A RAD-Tag Genetic Map for the Platyfish (Xiphophorus maculatus) Reveals Mechanisms of Karyotype Evolution Among Teleost Fish

Abstract

Mammalian genomes can vary substantially in haploid chromosome number even within a small taxon (e.g., 3-40 among deer alone); in contrast, teleost fish genomes are stable (24-25 in 58% of teleosts), but we do not yet understand the mechanisms that account for differences in karyotype stability. Among perciform teleosts, platyfish (Xiphophorus maculatus) and medaka (Oryzias latipes) both have 24 chromosome pairs, but threespine stickleback (Gasterosteus aculeatus) and green pufferfish (Tetraodon nigroviridis) have just 21 pairs. To understand the evolution of teleost genomes, we made a platyfish meiotic map containing 16,114 mapped markers scored on 267 backcross fish. We tiled genomic contigs along the map to create chromosome-length genome assemblies. Genome-wide comparisons of conserved synteny showed that platyfish and medaka karyotypes remained remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged 120 million years ago. Comparative genomics with platyfish shows how reduced chromosome numbers in stickleback and green pufferfish arose by fusion of pairs of ancestral chromosomes after their lineages diverged from platyfish 195 million years ago. Zebrafish and human genomes provide outgroups to root observed changes. These studies identify likely genome assembly errors, characterize chromosome fusion events, distinguish lineage-independent chromosome fusions, show that the teleost genome duplication does not appear to have accelerated the rate of translocations, and reveal the stability of syntenies and gene orders in teleost chromosomes over hundreds of millions of years.

Constructing Genetic Linkage Maps Using the Whole Genome Sequence of Pacific Bluefin Tuna (<i>Thunnus orientalis</i>) and a Comparison of Chromosome Structure among Teleost Species

“…Tongue sole also experienced three major chromosomal fusion events after divergence from the common ancestor with medaka, Tetraodon, and fugu [26]. A high density genetic map with tiled genomic platyfish contigs revealed that the platyfish and medaka karyotypes are remarkably similar with few interchromosomal translocations but with numerous intrachromosomal rearrangements (transpositions and inversions) since their lineages diverged about 120 Mya [27]. That study also suggested that stickleback and Tetraodon arose by fusion of pairs of ancestral chromosomes.…”

“…Restriction site-associated DNA (RAD) tag sequencing [41] using a next- generation sequencer is useful to develop several thousand single nucleotide polymorphism markers close to restriction endonuclease sites. This method has been applied to construct linkage maps for several teleosts [27] [42]- [45]. The integrated map in this study provides a framework for constructing high density-linkage map using RAD tag sequencing.…”

“…Stickleback [27], fugu, and Tetraodon [12] have experienced chromosome fusion events two or three times since diverging from the MTZ ancestor, which presumably had 24 chromosome pairs. Stickleback chromosome 1 corresponded to LG2 and LG13 in Pacific bluefin tuna.…”

A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed BugCimex lectularius

“…In order to combine our genetic map with the recently published C. lectularius reference genome, we used Chromonomer (Amores et al 2014). Chromonomer first removes markers that are inconsistent with local assembly order on the genetic map, and then anchors genome scaffolds to LG based on marker mapping position before finally reassembling the genome accordingly.…”

Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps

“…homologous chromosomes) between species (Naish et al 2013; Kodama et al 2014). Furthermore, high quality, dense linkage maps are valuable for validating and orienting genomic scaffolds (Mascher & Stein 2014; Fierst 2015), especially for cases of residual polyploidy, large genome size, and high repeat content (Amores et al 2014; Ming & Man Wai 2015). Recent advances in sequencing, such as through reduced-representation library sequencing (e.g.…”