Evolutionary changes in vertebrate genome signatures with special focus on coelacanth.
Evolutionary changes in vertebrate genome signatures with special focus on coelacanth.
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DOI：
10.1093/dnares/dsu012
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发表时间：
2014-10
期刊：
影响因子：
--
通讯作者：
Ikemura T
中科院分区：
文献类型：
--
作者：
Iwasaki Y;Abe T;Okada N;Wada K;Wada Y;Ikemura T
随着多种物种的基因组序列数据显着增加，需要新的工具来对大序列数据进行综合分析。自组织映射（SOM）是一种在一个平面上聚类高维数据的强大工具。对于作为高维数据处理的寡核苷酸组合物，我们之前修改了用于基因组信息学的传统 SOM：BLSOM。在本研究中，我们为包括腔棘鱼在内的多种脊椎动物的片段序列（例如 100 kb）中的寡核苷酸组成构建了 BLSOM，并发现序列主要根据物种进行聚类，没有物种信息。作为四足动物祖先的现存近亲之一，腔棘鱼被认为提供了导致四足动物出现的表型和基因组转变的途径。腔棘鱼的特征寡核苷酸组成与鱼类中最低的二核苷酸 CG 出现率（即最高的 CG 抑制）有关，这与四足动物相当。腔棘鱼中这种明显的 CG 抑制应该反映了表观遗传系统的分子进化过程，包括脊椎动物进化过程中的 DNA 甲基化。与其他鱼类相比，腔棘鱼的从头 DNA 甲基化酶 (Dntm3a) 序列被发现与四足动物的相关性更为密切。
With a remarkable increase in genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-organizing map (SOM) is a powerful tool for clustering high-dimensional data on one plane. For oligonucleotide compositions handled as high-dimensional data, we have previously modified the conventional SOM for genome informatics: BLSOM. In the present study, we constructed BLSOMs for oligonucleotide compositions in fragment sequences (e.g. 100 kb) from a wide range of vertebrates, including coelacanth, and found that the sequences were clustered primarily according to species without species information. As one of the nearest living relatives of tetrapod ancestors, coelacanth is believed to provide access to the phenotypic and genomic transitions leading to the emergence of tetrapods. The characteristic oligonucleotide composition found for coelacanth was connected with the lowest dinucleotide CG occurrence (i.e. the highest CG suppression) among fishes, which was rather equivalent to that of tetrapods. This evident CG suppression in coelacanth should reflect molecular evolutionary processes of epigenetic systems including DNA methylation during vertebrate evolution. Sequence of a de novo DNA methylase (Dntm3a) of coelacanth was found to be more closely related to that of tetrapods than that of other fishes.
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影响因子：
64.8
作者：
通讯作者：
--
影响因子：
7
作者：
Nikaido M;Noguchi H;Nishihara H;Toyoda A;Suzuki Y;Kajitani R;Suzuki H;Okuno M;Aibara M;Ngatunga BP;Mzighani SI;Kalombo HW;Masengi KW;Tuda J;Nogami S;Maeda R;Iwata M;Abe Y;Fujimura K;Okabe M;Amano T;Maeno A;Shiroishi T;Itoh T;Sugano S;Kohara Y;Fujiyama A;Okada N
通讯作者：
Okada N
影响因子：
14.9
作者：
NUSSINOV, R
通讯作者：
NUSSINOV, R
影响因子：
3.5
作者：
Abe, T;Sugawara, H;Ikemura, T
通讯作者：
Ikemura, T
影响因子：
11.4
作者：
Gowher, H;Leismann, O;Jeltsch, A
通讯作者：
Jeltsch, A