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

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.

A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species

“…The National Center for Biotechnology Information (NCBI) database contains three D. farinae genomes: (1) GCA_000767015.2 [ 47 ], with a total length of 60.39 Mb and a scaffold N50 value of 8.98 Mb; (2) GCA_002085665.2 [ 48 ], with a total ungapped length of 91.9 Mb and a scaffold N50 value of 0.19 Mb; and (3) GCA_020809275.1 [ 9 ], with a total length of 58.8 Mb and a Contig N50 value of 9.3 Mb. Due to PacBio technology, this scaffold-level genome assembly includes 10 contigs scaffolds [ 9 ], but no assembled chromosomes. These D. farinae genome data were downloaded from NCBI, reassembled and annotated, and compared with our current findings ( Table 1 ).…”

“…In 2021, Chen et al extracted genetic material from D. farinae bodies and eggs and sequenced with short reads from next-generation sequencing (NGS) and long reads from PacBio/nanopore sequencing; compared with the D. farinae draft genome, 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, 33 canonical allergens, and 2 novel allergens (Der f 37 and Der f 39) [ 9 ].…”