Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models

• 作者: Jie Wang Michael W.Itgen Huiju Wang Yuzhou Gong Jianping Jiang Jiatang Li Cheng Sun Stanley K.Sessions Rachel Lockridge Mueller
• 来源期刊: 基因组蛋白质组与生物信息学报（英文版）
• 年，卷（期）: 2021,（1）
• 所属期刊栏目: ORIGINAL RESEARCH
• 页码范围: 123-139
• 页数: 17页
• 语种: 英文

摘要

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 sys-tem 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 diver-sity 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.