开发用于旋毛虫的全基因组多态微卫星标记。

Development of genome-wide polymorphic microsatellite markers for Trichinella spiralis.

机构信息

Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun, 130062, Jilin, People's Republic of China.

State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, 730046, Gansu, People's Republic of China.

出版信息

Parasit Vectors. 2020 Feb 11;13(1):58. doi: 10.1186/s13071-020-3929-2.

DOI:10.1186/s13071-020-3929-2

PMID:32046770

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7014596/

Abstract

BACKGROUND

Trichinella nematodes are globally distributed food-borne pathogens, in which Trichinella spiralis is the most common species in China. Microsatellites are a powerful tool in population genetics and phylogeographic analysis. However, only a few microsatellite markers were reported in T. spiralis. Thus, there is a need to develop and validate genome-wide microsatellite markers for T. spiralis.

METHODS

Microsatellites were selected from shotgun genomic sequences using MIcroSAtellite identification tool (MISA). The identified markers were validated in 12 isolates of T. spiralis in China.

RESULTS

A total of 93,140 microsatellites were identified by MISA from 9267 contigs in T. spiralis genome sequences, in which 16 polymorphic loci were selected for validation by PCR with single larvae from 12 isolates of T. spiralis in China. There were 7-19 alleles per locus (average 11.25 alleles per locus). The observed heterozygosity (H) and expected heterozygosity (H) ranged from 0.325 to 0.750 and 0.737 to 0.918, respectively. The polymorphism information content (PIC) ranged from 0.719 to 0.978 (average 0.826). Among the 16 loci, markers for 10 loci could be amplified from all 12 international standard strains of Trichinella spp.

CONCLUSIONS

Sixteen highly polymorphic markers were selected and validated for T. spiralis. Primary phylogenetic analysis showed that these markers might serve as a useful tool for genetic studies of Trichinella parasites.

摘要

背景

旋毛虫线虫是全球分布的食源性病原体，其中旋毛虫是中国最常见的物种。微卫星是种群遗传学和系统地理学分析的有力工具。然而，在旋毛虫中仅报道了少数微卫星标记。因此，需要开发和验证旋毛虫的全基因组微卫星标记。

方法

使用 MIcroSAtellite identification tool (MISA) 从霰弹枪基因组序列中选择微卫星。在中国的 12 个旋毛虫分离株中验证了鉴定的标记。

结果

MISA 从旋毛虫基因组序列的 9267 个重叠群中鉴定出 93140 个微卫星，从中选择了 16 个多态性标记，通过 PCR 用来自中国的 12 个旋毛虫分离株的单个幼虫进行验证。每个位点有 7-19 个等位基因（平均每个位点 11.25 个等位基因）。观察杂合度（H）和预期杂合度（H）范围分别为 0.325-0.750 和 0.737-0.918。多态信息含量（PIC）范围为 0.719-0.978（平均 0.826）。在这 16 个标记中，10 个标记的产物可从 12 个国际标准旋毛虫株系中全部扩增出来。