Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi
Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi
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DOI：
10.1099/mgen.0.000177
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发表时间：
2018-05-01
影响因子：
3.9
通讯作者：
Robello, Carlos
中科院分区：
文献类型：
--
作者：
Berna, Luisa;Rodriguez, Matias;Robello, Carlos
尽管恰加斯病的病原体克氏锥虫的基因组于 2005 年首次公开，随后又报道了其他菌株，但这种寄生虫内在的基因组复杂性（串联组织的大量重复序列和基因）传统上阻碍了高质量的基因组组装和注释。这也限制了需要高精度的多种类型的分析。第三代测序技术生成的长读段特别适合解决与克氏锥虫基因组相关的挑战，因为它们允许直接确定大重复序列簇的完整序列，而不会破坏它们。反过来，这不仅可以准确估计基因拷贝数，还可以避免组装碎片。在这里，我们对两个克氏锥虫克隆的基因组序列进行了分析：杂交 TCC (TcVI) 和非杂交 Dm28c (Id)，由 PacBio 单分子实时 (SMRT) 技术测定。本文获得的改进组件使我们能够准确估计重复序列（包括卫星和逆转录元件）的基因拷贝数、丰度和分布。我们发现克氏锥虫的基因组由“核心区室”和“破坏性区室”组成，它们表现出相反的GC含量和基因组成。鉴定出新的串联和分散的重复序列，包括一些位于编码序列内部的序列。此外，同源染色体是单独组装的，使我们能够将单倍型作为单独的重叠群而不是独特的嵌合序列进行检索。最后，表面多基因家族、粘蛋白和转唾液酸酶的手动注释现在可以更好地概述这些复杂的基因组。
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T. cruzi's genome since they permit direct determination of the full sequence of large clusters of repetitive sequences without collapsing them. This, in turn, not only allows accurate estimation of gene copy numbers but also circumvents assembly fragmentation. Here, we present the analysis of the genome sequences of two T. cruzi clones: the hybrid TCC (TcVI) and the non-hybrid Dm28c (Id), determined by PacBio Single Molecular Real-Time (SMRT) technology. The improved assemblies herein obtained permitted us to accurately estimate gene copy numbers, abundance and distribution of repetitive sequences (including satellites and retroelements). We found that the genome of T. cruzi is composed of a 'core compartment' and a 'disruptive compartment' which exhibit opposite GC content and gene composition. Novel tandem and dispersed repetitive sequences were identified, including some located inside coding sequences. Additionally, homologous chromosomes were separately assembled, allowing us to retrieve haplotypes as separate contigs instead of a unique mosaic sequence. Finally, manual annotation of surface multigene families, mucins and trans-sialidases allows now a better overview of these complex groups of genes.