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.

Keywords: conserved synteny; genome evolution; medaka; stickleback; swordtail; zebrafish.

Figure 1

Phylogenetic relationships among species discussed in this report. Relationships after Miya et al. (2003), Steinke et al. (2006), Ross et al. (20090, and Near et al. (2012). (Ninespine stickleback are from the Canadian Registry of Marine Species; fourspine stickleback, from R. Winterbottom.)

Figure 2

New linkage group 21. The prior LG21 (A) and prior LG24 (B) of the published microsatellite-based platyfish meiotic map (Walter et al. 2004) are consolidated into the RAD-tag map on new LG21 (C). RAD-tag markers are colored differently for different scaffolds. The black arrow indicates markers for which the genome assembly is incorrect according to the meiotic map. Markers with LG in their names are in a contig that also has a previously mapped microsatellite (Walter et al. 2004); e.g., marker 51316LG1Msd073C145 is RAD-tag no. 51316 on LG1 in the previous map along with microsatellite Msd073, and is located in contig 145. Markers that lack an LG in their name were located in contigs containing no prior mapped microsatellite; e.g., 35650C2939 is RAD-tag no. 35650, which is located in contig 2939. Markers with no contig number gave ambiguous BLAST results against the genome assembly. (D) Two color fluorescent in situ hybridization depicting the locations of BAC XMAA-106I17 (red, previous LG21) and XMAA-37L10 (green, previous LG24) on a single cytogenetic chromosome, the sex chromosome, new LG21.

Figure 3

The distribution of paralogs along the platyfish karyotype reveals ohnologous chromosomes arising in the teleost genome duplication event. (A) Platyfish chromosome 1 (Xma1) has numerous paralogs that are located on Xma20. (B) Reciprocally, Xma20 has numerous paralogs that map on Xma1. (C) Xma16 has many paralogs that map onto Xma10 and, in the middle of Xma16, paralogs that are mostly on Xma5. (D) Reciprocally, most of Xma10 has paralogs lying on Xma16, but two short stretches of Xma10 have paralogs on Xma22. (E) Xma5 has groups of paralogs on several other chromosomes, including Xma16, Xma14, and Xma22.

Figure 4

Conserved syntenies reveal few translocations between platyfish and medaka. (A) Dot plot of platyfish chromosome Xma9 vs. the medaka genome showing that Ola4 is its ortholog and Ola17 is a paralog. (B) Dot plot of medaka chromosome Ola4 vs. the platyfish genome showing that Xma9 is its ortholog and Xma6 is a paralog. (C) Dot plot of Xma19 vs. the medaka genome showing that Ola22 is its ortholog with a 1-Mb segment at ∼20 Mb of Xma19 that is orthologous to a portion of Ola24; this segment could arise from translocation or assembly error. (D) Dot plot of Xma19 vs. the threespine stickleback genome showing that GacXV is the ortholog, which also contains orthologs of loci at ∼20 Mb on Xma19 rather than a different chromosome as in medaka, suggesting that the medaka state is derived. (E) Comparative plot of Xma9 and Ola4 revealing many transpositions (region a vs. bc) and inversions (region c). (F) Dot plot of threespine stickleback chromosome GacIV vs. the platyfish genome showing orthologs on Xma17 and Xma23, suggesting a chromosome fusion in the threespine stickleback lineage. The 2-Mb portion of GacIV located at 27 Mb that has orthologs on Xma23 would have originally been contiguous with the section of GacIV from 0–18 Mb but after the fusion of the two ancestral chromosomes represented by Xma23 and Xma17, would have moved due to either a transposition of that 2 Mb or an inversion involving the entire section from 18 to ∼28 Mb. (G) The genetic content of Xma23 resides fully on stickleback chromosome GacIV. (H) The genetic content of Xma17 also resides fully on stickleback chromosome GacIV, as would be expected by the fusion of two ancestral chromosomes in the threespine stickleback lineage.

