High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions.
High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions.
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巨片形吸虫的高质量参考基因组：深入了解热带地区转座子介导的进化和特定寄生适应的基因组特征
DOI：
10.1371/journal.pntd.0009750
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发表时间：
2021-10
影响因子：
3.8
通讯作者：
Liu Q
中科院分区：
文献类型：
--
作者：
Luo X;Cui K;Wang Z;Li Z;Wu Z;Huang W;Zhu XQ;Ruan J;Zhang W;Liu Q
巨大片形吸虫和肝片形吸虫是片形吸虫病的致病菌，其纬度、纵向和海拔分布最广；然而，在寄生虫中，它们拥有最大的测序基因组，阻碍了基因组研究。在本研究中，我们使用各种测序和组装技术来生成新的高质量巨片形吸虫参考基因组。我们改进了基因结构预测的整合，并确定了两个独立的转座元件扩展事件，这些事件有助于（1）白垩纪-古近纪边界大规模灭绝期间片形吸虫和片形吸虫之间的物种形成，以及（2）古新世-始新世热最大值期间栖息地切换到肝脏，并伴随着基因长度的增加。长散布元件（LINE）重复导致了第二次转座子介导的改变，显示出明显的插入基因区域的趋势，无论强纯化选择如何。对具有长 LINE 插入的基因进行基因本体分析，鉴定出膜相关蛋白和囊泡分泌过程蛋白，进一步暗示基因网络的功能改变。我们鉴定了巨片形吸虫与其宿主之间的 852 个排泄/分泌蛋白和 3300 个蛋白质-蛋白质相互作用。其中，铜/锌超氧化物歧化酶基因具有特定的基因拷贝数变异，可能在第一阶段解毒过程中发挥核心作用。对 559 个单拷贝直系同源物的分析表明，Fasciola gigantica 和 Fasciola hepatica 在中新世中晚期边界附近的 11.8 Ma 处出现分歧。我们鉴定了 98 个快速进化的基因家族，包括肌动蛋白和水通道蛋白，这可能解释了导致这些肝吸虫在热带和亚热带地区流行的巨大体型和寄生适应性特征。
Fasciola gigantica and Fasciola hepatica are causative pathogens of fascioliasis, with the widest latitudinal, longitudinal, and altitudinal distribution; however, among parasites, they have the largest sequenced genomes, hindering genomic research. In the present study, we used various sequencing and assembly technologies to generate a new high-quality Fasciola gigantica reference genome. We improved the integration of gene structure prediction, and identified two independent transposable element expansion events contributing to (1) the speciation between Fasciola and Fasciolopsis during the Cretaceous-Paleogene boundary mass extinction, and (2) the habitat switch to the liver during the Paleocene-Eocene Thermal Maximum, accompanied by gene length increment. Long interspersed element (LINE) duplication contributed to the second transposon-mediated alteration, showing an obvious trend of insertion into gene regions, regardless of strong purifying selection. Gene ontology analysis of genes with long LINE insertions identified membrane-associated and vesicle secretion process proteins, further implicating the functional alteration of the gene network. We identified 852 excretory/secretory proteins and 3300 protein-protein interactions between Fasciola gigantica and its host. Among them, copper/zinc superoxide dismutase genes, with specific gene copy number variations, might play a central role in the phase I detoxification process. Analysis of 559 single-copy orthologs suggested that Fasciola gigantica and Fasciola hepatica diverged at 11.8 Ma near the Middle and Late Miocene Epoch boundary. We identified 98 rapidly evolving gene families, including actin and aquaporin, which might explain the large body size and the parasitic adaptive character resulting in these liver flukes becoming epidemic in tropical and subtropical regions.
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