Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
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DOI：
10.1186/gb-2011-12-2-r20
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发表时间：
2011
期刊：
影响因子：
12.3
通讯作者：
Grigoriev IV
中科院分区：
文献类型：
--
作者：
Sucgang R;Kuo A;Tian X;Salerno W;Parikh A;Feasley CL;Dalin E;Tu H;Huang E;Barry K;Lindquist E;Shapiro H;Bruce D;Schmutz J;Salamov A;Fey P;Gaudet P;Anjard C;Babu MM;Basu S;Bushmanova Y;van der Wel H;Katoh-Kurasawa M;Dinh C;Coutinho PM;Saito T;Elias M;Schaap P;Kay RR;Henrissat B;Eichinger L;Rivero F;Putnam NH;West CM;Loomis WF;Chisholm RL;Shaulsky G;Strassmann JE;Queller DC;Kuspa A;Grigoriev IV
社会性变形虫是变形虫的一个多样化的群体，通过聚集实现多细胞，并经历形态发生，形成具有终末分化的孢子和柄细胞的子实体。盘形骨类有四组，其中衍生最多的一组包含模式物种盘形骨。我们制作了另一组盘状骨鞘（Dictyostelium purpureum）的基因组序列草图，并将其与盘状骨鞘基因组进行了比较。该组装（8.41 ×覆盖度）包含799个支架，总计33.0 Mb，与盘状龙脑的基因组大小相当。序列比较表明，这两种盘骨类动物在大约4亿年前有一个共同的祖先。尽管存在这种差异，但大多数同源词都存在于保守同构的小簇中。比较分析揭示了一组核心的同源基因，阐明了盘状骨细胞生理，以及基因家族含量的差异。有趣的基因保存和分化模式也很明显，表明功能差异；一些蛋白质家族，如组氨酸激酶，几乎没有发生功能变化，而另一些蛋白质家族，如聚酮合成酶，则经历了广泛的多样化。在两个基因组中编码的丰富的氨基酸均聚物通常在蛋白质的同源位置上没有发现，因此它们不太可能来自祖先的DNA三联体重复序列。参与社会阶段的基因比其他基因进化得更快，这与宽松的选择或由于社会冲突而加速的进化是一致的。这个新的基因组序列和比较分析的发现揭示了盘齿钢门的生物学和进化。
The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. There are four groups of dictyostelids, with the most derived being a group that contains the model species Dictyostelium discoideum. We have produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. The assembly (8.41 × coverage) comprises 799 scaffolds totaling 33.0 Mb, comparable to the D. discoideum genome size. Sequence comparisons suggest that these two dictyostelids shared a common ancestor approximately 400 million years ago. In spite of this divergence, most orthologs reside in small clusters of conserved synteny. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification. The abundant amino acid homopolymers encoded in both genomes are generally not found in homologous positions within proteins, so they are unlikely to derive from ancestral DNA triplet repeats. Genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict. The findings from this new genome sequence and comparative analysis shed light on the biology and evolution of the Dictyostelia.
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DOI：
10.1073/pnas.040565697
发表时间：
2000-02-29
影响因子：
11.1
作者：
Blanton, RL;Fuller, D;Loomis, WF
通讯作者：
Loomis, WF
影响因子：
--
作者：
Anjard, C;Loomis, WF
通讯作者：
Loomis, WF
影响因子：
4.3
作者：
Banerjee, Sulagna;Robbins, Phillips W.;Samuelson, John
通讯作者：
Samuelson, John
DOI：
10.1073/pnas.0501820102
发表时间：
2005-05-24
影响因子：
11.1
作者：
Anjard, C;Loomis, WF
通讯作者：
Loomis, WF
DOI：
10.1073/pnas.032662799
发表时间：
2002-02-05
影响因子：
11.1
作者：
Bapteste, E;Brinkmann, H;Philippe, H
通讯作者：
Philippe, H