DataSheet_13_Repeat-Driven Generation of Antigenic Diversity in a Major Human Pathogen, Trypanosoma cruzi.pdf

Trypanosoma cruzi, a zoonotic kinetoplastid protozoan parasite, is the causative agent of American trypanosomiasis (Chagas disease). Having a very plastic, repetitive and complex genome, the parasite displays a highly diverse repertoire of surface molecules, with pivotal roles in cell invasion, immune evasion and pathogenesis. Before 2016, the complexity of the genomic regions containing these genes impaired the assembly of a genome at chromosomal level, making it impossible to study the structure and function of the several thousand repetitive genes encoding the surface molecules of the parasite. We here describe the genome assembly of the Sylvio X10/1 genome sequence, which since 2016 has been used as a reference genome sequence for T. cruzi clade I (TcI), produced using high coverage PacBio single-molecule sequencing. It was used to analyze deep Illumina sequence data from 34 T. cruzi TcI isolates and clones from different geographic locations, sample sources and clinical outcomes. Resolution of the surface molecule gene distribution showed the unusual duality in the organization of the parasite genome, a synteny of the core genomic region with related protozoa flanked by unique and highly plastic multigene family clusters encoding surface antigens. The presence of abundant interspersed retrotransposons in these multigene family clusters suggests that these elements are involved in a recombination mechanism for the generation of antigenic variation and evasion of the host immune response on these TcI strains. The comparative genomic analysis of the cohort of TcI strains revealed multiple cases of such recombination events involving surface molecule genes and has provided new insights into T. cruzi population structure.

克氏锥虫（Trypanosoma cruzi）是一种人畜共患的动质体原生寄生虫，为美洲锥虫病（American trypanosomiasis，又称恰加斯病）的致病病原体。该寄生虫基因组具有高度可塑性、重复序列富集且结构复杂的特征，其表面分子组库极为多样，在细胞入侵、免疫逃逸与致病过程中发挥关键作用。2016年以前，由于携带此类编码基因的基因组区域结构极为复杂，无法完成染色体级别的基因组组装，导致难以解析该寄生虫数千个编码表面分子的重复基因的结构与功能。本研究报道了Sylvio X10/1的基因组组装结果，该序列自2016年起被用作克氏锥虫I支（T. cruzi clade I，缩写为TcI）的参考基因组，其组装采用了高覆盖度PacBio单分子测序技术（PacBio single-molecule sequencing）。该参考基因组被用于分析来自34株不同地理来源、样本来源及临床表型的克氏锥虫I支分离株与克隆的深度Illumina测序数据（Illumina sequencing）。对表面分子基因分布的解析揭示了该寄生虫基因组组织的独特二元性：核心基因组区域与相关原生动物存在共线性（synteny），其两侧则分布着编码表面抗原的独特且高度可塑性的多基因家族簇。这些多基因家族簇中存在大量散在分布的反转录转座子（retrotransposons），提示此类元件参与了重组机制，以促成I支菌株的抗原变异与宿主免疫逃逸。对该组I支菌株的比较基因组分析揭示了多起涉及表面分子基因的此类重组事件，并为解析克氏锥虫的种群结构提供了全新视角。