Cold Fusion: Massive Karyotype Evolution in the Antarctic Bullhead Notothen Notothenia coriiceps

Abstract

Half of all vertebrate species share a series of chromosome fusions that preceded the teleost genome duplication (TGD), but we do not understand the causative evolutionary mechanisms. The "Robertsonian-translocation hypothesis" suggests a regular fusion of each ancestral acro- or telocentric chromosome to just one other by centromere fusions, thus halving the karyotype. An alternative "genome-stirring hypothesis" posits haphazard and repeated fusions, inversions, and reciprocal and nonreciprocal translocations. To study large-scale karyotype reduction, we investigated the decrease of chromosome numbers in Antarctic notothenioid fish. Most notothenioids have 24 haploid chromosomes, but bullhead notothen (Notothenia coriiceps) has 11. To understand mechanisms, we made a RAD-tag meiotic map with ∼10,000 polymorphic markers. Comparative genomics aligned about a thousand orthologs of platyfish and stickleback genes along bullhead chromosomes. Results revealed that 9 of 11 bullhead chromosomes arose by fusion of just two ancestral chromosomes and two others by fusion of three ancestral chromosomes. All markers from each ancestral chromosome remained contiguous, implying no inversions across fusion borders. Karyotype comparisons support a history of: (1) Robertsonian fusions of 22 ancestral chromosomes in pairs to yield 11 fused plus two small unfused chromosomes, like N. angustata; (2) fusion of one of the remaining two ancestral chromosomes to a preexisting fused pair, giving 12 chromosomes like N. rossii; and (3) fusion of the remaining ancestral chromosome to another fused pair, giving 11 chromosomes in N. coriiceps These results raise the question of what selective forces promoted the systematic fusion of chromosomes in pairs and the suppression of pericentric inversions in this lineage, and provide a model for chromosome fusions in stem teleosts.

Keywords: Antarctica; Notothenioid; Robertsonian translocation; karyotype reduction; teleost genome duplication.

Figure 1

Cladogram and chromosome numbers for Antarctic fish. The phylogeny is modified from (Near 2008; Near 2015; Near 2004; Papetti 2016). Abbreviations: 2N, diploid chromosome number; NF, the number of chromosome arms (nombre fundamental). References: 1: (Mazzei et al. 2006). 2: (Pisano et al. 1995). 3: (Mazzei et al. 2008). 4: (Ghigliotti et al. 2007). 5: (Phan et al. 1987). 6: (Tomaszkiewicz et al. 2011). 7: (Morescalchi et al. 1992a). 8: (Ozouf-Costaz et al. 1991). 9: (Pisano et al. 2003b). 10: (Doussau de Bazignan and ozouf-Costaz 1985). 11: (Prirodina and Neyelov 1984). 12: (Prirodina 1997). 13: (Morescalchi et al. 1996). 14: (Pisano et al. 2001). 15: (Morescalchi et al. 1992a,b). 16: (Ghigliotti et al. 2015).

Figure 2

Male and female linkage maps for N. coriiceps chromosomes Nco1. The position of the centromere (Cen, gray box) is estimated based on published karyotype information and greatly reduced recombination rates. Connecting lines indicate the position of markers present in both the male and female chromosomes. Markers with sequence conservation to stickleback (Gac) or platyfish (Xma) sequences are color coded based on chromosome origin within these two species. For clarity, some loci do not list all polymorphic RAD-tags that mapped to the indicated position. Note sex-specific recombination rates across the chromosome. RAD, restriction site-associated DNA.

Figure 3

Patterns of sex-specific segregation distortion in bullhead chromosomes. (A and B), Nco11; (C and D), Nco1; and (E and F), Nco4. (A, C, and E) male map; (B, D, and F), female map. Distortion is plotted as a function of χ²-squared values for the hypothesis of Mendelian segregation vs. marker position along the linkage group. Horizontal lines represent levels of significance of P = 0.01 and P = 0.001. Fused chromosomes are displayed across the horizontal axis, color key in Figure 6. Nco11 has a small region that barely reaches significance; Nco1 has a large region of segregation distortion for meiosis in the male parent and Nco4 has a large region of segregation distortion for meiosis in the female parent.

Figure 4

Oxford grids showing conservation of synteny between (A) bullhead and stickleback (G. aculeatus) and (B) between bullhead and platyfish (X. maculatus). Numbers in boxes indicate the number of mapped bullhead RAD-tag markers with sequence conservation to the genomes of stickleback and platyfish. Bullhead chromosomes Nco2 and Nco4 each have conserved synteny to three stickleback and three platyfish chromosomes (red boxes). Each of the remaining bullhead linkage groups conserve synteny to two stickleback and the orthologous two platyfish chromosomes (yellow boxes). “Scaffolds” and “U” represent contigs not assembled into the official genome assemblies of stickleback and platyfish, respectively. RAD, restriction site-associated DNA.

Figure 5

Comparison of male and female linkage maps for bullhead chromosome Nco4. Markers with sequence conservation to the genome of stickleback and platyfish are color coded according to chromosomes with conserved synteny. The position of the centromere (Cen) is estimated based on published chromosome morphology (Ozouf-Costaz et al. 1991; Tomaszkiewicz et al. 2011). RAD markers with sequence conservation to chromosomes GacV or Xma10 are in red; RAD markers with sequence conservation to GacXIV or Xma8 are colored in green; and RAD markers with sequence conservation to GacI or Xma24 are colored in blue. Lines between the female and male linkage groups represent shared markers present in meiosis of both sexes. RAD, restriction site-associated DNA.

Figure 6

Conserved synteny relationship among chromosomes of (A) bullhead (Nco), (B) platyfish (Xma), and (C) stickleback (Gac). Note that stickleback LGs I, IV, and VII consist of fusions of two platyfish chromosomes.

Figure 7

A model for the history of chromosome fusions in bullhead notothen N. coriiceps. (A) Presumed ancestral state. (B) In step 2, a pericentromeric inversion of a small acrocentric chromosome created a small metacentric. (C) After step 2, the fusion of 22 chromosomes one-to-one gave 11 large metacentrics, one unfused acrocentric, and one small unfused metacentric, as in today’s N. angustata and N. magellanica. (D) Fusion of first one (step 4, as in N. rossii) and then the other (step 5, as in N. coriiceps) of the unfused chromosomes from (C) to form Nco2 and Nco4.