像我们一样，鸡容易受到各种害虫和病原体的攻击。有有效的疫苗，药物或消毒剂针对某些鸡肉疾病，但对许多其他鸡肉疾病的控制仍然是遥远的前景。测序病原体基因组可能是制定新的控制措施的宝贵步骤。经过十多年的工作，我们很高兴地报告说，目前为感染鸡的最重要的寄生虫组完成了基因组。这种新知识为更好地控制了全球毁灭性鸡肉肠道疾病，球虫病。

In a study between scientists at the Royal Veterinary College and Wellcome Trust Sanger Institute in the UK, the King Abdullah University of Science and Technology in Saudi Arabia, the University Kebangsaan in Malaysia and the University of São Paulo in Brazil, we sequenced and analysed genomes of all seven species of theEimeria引起鸡肉球虫病的寄生虫。鸡是世界上最受欢迎的食物动物。在过去的20年中，全球家禽产量增加了两倍，现在每年生产超过600亿只鸡，提供1.1万亿卵和9000万吨肉。预计禽类部门的增长将在未来几年内持续几年，并且与安全，福利友好，可持续的肉类和鸡蛋生产相关的挑战非常巨大。一个主要问题是损害鸟类健康和福利并降低生产力的地方性传染病。这些“生产”疾病中的许多疾病对全球粮食供应链构成了严重威胁，并直接促进了发展中农村经济的贫困，在这种农村经济中，可以通过疾病消除小农生计。Eimeria是单细胞原生动物，与引起疟疾，隐孢子虫病和弓形虫病的寄生虫密切相关。球虫病会影响所有牲畜，但在鸡中最有问题，主要是因为寄生虫具有直接的粪便/口服生命周期，并且当大量宿主在近距离内容纳大量宿主时，它们会迅速扩散。如果不受控制，球虫病会导致严重的肠道疾病，发病率和死亡率非常高（图1）。当前的控制主要基于使用抗癌药物的使用，which account for more than 40% of the total antimicrobials usage in UK animals（图2）。毫不奇怪，可能会发生对所有类别的抗癌药物的寄生虫遗传抗性，并且在世界各地的抗药性无处不在，这意味着通过药物控制始终是优势的，可能是完全无效的。还可以使用实时寄生虫疫苗，尽管这些疫苗的作用良好，但与药物相比，它们相对昂贵，并且由于必须在鸡中生产它们，但对可以实际制造的剂量数量有严重的限制。

SevenEimeria物种可以感染鸡，每个鸡都会在肠道中引起肠道的首选区域，导致严重程度不同。所有七个物种都会引起疾病，但四种（E. acervulina,E. maxima,E. Necatrix和E. tenella) are of most importance because they occur frequently, replicate to high levels and are highly pathogenic.We generated high quality ‘complete’ genome sequences for these four species, and less comprehensive sequences for the remaining three species (E. brunetti,E. Mitis,E. praecox），在所有情况下都通过编码序列注释表示赞赏。这些资源的发布意味着Eimeria属属加入了一个测序的Apicomplexan原生动物联盟，该联盟已经包括隐孢子虫,Neospora,Plasmodium,肌肉藻,Theileria和弓形虫genera. These resources are publically available through the web databaseeupathdb，它提供了多种生物信息学工具，可让用户对比较基因组学进行深入分析和研究。人们期望理解这些类型的寄生虫的详细比较生物学将通过允许重建和询问基本寄生虫代谢途径，鉴定潜在的药物或疫苗靶标和鉴定寄生虫基因，从而改善新的控制措施的“理性”发展。我们使用了Sanger和Illumina Technologies的组合来生成基因组序列，并由基于计算机的组装支持光学映射的物理技术。为了E. tenella，最彻底的所有Eimeriagenomes we worked on, there are significantly more protein-coding genes predicted than in the closely related弓形虫gondii， 尽管E. tenellahaving a smaller nuclear genome.

我们分析中的一个关键发现是范围范围的保守性，对重复/重复段段内部的保存Eimeria基因组，重复在蛋白质编码序列中比在自然界中任何其他生物报道的序列更为普遍。编码区域中重复的无处不在，意味着Eimeria寄生虫产生许多蛋白质，这些蛋白质含有广泛的均聚糖氨基酸重复序列（HAARS）。详细的基因本体分析未识别与这些HAAR相关的任何特定功能类别。但是，在所有已知真核生物中保守的“核心”基因的重复量少于非核心基因。我们还发现Eimeria基因组具有逆转座子序列，其中包含来自铬病毒组的主要碎片长期重复（LTR）逆转录子。这是第一次在Apicomplexan基因组中发现。所有Eimeria基因组包含编码多态性，膜连接表面抗原（SAGS）的基因家族。这些以前已经在某种程度上进行了研究E. tenella和shown to localise to the outermost membrane of the invading stages of parasites where they can interact directly with host cell surface molecules during the process of parasite attachment and host cell invasion. Comparing between the genomes it is of considerable interest that the total numbers of SAGs, as well as the representation of different types of SAG families, differs between species. The most pathogenic parasites have relatively high numbers of SAGs and the most immunogenic parasites have relatively low numbers. This may indicate key roles for parasite surface antigens in the outcome of infection, including the degree of damage caused to the gut and the susceptibility of recovered chickens to later parasite challenge.

The data generated from genome sequencing will be invaluable for pursing new cost-effective drugs and vaccines, and also to support longevity of any new products. European and North American poultry production currently leads the global demand for anti-coccidial products, but the biggest futureexpansion of the poultry industry is set to occur in Africa and Asia, thus new priorities are emerging. Shifts from traditional to intensive poultry production using indigenous and hybrid birds are increasingly common in these regions (Figure 3), although the inherent resistance or susceptibility of these breeds to eimerian infection is unknown. Genome sequences fromEimeriafield isolates collected from India and Nigeria will soon be available and comparisons with the reference genome sequences we have generated provides a foundation on which modern molecular biological tools can be used to gain insights into genome evolution, naturally occurring genetic diversity and host/pathogen interactions.