Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure
Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure
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DOI：
10.1016/j.cub.2013.05.062
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发表时间：
2013-08-05
期刊：
影响因子：
9.2
通讯作者：
Satoh, Nod
中科院分区：
文献类型：
--
作者：
Shoguchi, Eiichi;Shinzato, Chuya;Satoh, Nod
背景：鞭毛藻以其形成有害藻华（例如“赤潮”）的能力而闻名，并作为珊瑚的共生和光合伙伴。这些单细胞真核生物拥有永久浓缩的液晶染色体和巨大的核基因组，通常是人类基因组的几倍。在这里，我们描述了甲藻核基因组的初稿组装，提供了对其基因组组织和基因清单的见解。结果：来自共生菌的测序读数被组装成616 Mbp的富含基因的DNA区域，这大约代表了该物种估计的1500 Mbp基因组的一半。该组合编码了42,000个蛋白质编码基因，与先前使用转录组学数据估计的鞭毛藻基因数量一致。共生菌基因组包含染色体凝聚蛋白调控的重复基因，其中近三分之一具有真核同源，而其余的很可能是通过细菌水平基因转移获得的。共生基因在剪接体内含子中富集（平均18.6个内含子/基因）。供体和受体的剪接位点是独特的，其中5‘位点不仅利用GT，还利用GC和GA，而在3’位点，AG之后存在一个保守的G。所有剪接体snRNA基因（U1-U6）都聚集在基因组中。令人惊讶的是，共生菌基因组在整个基因组中显示了单向排列的基因，形成了一个簇状的基因排列。结论：我们在这里展示了鞭毛藻基因组与其他真核生物相比具有独特和不同的特征。我们的数据阐明了鞭毛藻的组织和基因清单，并为这一非凡的真核生物的未来研究奠定了基础。
Background: Dinoflagellates are known for their capacity to form harmful blooms (e.g., "red tides") and as symbiotic, photosynthetic partners for corals. These unicellular eukary-otes have permanently condensed, liquid-crystalline chromosomes and immense nuclear genome sizes, often several times the size of the human genome. Here we describe the first draft assembly of a dinoflagellate nuclear genome, providing insights into its genome organization and gene inventory.Results: Sequencing reads from Symbiodinium minutum were assembled into 616 Mbp gene-rich DNA regions that represented roughly half of the estimated 1,500 Mbp genome of this species. The assembly encoded similar to 42,000 protein-coding genes, consistent with previous dinoflagellate gene number estimates using transcriptomic data. The Symbiodinium genome contains duplicated genes for regulator of chromosome condensation proteins, nearly one-third of which have eukaryotic orthologs, whereas the remainder have most likely been acquired through bacterial horizontal gene transfers. Symbiodinium genes are enriched in spliceosomal introns (mean = 18.6 introns/gene). Donor and acceptor splice sites are unique, with 5' sites utilizing not only GT but also GC and GA, whereas at 3' sites, a conserved G is present after AG. All spliceosomal snRNA genes (U1-U6) are clustered in the genome. Surprisingly, the Symbiodinium genome displays unidirectionally aligned genes throughout the genome, forming a cluster-like gene arrangement.Conclusions: We show here that a dinoflagellate genome exhibits unique and divergent characteristics when compared to those of other eukaryotes. Our data elucidate the organization and gene inventory of dinoflagellates and lay the foundation for future studies of this remarkable group of eukaryotes.