Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement

Abstract

Researchers, supported by data from polyploid plants, have suggested that whole genome duplication (WGD) may induce genomic instability and rearrangement, an idea which could have important implications for vertebrate evolution. Benefiting from the newly released amphioxus genome sequence (Branchiostoma floridae), an invertebrate that researchers have hoped is representative of the ancestral chordate genome, we have used gene proximity conservation to estimate rates of genome rearrangement throughout vertebrates and some of their invertebrate ancestors. We find that, while amphioxus remains the best single source of invertebrate information about the early chordate genome, its genome structure is not particularly well conserved and it cannot be considered a fossilization of the vertebrate preduplication genome. In agreement with previous reports, we identify two WGD events in early vertebrates and another in teleost fish. However, we find that the early vertebrate WGD events were not followed by increased rates of genome rearrangement. Indeed, we measure massive genome rearrangement prior to these WGD events. We propose that the vertebrate WGD events may have been symptoms of a preexisting predisposition toward genomic structural change.

Figure 1.

Identifying and grouping pairs of syntenic genes. Syntenic gene pairs were identified in three steps. First, genes from the two genomes are grouped into orthologous families (A, B, and C). Next, both genomes are searched for syntenic “family combinations”—pairs of genes from two ortholog families that are found in close proximity in more than one genomic location. Genes are in close proximity if they have no more than 10 intervening genes (shown here as red x’s). In this example, three syntenic family combinations are identified (A–B, A–C, and B–C). The A–B combination is present in both amphioxus and humans, while the A–C and B–C combinations are only present in humans. These syntenic gene pairs can then be merged to generate segments of syntenic genes (A1–B1, A2–B2–C1, and A3–B3–C2). In the human genome these syntenic segments form a “synteny group,” which contains three gene families and is present on two chromosomes.

Figure 2.

Synteny group distributions reveal vertebrate duplication events. The size of each syntenic group, measured by the number of gene families in the group, is plotted against the number of chromosomes over which the group is spread. The bubble sizes are proportional to the number syntenic groups at each point. (A–C) Vertebrate synteny groups built by comparison to amphioxus: (A) human, (B) chicken, and (C) zebrafish. In A and B, the largest groups, with the most conserved synteny, are present on four chromosomes, and a steady reduction in chromosome coverage is seen as the group size decreases. (C) The zebrafish groups are spread out past four chromosomes. (D) As a control, the chromosome coverage of the human groups shown in A was doubled, creating a simulation of a new WGD event on top of the early chordate duplications. This plot shows a similar chromosome spread to C, and post-WGD gene loss in zebrafish could account for the sparser plot. (E) Zebrafish synteny groups, built by comparison to the human genome, show that the largest synteny groups cover two to three chromosomes. (F) Human synteny groups, built by comparison to the zebrafish genome, show a strong peak at one chromosome, as expected in the absence of WGD events. Arrowheads within the plots indicate the bubbles that contain the Hox clusters. In comparisons between amphioxus and vertebrates (A–D), the Hox genes form a single synteny group, while, in comparisons between fish and tetrapods (E–F), they subdivide into four separate groups, indicating that the cluster duplicated twice within the early vertebrate lineage.

Figure 3.

Estimating the amount of synteny conservation between two genomes. This figure illustrates the method we use to calculate the “syntenic distance” between pairs of genomes. (A) Two genomes, X and Y, share eight orthologous genes, present on three genome fragments in the genome X, and two in genome Y. (B) These orthologous genes can be decomposed into proximate gene pairs (see Methods and Fig. 1). (C) From these gene pairs, we can calculate the shared synteny proportion and convert this proportion into a time-linear distance measure by taking the negative natural logarithm. This is a highly simplified case—for analyses of real genomes, genome fragments are required to have at least 10 genes.

Figure 4.

Rates of synteny loss throughout vertebrates and their ancestors. (A) Estimates of conserved synteny are robust to genome fragmentation. The human genome was artificially fragmented into scaffolds of random lengths according to a Pareto distribution where k satisfies the equation, scaffold size = 1/U^1/k, and U is a random number between 0 and 1. These fragmented human genomes were then compared to amphioxus (Bf), chicken (Gg), or zebrafish (Dr). As k increases, the G50 size of the fragmented human genome decreases (dashed lines), but the syntenic shared pair metric remains relatively consistent (solid lines). G50 is the gene number such that 50% of the assembled genome lies in scaffolds containing at least G50 genes. (B) Conserved synteny was measured between all pairwise combinations of human, fugu, zebrafish, chicken, mouse, amphioxus, sea urchin, and sea anemone and then plotted relative to the divergence age of the comparison. The values are well fit by an exponential curve. (C) Syntenic distances were apportioned to the known species tree and then divided by the estimated evolutionary time in each branch to obtain rates of synteny loss. Internal nodes are labeled n1–n6. The highest rates of loss are observed in the period after the vertebrate divergence from amphioxus but before the early vertebrate WGD events (n2–2R WGD), and in the terminal zebrafish lineage (n6–Dr). Species abbreviations are human (Hs), mouse (Mm), chicken (Gg), fugu (Tr), zebrafish (Dr), amphioxus (Bf), sea urchin (Sp), sea anemone (Nv).