High-quality reference genome of < i > Fasciola gigantica < /i > : Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions

by Xier Luo, Kuiqing Cui, Zhiqiang Wang, Zhipeng Li, Zhengjiao Wu, Weiyi Huang, Xing-Quan Zhu, Jue Ruan, Weiyu Zhang, Qingyou LiuFasciola gigantica andFasciola hepatica are causative pathogens offascioliasis, 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-qualityFasciola gigantica reference genome. We improved the integration of gene structure prediction, and identified two independent transposable element expansion events contributing to (1) the speciation betweenFasciola andFasciolopsis 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 effect. 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 predicted excretory/secretory proteins and 3300 protein-protein interactions betweenFasciola gigantica and its host. Among them, copper/zinc superoxide dismutase genes, with specific gene copy ...
Source: PLoS Neglected Tropical Diseases - Category: Tropical Medicine Authors: Source Type: research