14CONFAP From Comparative genomics to Phylogenomics: uncovering the genomic complexity and evolutionary adaptations of twenty species of protozoa 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. The Newton Fund builds research and innovation partnerships with developing countries across the world to promote the economic development and social welfare of the partner countries.