Abstract：
Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames, with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.
摘要：
锥虫属于一个非凡的单细胞群体，类寄生虫，真核生物系统发育树的早期分支，表现出影响基因表达的有趣的生物学特征(无内含子多顺反子转录，转接,和RNA编辑)，新陈代谢，表面分子,和细胞器(糖酵解的分隔，表面分子的变化，和独特的线粒体DNA)，细胞生物学和生命周期（吞噬液泡逃避和细胞形态发生的复杂模式）。自2005年以来，几种锥虫的大量基因组规模数据变得可用(基因组，转录组，和蛋白质组)，科学界可以进一步研究这些不寻常特征的潜在机制，并解决可能揭示真核生物早期进化生物学方面的其他未探索现象。一个基本方面包括在这些原始微生物的整个进化史中涉及基因的获取和丢失的过程和机制。这里,我们对该组的三个主要代表的假基因进行了全面的计算机分析：利什曼原虫，布鲁氏锥虫,和克氏锥虫.假基因，DNA片段源自改变的基因，这些基因失去了原有的功能，是基因组遗物，可以提供功能基因进化史的基本记录，以及有关宿主基因组的动态和进化的线索。用功能蛋白作为代理扫描这些基因组，以揭示具有蛋白质编码特征的基因间区域，依靠定制的阈值来区分统计和生物学上显著的序列相似性，从碎片中重新组装剩余序列，我们发现了成千上万的伪基因和数百个开放阅读框架，每个锥虫都有特殊的特征：突变谱，number,内容,密度,密码子偏倚，平均大小,单拷贝或多拷贝基因起源，突变的数量和类型，假定的原始函数，和转录活性。这些特征表明假基因形成的共同过程，假基因进化的不同模式和现存的生物学功能，和/或这些寄生虫在进化过程中进行的独特基因组组织，以及作用于不同谱系的不同进化和/或选择压力。
