Jayaswal Pawan Kumar, Dogra Vivek, Shanker Asheesh, Sharma Tilak Raj, Singh Nagendra Kumar
National Research Centre on Plant Biotechnology, IARI, Pusa, New Delhi, India.
Banasthali University, Banasthali, Rajasthan, India.
PLoS One. 2017 Sep 18;12(9):e0184276. doi: 10.1371/journal.pone.0184276. eCollection 2017.
Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed. The 98 genes conserved across diverse eukaryotes mostly exhibited binding and catalytic activities and shared common sequence motifs; and hence appeared to have a common origin. The 98 conserved genes belonged to 22 functional gene families including 26S protease, actin, ADP-ribosylation factor, ATP synthase, casein kinase, DEAD-box protein, DnaK, elongation factor 2, glyceraldehyde 3-phosphate, phosphatase 2A, ras-related protein, Ser/Thr protein phosphatase family protein, tubulin, ubiquitin and others. The consensus Bayesian eukaryotic tree of life developed in this study demonstrated widely separated clades of plants, fungi, and animals. Musa acuminata provided an evolutionary link between monocotyledons and dicotyledons, and Salpingoeca rosetta provided an evolutionary link between fungi and animals, which indicating that protozoan species are close relatives of fungi and animals. The divergence times for 1176 species pairs were estimated accurately by integrating fossil information with synonymous substitution rates in the comprehensive set of 98 genes. The present study provides valuable insight into the evolution of eukaryotes.
DNA测序技术的飞速发展导致公共领域积累了大量数据集，推动了比较研究，为生命进化提供了新的见解。已经报道了跨真核生物类群的系统发育研究，但这些研究基于有限数量的基因。在此，我们参照水稻基因组的36002个表达基因，对不同的植物、真菌、原生生物和动物物种进行了全基因组分析。我们的分析揭示了水稻特有的9831个基因以及在所有49种被分析的真核生物中都保守的98个基因。在不同真核生物中保守的这98个基因大多表现出结合和催化活性，并共享共同的序列基序；因此似乎有共同的起源。这98个保守基因属于22个功能基因家族，包括26S蛋白酶、肌动蛋白、ADP核糖基化因子、ATP合酶、酪蛋白激酶、DEAD盒蛋白、DnaK、延伸因子2、甘油醛3 - 磷酸、磷酸酶2A、ras相关蛋白、丝氨酸/苏氨酸蛋白磷酸酶家族蛋白、微管蛋白、泛素等。本研究构建的共识贝叶斯真核生物生命树显示，植物、真菌和动物的进化分支相距甚远。尖叶蕉在单子叶植物和双子叶植物之间提供了进化联系，而玫瑰领鞭毛虫在真菌和动物之间提供了进化联系，这表明原生动物物种是真菌和动物的近亲。通过将化石信息与这98个基因的综合集合中的同义替换率相结合，准确估计了1176个物种对的分歧时间。本研究为真核生物的进化提供了有价值的见解。
