14CONFAP From Comparative genomics to Phylogenomics: uncovering the genomic complexity and evolutionary adaptations of twenty species of protozoa

在像我们这样含有细胞核的细胞（真核生物）和不含细胞核的细菌细胞之间存在着根本的分裂。绝大多数真核生物是单细胞生物或原生动物，具有巨大的遗传多样性，导致生物学上的巨大变化，形态和功能千差万别。在少数原生动物群体中，出现了寄生动物（如我们人类）的能力。动质体和双胞体是两个这样的原生动物群，它们被认为是在最后一个真核生物共同祖先（接近真核生物树的根）之后不久从动物谱系中分化出来的。在这两组中都有重要但被忽视的人类病原体——导致致命的病媒传播锥虫病和利什曼病的病原体；那些引起水传播腹泻，贾第虫病和各种其他致病物种和自由生活的物种是自由生活的而不是寄生的。对这些群体的致病性和致病性成员的基因组进行比较，将突出显示编码蛋白质的基因群的进化，这些蛋白质的作用是绕过动物宿主的防御，这些生物体的致病性和毒性取决于这些基因群。这些基因也是疫苗接种、药物和单克隆治疗的关键靶点。该提案汇集了来自巴西FioCruz研究所、TGAC和英国东安格利亚大学的寄生虫学家、原生动物学家、进化生物学家、基因组生物学家和生物信息学家的专家团队。该项目承诺提供首批高质量的20个着丝体和双胞体基因组序列。所选择的基因组将涵盖这些群体的遗传多样性，并将与来自主要致病物种的现有基因组数据一起进行分析。所涉及的技术是最先进的，并且不断升级，期望产生的基因组和转录组将具有最高的质量。双方将相互交换专门知识，主要人员和学生的互访将促进技术和分析技术的双向知识转移。我们的基本策略是培养生物体，利用东英吉利大学沃尔夫森实验室的新兴病原体来培养该组的致病成员。我们将采集和纯化核酸，使用朝乱性缓冲液破坏细胞和二氧化硅亲和力进行核酸纯化。我们将使用混合的方法和技术来组装高质量的基因组，包括全基因组测序和基因组的光学作图以及RNA-seq来划分转录组。最后，我们将结合每个谱系的数据集，从与寄生生活方式的进化适应有关的基因组复杂性中推断细节。在这样做的过程中，我们将在英国和巴西的研究人员之间建立可持续的合作，这将导致出版物，并在新的合作可以建立未来项目的领域取得实质性进展。总的来说，这些分析的目的是为了深入了解两组不同的鞭毛原生动物的功能生物学，这两组鞭毛原生动物独立地从自由生物体进化为主要的人类和动物病原体。每个群体在生物学上都是独特的，并由细胞和分子生物学的特性来定义——阐明这些特性是如何进化和继续发展的，以及它们对这些不同谱系中寄生进化的贡献是基础生物学，也是这项工作的主要目标。

A fundamental schism exists between organisms with cells such as our own which contain nuclei (eukaryotes), and bacterial cells which do not. The vast majority of eukaryote species are single celled organisms or protozoa displaying enormous genetic diversity leading to huge variation in biology, myriad form and function. In just a few groups of protozoa the ability to parasitize animals such as ourselves has arisen. Kinetoplastids and Diplomonads are two such groups of protozoa which are believed to have diverged from the animal lineage not long after the last eukaryotic common ancestor (close to the root of the eukaryotic tree). Within both groups are important but neglected pathogens of humans - those which cause the deadly vector-borne trypanosomiases and leishmanias; and those that cause the waterborne diahorrea, giardiasis and a variety of other pathogenic species and free living species which are free living rather than parasitic. Comparison of the genomes from pathogenic and apathogenic members of these groups will highlight the evolution of groups of genes encoding proteins which act to circumvent the defences of animal hosts and upon which the pathogenicity and virulence of these organisms depends. Such genes are also key targets for vaccination, drug and monoclonal therapeutics.The proposal brings together an expert team of parasitologists, protozoologists, evolutionary biologists, genome biologists and bioinformaticians from the FioCruz Institute in Brazil and from TGAC and the University of East Anglia in the United Kingdom. The project undertakes to deliver the first high quality genome sequences of twenty kinetoplastid and diplomonad genomes. The genomes selected will span the breadth of the genetic diversity in these groups and will be analysed in concert with existing genomic data from the key pathogenic species. The technology involved is state of the art and constantly upgraded and the expectation is that the genomes and transcriptomes produced will be of the highest possible quality. There will be a reciprocal exchange of expertise, with bidirectional knowledge transfer of technical and analytical techniques facilitated by exchange visits of key personnel and students.Our basic strategy will be to culture the organisms, making use of the Wolfson laboratory for emerging pathogens at UEA for the culture of the pathogenic members of the group. We will harvest and purify the nucleic acid using a chaotropic buffer to disrupt the cells and silica affinity for nucleic acid purification. Will we use a mixture of methods and technologies to assemble high quality genomes including whole genome sequencing and optical mapping for the genomes and RNA-seq to delimit the transcriptome. Finally, we will combine the data sets for each lineage to infer details from the genomic complexity relating to evolutionary adaptations for parasitic lifestyle. In so doing we will establish sustainable collaborations between UK and Brazilian researchers that will lead to publications, and substantial advances in the field upon which the new collaborations can build future projects.Overall, the purpose of these analyses is to add insight into the functional biology of two groups of divergent flagellated protozoans which have independently evolved from free living organisms to major human and animal pathogens. Each group is biologically distinctive and famously defined by peculiarities in cell and molecular biology - elucidating how these peculiarities have evolved and continue to do and their contribution to the evolution of parasitism in these distinct lineages is fundamental biology and will be the primary objective of this work.