Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

Abstract

Background: Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish.

Results: Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89%) and that in the Te. nigroviridis genome (4.66%). In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp) in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp).

Conclusion: Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different accumulation of non-homologous sequences. The length difference of intron is consistent with the genome size variation between D. holocanthus and the smooth pufferfish. Different transposable element accumulation is responsible for genome size variation between D. holocanthus and the smooth pufferfish.

Figure 1

The evolutionary history of the pufferfish. The tree topology was modified according to Li et al. [52], and the divergent times were adopted from Steinke et al. [53] and Tyler and Santini [54]. The genome sizes of the species used in analysis are shown.

Figure 2

Microsynteny between the sequences of clone ctfh in D. holocanthus genome and its homologous region in T. rubripes and Te. nigroviridis genome. The length of the bar represents the relatively length of the sequence, and the lines between the bars represent the high-scoring segment pair (HSP) of the BLASTN searches between the sequences. Other microsyntenic relationships between the BAC clone sequences of D. holocanthus and the smooth pufferfish genomes were given in additional file 1.

Figure 3

Distribution patterns of intron size. Distributions of the intron lengths used for the comparison in D. holocanthus (Diodon), T. rubripes (Fugu), Te. nigroviridis (Tetraodon), and G. aculeatus (Gasterosteus).