Abstract
BackgroundTeleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The cause of the difference in genome size remains largely unexplained.ResultsIn this study, we reveal that the differential success of transposable elements (TEs) correlates with the variation of genome size across four representative teleost species (zebrafish, medaka, stickleback, and tetraodon). The larger genomes represent a higher diversity within each clade (superfamily) and family and a greater abundance of TEs compared with the smaller genomes; zebrafish, representing the largest genome, shows the highest diversity and abundance of TEs in its genome, followed by medaka and stickleback; while the tetraodon, representing the most compact genome, displays the lowest diversity and density of TEs in its genome. Both of Class I (retrotransposons) and Class II TEs (DNA transposons) contribute to the difference of TE accumulation of teleost genomes, however, Class II TEs are the major component of the larger teleost genomes analyzed and the most important contributors to genome size variation across teleost lineages. The hAT and Tc1/Mariner superfamilies are the major DNA transposons of all four investigated teleosts. Divergence distribution revealed contrasting proliferation dynamics both between clades of retrotransposons and between species. The TEs within the larger genomes of the zebrafish and medaka represent relatively stronger activity with an extended time period during the evolution history, in contrast with the very young activity in the smaller stickleback genome, or the very low level of activity in the tetraodon genome.ConclusionOverall, our data shows that teleosts represent contrasting profiles of mobilomes with a differential density, diversity and activity of TEs. The differences in TE accumulation, dominated by DNA transposons, explain the main size variations of genomes across the investigated teleost species, and the species differences in both diversity and activity of TEs contributed to the variations of TE accumulations across the four teleost species. TEs play major roles in teleost genome evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0059-7) contains supplementary material, which is available to authorized users.
Highlights
Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon
The initial annotations of four teleost genomes have suggested that major differences in transposable elements (TEs) content exist between lineages [13,14,15,16]; and comparisons of TE diversity and evolution have revealed that teleost genomes contain the highest diversity of TE superfamilies in vertebrates [18], the TE contents in the early assembles of medaka, stickleback, and tetraodon tent to be underestimated and inaccurate due to the repeat database is far from complete; information on the distribution of TE diversity and density, and the evolution dynamics intraspecies of teleosts, and the knowledge of the roles of TEs in teleost genome architecture and evolution is still reduced and fragmented
Different expansion of TEs across the four teleost genomes The joint annotation of teleost mobilomes with the species-specific custom TE libraries, which combined the previously-known elements from RepBase and the elements newly identified by multiple de novo methods as described in the Methods section, revealed a significantly different expansion of TEs within four teleost species (Table 1 and Fig. 1)
Summary
Teleosts are unique among vertebrates, with a wide range of haploid genome sizes in very close lineages, varying from less than 400 mega base pairs (Mb) for pufferfish to over 3000 Mb for salmon. The initial annotations of four teleost (zebrafish, medaka, stickleback, and tetraodon) genomes have suggested that major differences in TE content exist between lineages [13,14,15,16]; and comparisons of TE diversity and evolution have revealed that teleost genomes contain the highest diversity of TE superfamilies in vertebrates [18], the TE contents in the early assembles of medaka, stickleback, and tetraodon tent to be underestimated and inaccurate due to the repeat database is far from complete; information on the distribution of TE diversity and density, and the evolution dynamics intraspecies of teleosts, and the knowledge of the roles of TEs in teleost genome architecture and evolution is still reduced and fragmented. To better understand the different success rates of TEs and the evolution of genomes within teleosts, in this study we re-annotated the mobilomes of four representative teleost species (zebrafish, medaka, stickleback, and tetraodon) by using multiple de novo repeat prediction pipelines
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