Lo Rosalyn, Dougan Katherine E, Chen Yibi, Shah Sarah, Bhattacharya Debashish, Chan Cheong Xin
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia.
Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States.
Front Plant Sci. 2022 Apr 26;13:815714. doi: 10.3389/fpls.2022.815714. eCollection 2022.
Dinoflagellates of the family Symbiodiniaceae are predominantly essential symbionts of corals and other marine organisms. Recent research reveals extensive genome sequence divergence among Symbiodiniaceae taxa and high phylogenetic diversity hidden behind subtly different cell morphologies. Using an alignment-free phylogenetic approach based on sub-sequences of fixed length (i.e. -mers), we assessed the phylogenetic signal among whole-genome sequences from 16 Symbiodiniaceae taxa (including the genera of , , , and ) and two strains of as outgroup. Based on phylogenetic trees inferred from -mers in distinct genomic regions (i.e. repeat-masked genome sequences, protein-coding sequences, introns and repeats) and in protein sequences, the phylogenetic signal associated with protein-coding DNA and the encoded amino acids is largely consistent with the Symbiodiniaceae phylogeny based on established markers, such as large subunit rRNA. The other genome sequences (introns and repeats) exhibit distinct phylogenetic signals, supporting the expected differential evolutionary pressure acting on these regions. Our analysis of conserved core -mers revealed the prevalence of conserved -mers (>95% core 23-mers among all 18 genomes) in annotated repeats and non-genic regions of the genomes. We observed 180 distinct repeat types that are significantly enriched in genomes of the symbiotic versus free-living taxa, suggesting an enhanced activity of transposable elements linked to the symbiotic lifestyle. We provide evidence that representation of alignment-free phylogenies as dynamic networks enhances the ability to generate new hypotheses about genome evolution in Symbiodiniaceae. These results demonstrate the potential of alignment-free phylogenetic methods as a scalable approach for inferring comprehensive, unbiased whole-genome phylogenies of dinoflagellates and more broadly of microbial eukaryotes.
共生甲藻科的甲藻主要是珊瑚和其他海洋生物的重要共生体。最近的研究揭示了共生甲藻科分类群之间广泛的基因组序列差异，以及隐藏在细微不同细胞形态背后的高系统发育多样性。我们使用基于固定长度子序列（即k-mers）的无比对系统发育方法，评估了16个共生甲藻科分类群（包括Symbiodinium、Cladocopium、Durusdinium、Gerakladium和Fugacium属）以及作为外群的两个Amphidinium菌株全基因组序列中的系统发育信号。基于从不同基因组区域（即重复序列掩码基因组序列、蛋白质编码序列、内含子和重复序列）的k-mers以及蛋白质序列推断出的系统发育树，与蛋白质编码DNA和编码氨基酸相关的系统发育信号在很大程度上与基于既定标记（如大亚基rRNA）的共生甲藻科系统发育一致。其他基因组序列（内含子和重复序列）表现出不同的系统发育信号，支持了作用于这些区域的预期差异进化压力。我们对保守核心k-mers的分析揭示了基因组注释重复序列和非基因区域中保守k-mers的普遍性（在所有18个基因组中>95%的核心23-mers）。我们观察到180种不同的重复类型，这些类型在共生与自由生活的Fugacium分类群的基因组中显著富集，表明与共生生活方式相关的转座元件活性增强。我们提供的证据表明，将无比对系统发育表示为动态网络增强了生成关于共生甲藻科基因组进化新假设的能力。这些结果证明了无比对系统发育方法作为一种可扩展方法用于推断甲藻以及更广泛的微生物真核生物全面、无偏全基因组系统发育的潜力。
