期刊
JOURNAL OF BIOSCIENCES
卷 44, 期 4, 页码 -出版社
INDIAN ACAD SCIENCES
DOI: 10.1007/s12038-019-9917-z
关键词
2b-RAD sequencing; genome-wide SNP analysis; Haemonchus contortus; selective sweeps; signature of selection
类别
资金
- National Key Basic Research Program (973 program) of China [2015CB150303]
- Special Fund for Agroscientific Research in the Public Interest, China [201303037]
- Fund on Basic Scientific Research Project of Non-profit Central Research Institutions of China [2018JB08]
- Innovation Program of the Chinese Academy of Agricultural Sciences
The parasitic nematode Haemonchus contortus is one of the world's most important parasites of small ruminants that causes significant economic losses to the livestock sector. The population structure and selection in its various strains are poorly understood. No study so far compared its different populations using genome-wide data. Here, we focused on different geographic populations of H. contours from China (Tibet, TB; Hubei, HB; Inner Mongolia, IM; Sichuan, SC), UK and Australia (AS), using genome-wide population-genomic approaches, to explore genetic diversity, population structure and selection. We first performed next-generation high-throughput 2b RAD pool sequencing using Illumina technology, and identified single-nucleotide polymorphisms (SNPs) in all the strains. We identified 75,187 SNPs for TB, 82,271 for HB, 82,420 for IM, 79,803 for SC, 83,504 for AS and 78,747 for UK strain. The SNPs revealed low-nucleotide diversity (pi = 0.0092-0.0133) within each strain, and a significant differentiation level (average F-st = 0.34264) among them. Chinese populations TB and SC, along with the UK strain, were more divergent populations. Chinese populations IM and HB showed affinities to the Australian strain. We then analysed signature of selection and detected 44 (UK) and 03 (AS) private selective sweeps containing 49 and 05 genes, respectively. Finally, we performed the functional annotation of selective sweeps and proposed biological significance to signature of selection. Our data suggest that 2b-RAD pool sequencing can be used to assess the signature of selection in H. contortus.
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