Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilian Ichthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.
转座子是决定真核生物基因组大小的主要因素。对基因组中转座子的特征进行研究，不仅能反映出转座子与宿主的动态进化历史，还能在基因组乃至整个生物水平揭示转座子对宿主结构与功能的影响。只有少数的动物中转座子的含量及基因组的大小发生显著的扩增，而这些扩增与它们细胞的尺寸扩张及形态与生理的改变紧密相关。两栖动物版纳鱼螈（Ichthyophis bannanicus）具有超大的基因组（约12.2G）。我们的研究发现，其基因组中的转座子组成与其它两栖类甚为不同；但被易位重组介导的转座子的删除速率与其它两栖类相似，都非常低，并且它的大多数转座子超家族依然活跃，表达量达体细胞总表达量的15%。我们进而整合以往研究中关于转座子数量、多样性及活力的模型，并统一计算版纳鱼螈与其它模式动物中转座子的多样性指数，以验证是否符合这些模型的预期。我们提出今后应对转座子的特征进行一致性地分析，这对不同基因组中千差万别转座子的比较研究甚为必要，并将最终反映转座子与宿主博弈的共性特征。





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