title: The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens.
abstract: BACKGROUND
  A sequenced house dust mite (HDM) genome would advance our understanding of HDM allergens, a common cause of human allergies.
  
  
  OBJECTIVE
  We sought to produce an annotated Dermatophagoides farinae draft genome and develop a combined genomic-transcriptomic-proteomic approach for elucidation of HDM allergens.
  
  
  METHODS
  A D farinae draft genome and transcriptome were assembled with high-throughput sequencing, accommodating microbiome sequences. The allergen gene structures were validated by means of Sanger sequencing. The mite's microbiome composition was determined, and the predominant genus was validated immunohistochemically. The allergenicity of a ubiquinol-cytochrome c reductase binding protein homologue was evaluated with immunoblotting, immunosorbent assays, and skin prick tests.
  
  
  RESULTS
  The full gene structures of 20 canonical allergens and 7 noncanonical allergen homologues were produced. A novel major allergen, ubiquinol-cytochrome c reductase binding protein-like protein, was found and designated Der f 24. All 40 sera samples from patients with mite allergy had IgE antibodies against rDer f 24. Of 10 patients tested, 5 had positive skin reactions. The predominant bacterial genus among 100 identified species was Enterobacter (63.4%). An intron was found in the 13.8-kDa D farinae bacteriolytic enzyme gene, indicating that it is of HDM origin. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed a phototransduction pathway in D farinae, as well as thiamine and amino acid synthesis pathways, which is suggestive of an endosymbiotic relationship between D farinae and its microbiome.
  
  
  CONCLUSIONS
  An HDM genome draft produced from genomic, transcriptomic, and proteomic experiments revealed allergen genes and a diverse endosymbiotic microbiome, providing a tool for further identification and characterization of HDM allergens and development of diagnostics and immunotherapeutic vaccines.
authors.affiliation: School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Ting-Fung
authors.initials: TF
authors.lastname: Chan
authors.affiliation: State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen, China.
authors.forename: Kun-Mei
authors.initials: KM
authors.lastname: Ji
authors.affiliation: School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China; Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Aldrin Kay-Yuen
authors.initials: AK
authors.lastname: Yim
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Xiao-Yu
authors.initials: XY
authors.lastname: Liu
authors.affiliation: School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Jun-Wei
authors.initials: JW
authors.lastname: Zhou
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Rui-Qi
authors.initials: RQ
authors.lastname: Li
authors.affiliation: Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Kevin Yi
authors.initials: KY
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.affiliation: School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Patrick Tik-Wan
authors.initials: PT
authors.lastname: Law
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Yu-Lan
authors.initials: YL
authors.lastname: Wu
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Ze-Lang
authors.initials: ZL
authors.lastname: Cai
authors.affiliation: School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China; Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Qin
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Bao
authors.affiliation: Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Ross Ka-Kit
authors.initials: RK
authors.lastname: Leung
authors.affiliation: School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China.
authors.forename: Patrick Kwok-Shing
authors.initials: PK
authors.lastname: Ng
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Ju
authors.initials: J
authors.lastname: Zou
authors.affiliation: Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China.
authors.forename: Xiao-Jun
authors.initials: XJ
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
authors.forename: Pi-Xin
authors.initials: PX
authors.lastname: Ran
authors.affiliation: State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China. Electronic address: nanshan@vip.163.com.
authors.forename: Nan-Shan
authors.initials: NS
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Respiratory Disease for Allergy at Shenzhen University, Shenzhen, China; Shenzhen Key Laboratory of Allergy and Immunology, School of Medicine, Shenzhen University, Shenzhen, China. Electronic address: lzg@szu.edu.cn.
authors.forename: Zhi-Gang
authors.initials: ZG
authors.lastname: Liu
authors.affiliation: Hong Kong Bioinformatics Centre, Chinese University of Hong Kong, Hong Kong, China; School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China. Electronic address: kwtsui@cuhk.edu.hk.
authors.forename: Stephen Kwok-Wing
authors.initials: SK
authors.lastname: Tsui
mesh_terms: D000485:Allergens / Q000235:genetics* / Q000276:immunology; D000818:Animals; D039741:Antigens, Dermatophagoides / Q000235:genetics* / Q000276:immunology; D040001:Dermatophagoides farinae / Q000033:anatomy & histology / Q000145:classification / Q000235:genetics* / Q000276:immunology* / Q000382:microbiology; D005260:Female; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D054892:Metagenome; D064307:Microbiota; D010802:Phylogeny; D040901:Proteomics; D059467:Transcriptome
chemical_list: D000485:Allergens; D039741:Antigens, Dermatophagoides
keywords: Der f 24; Enterobacter species; House dust mite; allergen; genome; microbiome; proteome; transcriptome; ubiquinol-cytochrome c reductase binding protein