Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
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DOI：
10.1038/s41598-018-37792-0
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发表时间：
2019-02-04
影响因子：
4.6
通讯作者：
Shoguchi, Eiichi
中科院分区：
文献类型：
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作者：
Beedessee, Girish;Hisata, Kanako;Shoguchi, Eiichi
共生甲藻科甲藻具有比其他甲藻小的核基因组，并产生结构特化的、具有生物活性的次级代谢产物。迄今为止，甲藻次级代谢的进化知之甚少，因为它们庞大的基因组尺寸阻碍了比较基因组方法的研究。在这里，我们克服了这一挑战，结合基因组学和代谢组学的方法来研究化学多样性如何出现在三个解码共生藻科基因组（分支A3，B1和C）。我们的分析确定了广泛的多样化的聚酮合酶和非核糖体肽合成酶基因从两个新解码的基因组的三节共生藻（A3）和Cladocopioid sp.（C）。系统发育分析表明，几乎所有的基因家族都来自谱系特异性基因重复，在所有的三个分支，表明环境适应的分歧。很少有代谢途径是保守的三个分支，我们检测代谢相似性，只有在最近分歧的分支，B1和C。我们建立了次级代谢蛋白质结构指导底物特异性，基因重复和结构域改组导致了次级代谢基因的多样化。
Symbiodiniaceae dinoflagellates possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Till date, little is known about the evolution of secondary metabolism in dinoflagellates as comparative genomic approaches have been hampered by their large genome sizes. Here, we overcome this challenge by combining genomic and metabolomics approaches to investigate how chemical diversity arises in three decoded Symbiodiniaceae genomes (clades A3, B1 and C). Our analyses identify extensive diversification of polyketide synthase and non-ribosomal peptide synthetase genes from two newly decoded genomes of Symbiodinium tridacnidorum (A3) and Cladocopium sp. (C). Phylogenetic analyses indicate that almost all the gene families are derived from lineage-specific gene duplications in all three clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.