Durand Pierre M, Oelofse Andries J, Coetzer Theresa L
Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School and National Health Laboratory Service, York Road, Parktown, 2193, South Africa.
BMC Genomics. 2006 Nov 4;7:282. doi: 10.1186/1471-2164-7-282.
The completed genome sequences of the malaria parasites P. falciparum, P. y. yoelii and P. vivax have revealed some unusual features. P. falciparum contains the most AT rich genome sequenced so far--over 90% in some regions. In comparison, P. y. yoelii is approximately 77% and P. vivax is approximately 55% AT rich. The evolutionary reasons for these findings are unknown. Mobile genetic elements have a considerable impact on genome evolution but a thorough investigation of these elements in Plasmodium has not been undertaken. We therefore performed a comprehensive genome analysis of these elements and their derivatives in the three Plasmodium species.
Whole genome analysis was performed using bioinformatic methods. Forty potential protein encoding sequences with features of transposable elements were identified in P. vivax, eight in P. y. yoelii and only six in P. falciparum. Further investigation of the six open reading frames in P. falciparum revealed that only one is potentially an active mobile genetic element. Most of the open reading frames identified in all three species are hypothetical proteins. Some represent annotated host proteins such as the putative telomerase reverse transcriptase genes in P. y. yoelii and P. falciparum. One of the P. vivax open reading frames identified in this study demonstrates similarity to telomerase reverse transcriptase and we conclude it to be the orthologue of this gene.
There is a divergence in the frequencies of mobile genetic elements in the three Plasmodium species investigated. Despite the limitations of whole genome analytical methods, it is tempting to speculate that mobile genetic elements might have been a driving force behind the compositional bias of the P. falciparum genome.
恶性疟原虫、约氏疟原虫和间日疟原虫的完整基因组序列已揭示出一些不同寻常的特征。恶性疟原虫拥有迄今为止测序的富含AT的基因组——某些区域超过90%。相比之下，约氏疟原虫约为77%，间日疟原虫约为55%富含AT。这些发现的进化原因尚不清楚。移动遗传元件对基因组进化有相当大的影响，但尚未对疟原虫中的这些元件进行全面研究。因此，我们对这三种疟原虫物种中的这些元件及其衍生物进行了全面的基因组分析。
使用生物信息学方法进行全基因组分析。在间日疟原虫中鉴定出40个具有转座元件特征的潜在蛋白质编码序列，在约氏疟原虫中鉴定出8个，在恶性疟原虫中仅鉴定出6个。对恶性疟原虫中的6个开放阅读框进行进一步研究发现，只有一个可能是活跃的移动遗传元件。在所有三个物种中鉴定出的大多数开放阅读框都是假设蛋白。有些代表注释的宿主蛋白，如约氏疟原虫和恶性疟原虫中假定的端粒酶逆转录酶基因。本研究中鉴定出的一个间日疟原虫开放阅读框与端粒酶逆转录酶具有相似性，我们认为它是该基因的直系同源物。
在所研究的三种疟原虫物种中，移动遗传元件的频率存在差异。尽管全基因组分析方法存在局限性，但很诱人推测移动遗传元件可能是恶性疟原虫基因组组成偏差背后的驱动力。
