Institute of computational modelling SB RAS, Akademgorodok, Krasnoyarsk, 660036, Russia.
Siberian federal university, Svobodny prosp. 79, Krasnoyarsk, 660041, Russia.
BMC Bioinformatics. 2020 Mar 11;21(Suppl 2):83. doi: 10.1186/s12859-020-3350-z.
Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast genomes.
Surprisingly, eight cluster structure has been found, for chloroplasts. The pattern observed for chloroplasts differs rather significantly, from bacterial one, and from that latter observed for cyanobacteria. The structure is provided by clustering of the fragments of equal length isolated within a genome so that each fragment is converted in triplet frequency dictionary with non-overlapping triplets with no gaps in frame tiling. The points in 63-dimensional space were clustered due to elastic map technique. The eight cluster found in chloroplasts comprises the fragments of a genome bearing tRNA genes and exhibiting excessively high GC-content, in comparison to the entire genome.
Chloroplasts exhibit very specific symmetry type in distribution of coding and non-coding fragments of a genome in the space of triplet frequencies: this is mirror symmetry. Cyanobacteria may have both mirror symmetry, and the rotational symmetry typical for other bacteria.
此前，曾报道过一种声称在细菌基因组中普遍存在的七聚类模式。考虑到叶绿体起源的最流行理论，我们检查了类似的模式是否在叶绿体基因组中观察到。
令人惊讶的是，我们发现叶绿体具有八聚类结构。与细菌和蓝细菌的模式相比，观察到的叶绿体模式差异非常大。该模式是通过将基因组内等长片段聚类而形成的，使得每个片段都转换为三联体频率字典，其中具有非重叠三联体，并且在框架平铺中没有间隙。由于弹性图技术，点在 63 维空间中聚类。在叶绿体中发现的八个聚类包含携带 tRNA 基因并表现出与整个基因组相比过高 GC 含量的基因组片段。
叶绿体在三联体频率空间中展示了基因组编码和非编码片段分布的非常特殊的对称类型：这是镜像对称。蓝细菌可能具有镜像对称和其他细菌典型的旋转对称。
