Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, 110 077, India.
Parasitol Res. 2011 Feb;108(2):451-8. doi: 10.1007/s00436-010-2086-5. Epub 2010 Oct 6.
Simple sequence repeats (SSRs) are known to be responsible for genetic complexities and play major roles in gene and genome evolution. To this respect, malaria parasites are known to have rapidly evolving and complex genomes with complicated and differential pathogenic behaviors. Hence, by studying the whole genome comparative SSRs patterns, one can understand genomic complexities and differential evolutionary patterns of these species. We herein utilized the whole genome sequence information of three Plasmodium species, Plasmodium falciparum, Plasmodium vivax, and Plasmodium knowlesi, to comparatively analyze genome-wide distribution of SSRs. The study revealed that despite having the smallest genome size, P. falciparum bears the highest SSR content among the three Plasmodium species. Furthermore, distribution patterns of different SSRs types (e.g., mono, di, tri, tetra, penta, and hexa) in term of relative abundance and relative density provide evidences for greater accumulation of di-repeats and marked decrease of mono-repeats in P. falciparum in comparison to other two species. Overall, the types and distribution of SSRs in P. falciparum genome was found to be different than that of P. vivax and P. knowlesi. The latter two species have quite similar SSR organizations in many aspects of the data. The results were discussed in terms of comparative SSR patterns among the three Plasmodium species, uniqueness of P. falciparum in SSR organization and general pattern of evolution of SSRs in Plasmodium.
简单序列重复（SSR）已知负责遗传复杂性，并在基因和基因组进化中发挥主要作用。在这方面，疟原虫已知具有快速进化和复杂的基因组，具有复杂和不同的致病行为。因此，通过研究整个基因组比较 SSR 模式，可以了解这些物种的基因组复杂性和不同的进化模式。我们在此利用三种疟原虫，即恶性疟原虫、间日疟原虫和疟原虫 knowlesi 的全基因组序列信息，比较分析 SSRs 的全基因组分布。研究表明，尽管疟原虫具有最小的基因组大小，但在三种疟原虫中，疟原虫具有最高的 SSR 含量。此外，不同 SSR 类型（如单、二、三、四、五和六核苷酸重复）的分布模式，无论是在相对丰度还是相对密度方面，都为疟原虫中二核苷酸重复的积累较多和单核苷酸重复的明显减少提供了证据，与其他两种疟原虫相比。总体而言，疟原虫基因组中的 SSR 类型和分布与间日疟原虫和疟原虫 knowlesi 不同。后两种物种在数据的许多方面具有非常相似的 SSR 组织。结果从三种疟原虫之间的比较 SSR 模式、疟原虫在 SSR 组织方面的独特性以及 SSR 在疟原虫中的进化一般模式进行了讨论。
