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标题：Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra
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作者：Wai Yee Wong ; Oleg Simakov ; Diane M. Bridge 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2019
卷号：116
期号：46
页码：22915-22917
DOI：10.1073/pnas.1910106116
出版社：The National Academy of Sciences of the United States of America
摘要：Transposable elements are one of the major contributors to genome-size differences in metazoans. Despite this, relatively little is known about the evolutionary patterns of element expansions and the element families involved. Here we report a broad genomic sampling within the genus Hydra , a freshwater cnidarian at the focal point of diverse research in regeneration, symbiosis, biogeography, and aging. We find that the genome of Hydra is the result of an expansion event involving long interspersed nuclear elements and in particular a single family of the chicken repeat 1 (CR1) class. This expansion is unique to a subgroup of the genus Hydra , the brown hydras, and is absent in the green hydra, which has a repeat landscape similar to that of other cnidarians. These features of the genome make Hydra attractive for studies of transposon-driven genome expansions and speciation. Transposable elements (TEs) were originally discovered by Barbara McClintock in maize ( 1 ) and later found to comprise a significant fraction of plant and animal genomes ( 2 ). Well-known for their contribution to total genome size (most recently in refs. 3 and 4 ), transposons are also sources of regulatory element evolution, modulators of gene expression ( 5 ), and a potential basis of large-scale genomic rearrangements ( 6 ). Hydra provides an intriguing system to study the evolutionary history of TEs. The genus is subdivided into 2 major groups: the brown hydras (comprised of the Vulgaris, Oligactis, and Braueri clades) and the algal symbiont-containing green hydra (comprised of the Viridissima clade) ( 7 ). Cnidarian genomes are typically smaller than 500 Mb in size ( 8 ), as in the Viridissima clade, which has a genome size of about 300 Mb. In contrast, the genomes of brown hydras are ∼1 Gb in size ( 9 ). High abundance of TEs in the Hydra vulgaris strain 105 genome ( 9 ) has led to the hypothesis that large genome size is due to their expansion in this taxon. However, genomic data from other Hydra lineages were required to determine the timing of TE expansion and to rule out other scenarios, such as genome duplication in brown hydras. To address this question, we sequenced genomes and transcriptomes from 4 brown hydras and 1 Hydra viridissima strain ( Materials and Methods ). Using the H. vulgaris strain 105 gene set as a reference ( 10 ), we constructed single-ortholog gene families using mutual best BLAST (basic local alignment search tool) hits to a select set of species ( Fig. 1 A ). We used RAxML ( 11 ) to construct a phylogeny ( Fig. 1 A ). The branching order for the 4 Hydra clades was identical to that found previously ( 7 ). We used r8s ( 12 ) to estimate divergence times, setting the cnidarian–bilaterian divergence as a calibration point to 550 Mya ( 13 ). We obtained 87 Mya for the beginning of the Hydra radiation and 59 Mya for the timing of the brown/green hydra split. These estimates for Hydra radiation times are based on transcriptome data and fall between previously reported estimates ( 7 , 14 ) ( Fig. 1 B ).