific genome duplication.ResultsWe generated the ddRAD-based linkage map of the Japanese eel, where the maps for female and male spanned 1748.8 cM and 1294.5 cM, respectively, and were arranged into 19 linkage groups. A total of 2,672 SNP markers and 115 Simple Sequence Repeat markers provide anchor points to 1,252 scaffolds covering 151 Mb (13%) of the current genome assembly of the Japanese eel. Comparisons among the Japanese eel, medaka, zebrafish and spotted gar genomes showed highly conserved synteny among teleosts and revealed part of the eight major chromosomal rearrangement events that occurred soon after the teleost-specific genome duplication.ConclusionsThe ddRAD-seq approach combined with the Ion Torrent Personal Genome Machine sequencing allowed us to conduct efficient and flexible SNP genotyping. The integration of the genetic map and the assembled sequence provides a valuable resource for fine mapping and positional cloning of quantitative trait loci associated with economically important traits and for investigating comparative genomics of the Japanese eel.

A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution

“…Chromosome preparations, spreads, staining, capture and amplification were generated with the same methods described for axolotl (Keinath et al, 2015) with a few modifications: newts were dechorionated shortly after late neurula stage of development, embryos were dechorionated in 40% Holtfreter’s solution to account for the higher internal pressure of chorionic fluid, and chromosome spreading was performed in a high-humidity chamber held at 60°C (Keinath et al, 2015). We collected 24 individual chromosomes using laser capture microdissection as previously done in salamander (Keinath et al, 2015). Library preparation was performed using a Rubicon whole genome amplification (WGA) PicoPLEX™ DNA-seq (R300381), a bioanalyzer was used to check for presence of DNA, and resulting amplicons were sequenced on a HiSeq 2000 platform at Hudson Alpha Institute for Biotechnology.…”

“…Estimates of salamander genome sizes range from 10 – 120 gigabases (Gregory, 2015; Smith et al, 2009), with the smallest salamander genome exceeding the size of the largest anuran genome. Because all salamanders have large to extremely large genomes, it seems likely that genome size increased in the basal lineage that gave rise to all extant salamanders, between ~300 and 180 MYA (Hedges et al, 2015; Keinath et al, 2015; Zhang and Wake, 2009). This increase in size is thought to reflect an ancient expansion of repetitive DNA sequences (Keinath et al, 2015).…”

“…Because all salamanders have large to extremely large genomes, it seems likely that genome size increased in the basal lineage that gave rise to all extant salamanders, between ~300 and 180 MYA (Hedges et al, 2015; Keinath et al, 2015; Zhang and Wake, 2009). This increase in size is thought to reflect an ancient expansion of repetitive DNA sequences (Keinath et al, 2015). This expansion appears to have affected salamander genome structure in a global sense because introns, intergenic regions and linkage map size are dramatically expanded in the axolotl (Smith et al, 2005; Smith et al, 2009; Voss et al, 2011).…”

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

“…Physical and linkage maps for yellowtail (Seriola quinqueradiata), an important species in fish aquaculture in Japan was constructed using SNP obtained from NGS results and synteny with four model fish species was analyzed (Aoki et al, 2015). A double digest RAD (ddRAD)-based genetic linkage map was generated for the Japanese eel Anguilla japonica (Kai et al, 2014). The map for female spanned 1748.8 cM, whereas the map span for males was 1294.5 cM.…”

Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

“…This method is popular and has been used in many studies since its inception (Figure S1). RAD sequencing has been used, particularly in fish, to identify population divergence (Boehm, Waldman, Robinson, & Hickerson, 2015; Ferchaud & Hansen, 2016; Larson et al., 2014), for SNP identification in polyploid fish (Hohenlohe, Amish, Catchen, Allendorf, & Luikart, 2011; Ogden et al., 2013; Palti et al., 2014), in phylogeographic studies (Macher et al., 2015; Reitzel, Herrera, Layden, Martindale, & Shank, 2013), for QTL analysis (Gagnaire, Normandeau, Pavey, & Bernatchez, 2013; Houston et al., 2012; Yoshizawa et al., 2015), for linkage mapping (Brieuc, Waters, Seeb, & Naish, 2014; Henning, Lee, Franchini, & Meyer, 2014), in hybridization studies (Hand et al., 2015; Lamer et al., 2014; Pujolar et al., 2014), for exploration of genome architecture and evolution (Brawand et al., 2014; Kai et al., 2014; Waples, Seeb, & Seeb, 2016), and in phylogenetic analyses (Gonen, Bishop, & Houston, 2015; Wagner et al., 2013). This methodology should be particularly suited to phylogeographic studies as the inference power from large numbers of markers may identify patterns that are not easily visible in traditional analyses based on relatively few loci (Davey et al., 2011).…”