title: Genetic variation between Schistosoma japonicum lineages from lake and mountainous regions in China revealed by resequencing whole genomes.
abstract: Schistosoma infection is a major cause of morbidity and mortality worldwide. Schistosomiasis japonica is endemic in mainland China along the Yangtze River, typically distributed in two geographical categories of lake and mountainous regions. Study on schistosome genetic diversity is of interest in respect of understanding parasite biology and transmission, and formulating control strategy. Certain genetic variations may be associated with adaptations to different ecological habitats. The aim of this study is to gain insight into Schistosoma japonicum genetic variation, evolutionary origin and associated causes of different geographic lineages through examining homozygous Single Nucleotide Polymorphisms (SNPs) based on resequenced genome data. We collected S. japonicum samples from four sites, three in the lake regions (LR) of mid-east (Guichi and Tonglin in Anhui province, Laogang in Hunan province) and one in mountainous region (MR) (Xichang in Sichuan province) of south-west of China, resequenced their genomes using Next Generation Sequencing (NGS) technology, and made use of the available database of S. japonicum draft genomic sequence as a reference in genome mapping. A total of 14,575 SNPs from 2059 genes were identified in the four lineages. Phylogenetic analysis confirmed significant genetic variation exhibited between the different geographical lineages, and further revealed that the MR Xichang lineage is phylogenetically closer to LR Guich lineage than to other two LR lineages, and the MR lineage might be evolved from LR lineages. More than two thirds of detected SNPs were nonsynonymous; functional annotation of the SNP-containing genes showed that they are involved mainly in biological processes such as signaling and response to stimuli. Notably, unique nonsynonymous SNP variations were detected in 66 genes of MR lineage, inferring possible genetic adaption to mountainous ecological condition.
authors.affiliation: Key Laboratory of Parasite and Vector Biology Ministry of Public Health, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai 200025, China; School of Life Sciences, Fudan University, 2005 Song Hu Road, Shanghai 200438, China.
authors.forename: Mingbo
authors.initials: M
authors.lastname: Yin
authors.affiliation: School of Life Sciences, Fudan University, 2005 Song Hu Road, Shanghai 200438, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: Key Laboratory of Parasite and Vector Biology Ministry of Public Health, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai 200025, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Xu
authors.affiliation: Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Huang
authors.affiliation: School of Life Sciences, Fudan University, 2005 Song Hu Road, Shanghai 200438, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zheng
authors.affiliation: School of Life Sciences, Fudan University, 2005 Song Hu Road, Shanghai 200438, China.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Yang
authors.affiliation: Key Laboratory of Parasite and Vector Biology Ministry of Public Health, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai 200025, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Feng
authors.affiliation: Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China; Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai 201203, China. Electronic address: hanzg@sjtu.edu.cn.
authors.forename: Ze-Guang
authors.initials: ZG
authors.lastname: Han
authors.affiliation: Key Laboratory of Parasite and Vector Biology Ministry of Public Health, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, 207 Rui Jin Er Road, Shanghai 200025, China; School of Life Sciences, Fudan University, 2005 Song Hu Road, Shanghai 200438, China. Electronic address: huw@fudan.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Hu
mesh_terms: D000818:Animals; D002681:China / Q000453:epidemiology; D014644:Genetic Variation; D023281:Genomics; D005843:Geography; D059014:High-Throughput Nucleotide Sequencing; D060106:Lakes / Q000469:parasitology*; D010802:Phylogeny; D012549:Schistosoma japonicum / Q000235:genetics*; D012554:Schistosomiasis japonica / Q000235:genetics* / Q000469:parasitology*
keywords: Adaptation; Divergence; Resequencing; SNPs; Schistosoma japonicum; Variation; Whole genome