Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates

Abstract

Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.

Figure 1.

Vertebrate chromosome evolution scenario. (A) For simplicity, we illustrate two proto-chromosomes (red and blue bars) duplicated by the first round of WGD. Subsequently, fission divided one of the duplicated chromosomes. (B) The second round of WGD doubled the proto-chromosomes. Blocks in chromosomes are labeled with their respective chromosome positions in the human genome. (C) After the second WGD, early vertebrates underwent slow changes in karyotype over a long evolutionary process. (D) In the ancestral mammalian lineage, intensive interchromosomal rearrangements occurred and the ancestral chromosomes were broken into smaller segments that were distributed across many human chromosomes. (E) In the ancient ray-finned fish lineage, intensive chromosome fusions merged the ancestral chromosomal segments into ancestral teleost chromosomes. (F) Another round of WGD in the ancestral teleost doubled proto-chromosomes, but afterward, few global rearrangements shaped the present medaka genome.

Figure 2.

Model of vertebrate genome evolution and reconstruction of the ancestral genome. (A) For simplicity, suppose that the ancestral chromosome had 10 genes. The 2R WGD produced ohnologs (blue dots along the diagonal line in the triangular dot plot) in the duplicated chromosomes. (B) Chromosome breaks and inversions may have altered the order of ohnologs on the sister chromosomes. (C) In the course of early vertebrate genome evolution, the ancestral gene order was disrupted by many inversions, resulting in scattered ohnolog dots. (D) Eventually, CVL blocks were distributed across several human chromosomes by intensive interchromosomal rearrangements. (a–d) A typical model of genome evolution involving the 2R WGD. In the next step, we handle real human genome data. (E) This is a real instance of the dot plot in D. CVL blocks were ordered from the human chromosomes 1 to X, and ohnologs shared among these CVL blocks were plotted. (Red) Regions representing pairs of paralogous CVL blocks with a great number of ohnologs (P < 10⁻⁴, see Methods). (F) This corresponds to the state in C. CVL blocks were reordered in such a way that paralogous CVL blocks were grouped so that each group represented one ancestral vertebrate chromosome (see Methods). (G) This state corresponds to that in B. CVL blocks within individual vertebrate groups were further reordered to obtain ancestral gnathostome subgroups (namely, chromosomes), which were duplicated from a single ancestral vertebrate chromosome by the 2R WGD events. The partition of subgroups that optimizes the significance defined in the Methods. Rectangles and triangles are colored in accordance with those in B to make the correspondence clear. (H) The vertebrate group A was decomposed into four gnathostome subgroups by statistical analysis, indicating that the ancestral chromosome underwent 2R WGD.

Figure 3.

Models of chromosome evolution during 2R WGD. (A) Vertebrate groups A, B, and E in Fig. 2F. Pairs of light blue boxes with few ohnologs may be the remains of genome rearrangements between the two WGD events. (B) Two distinct ancestor chromosomes (A and B) were duplicated by the first WGD, and duplicated chromosomes A1 and B1 underwent a chromosome fusion. (C) One ancestor chromosome consisting of two parts (A and B) was duplicated by the first WGD, and a copy of the duplicated chromosomes was split into two chromosomes (A1 and B1) by a chromosome fission event. (D) After the second round of WGD, two of the four sister chromosomes underwent two independent chromosome fissions. Because the two fissions split two chromosomes (A11 and A12) at different chromosome positions, blocks A21b and A22a have some ohnologs in common. (E) Both of the fusion and fission models in B and C produce the same distribution of ohnologs, especially pairs of light blue boxes without ohnologs. (F) The distribution originating from independent fission events in D is distinguishable from that in E as indicated by one light blue box.

Figure 4.

Reconstructed ancestral chromosomes. Ancestral vertebrate chromosomes A, B, and F had two alternative scenarios, fusions or fissions, between the 2R WGD events, as shown in Fig. 3. Thus, the number of proto-chromosomes ranges from 10 to 13 depending on the choice of two alternatives. The figure illustrates the scenario in which only fissions took place. Ten reconstructed proto-chromosomes in the vertebrate ancestor shown at the top are assigned distinct colors, and their daughter chromosomes in the gnathostome ancestor are distinguished by their respective vertical bars. In the genomes of the osteichthyan, teleost, and amniote ancestors, and human, chicken, and medaka genomes, genomic regions are assigned colors and vertical bars that represent correspondences of individual regions to the proto-chromosomes in the gnathostome ancestor from which respective regions originated. Unassigned blocks are shown in the rightmost chromosome (Un) in the osteichthyan and amniote ancestors.

Figure 5.

Syntenic chromosome correspondence between the chicken and gnathostome ancestor chromosomes. In the table, the number in a cell indicates the number of orthologous genes in syntenic regions (see Supplemental materials) between the chicken chromosome in the column and the reconstructed gnathostome proto-chromosome in the row. To emphasize chicken chromosomes that were primarily derived from a single ancestral gnathostome chromosome, cells with the maximum number of orthologs are colored yellow or red. In particular, red cells imply chicken chromosomes that have one-to-one correspondence to their ancestral gnathostome chromosomes.

Figure 6.

Changes in chromosome number during vertebrate karyotype evolution. The reconstructed proto-chromosomes in Fig. 4 allow us to discuss how the number of chromosomes has changed in individual vertebrate lineages. (Left) The phylogenetic tree of vertebrates, (right) the distribution of chromosome number in individual lineages (Gregory et al. 2007; Animal Genome Size Database, http://www.genomesize.com). Considering the numbers of proto-chromosomes in Fig. 4, two ancient whole-genome duplication events almost quadrupled the number of chromosomes; subsequently, chromosome numbers in individual lineages tended to decrease in many lineages, although not in the avian lineage.