PDF(Pubmed)
Abstract：
Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.
摘要：
Siphonophores（Cnidaria：Hydrozoa）是在整个海洋中发现的大量捕食者，是全球浮游动物群落的重要组成部分。它们的长度从几厘米到几十米不等。它们是凝胶状的，脆弱的,而且很难收集，因此，这大约200个物种的生物学的许多方面仍然知之甚少。为了调查虹吸体基因组多样性，我们对系统发育中广泛采样的32个物种进行了Illumina测序。测序深度足以从6个标本的k-mer光谱中估计核基因组大小，范围从0.7-2.3Gb，杂合度估计值在0.69-2.32%之间。增量k-mer计数表明k-mer峰可以不存在，具有近20倍的读段覆盖率，表明在k-mer光谱中没有峰的25个样品中最小基因组大小范围为1.4-5.6Gb。这项工作证实了大多数虹吸体核基因组相对于其他刺胞动物的基因组是大的，而且还确定了一些尺寸减小的目标，这些目标是未来的虹吸体核基因组组装项目。我们还从这些新数据中组装了33个样本的完整线粒体基因组，表明在非虹吸体水生动物之间共享保守的基因顺序，Cystonectae和一些Physonectae，揭示了虹吸子祖先的线粒体基因顺序。我们的结果还表明，线粒体基因组在其他Physonectae和Calycophorae中广泛重排。尽管虹吸虫只占刺胞动物物种的一小部分，这项调查大大扩展了我们对刺胞动物基因组多样性的理解。这项研究进一步说明了深度系统发育采样的重要性以及基于k-mer的基因组撇脂在理解进化枝的基因组多样性中的实用性。
