Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis. Scabies mite genome project

The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans or mange in other animal species. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where secondary Group A streptococcal and Staphylococcus aureus infections of scabies sores are thought to drive the high rate of rheumatic heart disease and chronic kidney disease. We sequenced the genome of two samples of Sarcoptes scabiei var. hominis obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of Sarcoptes scabiei var. suis from a pig model. Due to the small size of scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present Sarcoptes scabiei var. hominis and var. suis draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins. We have developed extensive genomic resources for the scabies mite, including reference genomes and a preliminary annotation.

疥螨（Sarcoptes scabiei）是一类寄生性蛛形纲动物，可引发人类的传染性皮肤病疥疮，以及其他动物的疥癣。疥疮感染是一项重大公共卫生问题，尤其在澳大利亚偏远原住民社区，据信疥疮破溃处继发的A组链球菌与金黄色葡萄球菌（Staphylococcus aureus）感染，是该地区风湿性心脏病与慢性肾病高发的核心驱动因素。我们采用Illumina HiSeq测序平台，对取自澳大利亚北部不同地区、无亲缘关系的结痂型疥疮患者体内的人疥螨（Sarcoptes scabiei var. hominis）的两份样本完成了基因组测序；同时还对猪模型中的猪疥螨（Sarcoptes scabiei var. suis）样本进行了测序。鉴于疥螨体型微小，本次测序数据源自数千只疥螨的混合样本，属于宏基因组（metagenomic）数据，涵盖宿主与微生物组的DNA。我们完成了数据清洗与从头组装（de novo assembly），并获得了人疥螨与猪疥螨的草图参考基因组。基于与已知蛋白的序列相似性，我们为该参考基因组构建了初步注释，共包含13226个推定编码序列。本研究为疥螨构建了丰富的基因组资源，包括参考基因组与初步注释信息。