Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39

Jiajie Chen; Zelang Cai; Dingding Fan; Jiayu Hu; Yibo Hou; Yongsen He; Zhen Zhang; Zhenfu Zhao; Pan Gao; Wanzhen Hu; Jinlyu Sun; Jiang Li; Kunmei Ji

doi:10.1016/j.waojou.2021.100590

Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39

World Allergy Organ J. 2021 Sep 28;14(10):100590. doi: 10.1016/j.waojou.2021.100590. eCollection 2021 Oct.

Authors

Jiajie Chen¹, Zelang Cai¹, Dingding Fan², Jiayu Hu¹, Yibo Hou¹, Yongsen He¹, Zhen Zhang¹, Zhenfu Zhao¹, Pan Gao³, Wanzhen Hu³, Jinlyu Sun⁴, Jiang Li², Kunmei Ji¹

Affiliations

¹ Department of Biochemistry and Molecular Biology, Laboratory Department of Pinghu Hospital, Health Science Center, Shenzhen University, Shenzhen, 518060, China.
² EasyATCG L.L.C, Shenzhen, 518000, China.
³ Shenzhen University General Hospital, Shenzhen, 518060, China.
⁴ Allergy Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, China.

Abstract

Accurate house dust mite (HDM) genome and transcriptome data would promote our understanding of HDM allergens. We sought to assemble chromosome-level genome and precise transcriptome profiling of Dermatophagoides farinae and identify novel allergens. In this study, genetic material extracted from HDM bodies and eggs were sequenced. Short-reads from next generation sequencing (NGS) and long-reads from PacBio/Nanopore sequencing were used to construct the D. farinae nuclear genome, transcriptome, and mitochondrial genome. The candidate homologs were screened through aligning our assembled transcriptome data with amino acid sequences in the WHO/IUIS database. Our results showed that compared with the D. farinae draft genome, bacterial DNA content in the presently developed sequencing reads was dramatically reduced (from 22.9888% to 1.5585%), genome size was corrected (from 53.55 Mb to 58.77 Mb), and the contig N50 was increased (from 8.54 kb to 9365.49 kb). The assembled genome has 10 contigs with minimal microbial contamination, 33 canonical allergens and 2 novel allergens. Eight homologs (≥50% homology) were cloned; 2 bound HDM allergic-sera and were identified as allergens (Der f 37 and Der f 39). In conclusion, a chromosome-level genome, transcriptome and mitochondrial genome of D. farinae was generated to support allergen identification and development of diagnostics and immunotherapeutic vaccines.

Keywords: Chromsome-scale genome; Der f 37; Der f 39; Dermatophagoides farinae; Dust mite; Nanopore sequencing; Transcriptome sequencing.