Figure 5

Conserved syntenies between platyfish and green pufferfish. (A) The left portion of pufferfish chromosome 1 (Tni1) is orthologous to platyfish chromosome Xma23 and the right part to Xma9, showing that Tni1 is either a fusion of two ancestral chromosomes or that Xma23 and Xma9 resulted from the fission of an ancestral chromosome. (B) Orthologs of Xma9 lie mostly on Tni1. (C) Orthologs of Xma23 are mainly on Tni1 with a short stretch on Tni20. (D) Tni20 orthologs lie on Xma23 with some on Xma14. (E) Xma14 orthologs reside only on Tni20. (F) A dot plot of Tni1 vs. threespine stickleback confirms that Tni1 is a fusion of two ancestral chromosomes.

Figure 6

Conserved syntenies between platyfish and zebrafish. (A) Orthologs of Xma16 genes lie on zebrafish chromosome Dre3 and paralogs of Xma16 genes are on Dre12, the TGD ohnolog of Dre3 (Postlethwait et al. 1998). (B) Reciprocally, orthologs of Dre3 lie on Xma16. (C) Orthologs of Xma17 are on Dre4. (D) Reciprocally, the orthologs of the left arm of Dre4 are on Xma17, but note that platyfish has few if any orthologs of genes on the right arm of Dre4, a heterochromatic arm that contains a major sex determinant in some zebrafish strains (Anderson et al. 2012). (E) Orthologs of Xma15 genes lie on Dre20 with paralogs on Dre17. (F) Orthologs of genes on Dre20 are mostly on Xma15 with several short stretches of 1 or 2 Mb on Xma9. (G) Most of the orthologs of genes on Xma14 are on Dre7 with the tip of the Xma14 chromosome bearing orthologs of Dre23 genes. (H) Some of the orthologs of Dre7 lie on Xma14, but others are on Xma4. The gray disk on zebrafish chromosomes indicates the location of the centromere.

Figure 7

Conserved syntenies reveal many translocations between platyfish and human genomes. (A) The orthologs of Xma2 reside mainly on five human chromosomes, revealing several translocations and many inversions or transpositions since their last common ancestor. (B) The orthologs of various regions of human chromosome Hsa12 reside on two platyfish chromosomes, as expected from the teleost genome duplication. Because most duplicated regions are coterminus, many translocations occurred before the teleost genome duplication. (C) Comparison of Hsa12 to the zebrafish genome identifies the same duplicated chromosome segments as found in platyfish (B), supporting the origin of many chromosome rearrangements before the divergence of zebrafish and platyfish lineages. (D) Comparison of the orders of paralogous genes on Xma2 and Xma17, which are paralogous chromosomes according to B, identifies many intrachromosomal rearrangements (transpositions and inversions) that occurred after the teleost genome duplication. (E) Comparison of ortholog orders along Xma17 and Hsa12 reveals a substantial number of transpositions and inversions in the 450 MY since their last common ancestor.

Figure 8

The evolution of gene orders along orthologous chromosomes. (A) Xma1 vs. medaka chromosome Ola7 shows mostly conserved gene orders with a few short inversions. (B) Xma1 gene order plot vs. green pufferfish Tni9 shows a few more irregularities and that the initial 4 Mb on Xma1 do not have any orthologs along Tni9, because these sequences that should be on Tni9 were not assembled into the chromosome. (C) Threespine stickleback chromosome Gac12 shows a few more rearrangements with respect to Xma1. (D) Although zebrafish chromosome Dre23 is reciprocally fully orthologous to Xma1, the order of genes along the chromosome is quite different. (E) The human orthologs of Xma1 genes lie mainly on four human chromosomes, Hsa1, -3, -12, and -20. (F–I) Gene order plots for human chromosomes Hsa1, -3, -12, and -20, respectively, resemble those for zebrafish. Inversions between medaka and platyfish are colored differently to compare fates in different species.