State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural SciencesLanzhou, China.
Front Cell Infect Microbiol. 2017 Sep 21;7:412. doi: 10.3389/fcimb.2017.00412. eCollection 2017.
Gene duplication (GD), thought to facilitate evolutionary innovation and adaptation, has been studied in many phylogenetic lineages. However, it remains poorly investigated in trematodes, a medically important parasite group that has been evolutionarily specialized during long-term host-parasite interaction. In this study, we conducted a genome-wide study of GD modes and contributions in , a pathogen causing human schistosomiasis. We combined several lines of evidence provided by duplicate age distributions, genomic sequence similarity, depth-of-coverage and gene synteny to identify the dominant drivers that contribute to the origins of new genes in this parasite. The gene divergences following duplication events (gene structure, expression and function retention) were also analyzed. Our results reveal that the genome lacks whole genome duplication (WGD) in a long evolutionary time and has few large segmental duplications, but is extensively shaped by the continuous small-scale gene duplications (SSGDs) (i.e., dispersed, tandem and proximal GDs) that may be derived from (retro-) transposition and unequal crossing over. Additionally, our study shows that the genes generated by tandem duplications have the smallest divergence during the evolution. Finally, we demonstrate that SSGDs, especially the tandem duplications, greatly contribute to the expansions of some preferentially retained pathogenesis-associated gene families that are associated with the parasite's survival during infection. This study is the first to systematically summarize the landscape of GDs in trematodes and provides new insights of adaptations to parasitism linked to GD events for these parasites.
基因复制（GD）被认为有助于进化创新和适应，已在许多系统发育谱系中进行了研究。然而，在吸虫中，这一现象的研究仍然很少，吸虫是一类具有医学重要性的寄生虫，它们在长期的宿主-寄生虫相互作用中已经进化得非常专业化。在这项研究中，我们对引起人类血吸虫病的病原体进行了全基因组范围内的 GD 模式和贡献研究。我们结合了重复年龄分布、基因组序列相似性、覆盖深度和基因同线性提供的几条证据，以确定导致寄生虫中新基因起源的主要驱动因素。还分析了复制事件后基因的分歧（基因结构、表达和功能保留）。我们的结果表明，该基因组在漫长的进化时间内缺乏全基因组复制（WGD），并且很少有大的片段重复，但广泛受到连续的小规模基因重复（SSGDs）的影响（即分散、串联和近端 GD），这些重复可能来自（ retro-）转座和不等交换。此外，我们的研究表明，串联重复产生的基因在进化过程中具有最小的分歧。最后，我们证明 SSGDs，特别是串联重复，极大地促进了一些优先保留的与发病机制相关基因家族的扩张，这些基因家族与寄生虫在感染过程中的生存有关。这项研究首次系统地总结了吸虫中 GD 的情况，并为这些寄生虫与 GD 事件相关的寄生适应性提供了新的见解。
