Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39
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 HD...
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2021
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oai:doaj.org-article:9ef74f3045eb479f80f66f6a873f750e2021-11-12T04:30:10ZChromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 391939-455110.1016/j.waojou.2021.100590https://doaj.org/article/9ef74f3045eb479f80f66f6a873f750e2021-10-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S1939455121000843https://doaj.org/toc/1939-4551Accurate 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.Jiajie ChenZelang CaiDingding FanJiayu HuYibo HouYongsen HeZhen ZhangZhenfu ZhaoPan GaoWanzhen HuJinlyu SunJiang LiKunmei JiElsevierarticleDermatophagoides farinaeDust miteChromsome-scale genomeNanopore sequencingTranscriptome sequencingDer f 37Immunologic diseases. AllergyRC581-607ENWorld Allergy Organization Journal, Vol 14, Iss 10, Pp 100590- (2021) |
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EN |
| topic |
Dermatophagoides farinae Dust mite Chromsome-scale genome Nanopore sequencing Transcriptome sequencing Der f 37 Immunologic diseases. Allergy RC581-607 |
| spellingShingle |
Dermatophagoides farinae Dust mite Chromsome-scale genome Nanopore sequencing Transcriptome sequencing Der f 37 Immunologic diseases. Allergy RC581-607 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 Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39 |
| description |
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. |
| format |
article |
| author |
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 |
| author_facet |
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 |
| author_sort |
Jiajie Chen |
| title |
Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39 |
| title_short |
Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39 |
| title_full |
Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39 |
| title_fullStr |
Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39 |
| title_full_unstemmed |
Chromosome-level assembly of Dermatophagoides farinae genome and transcriptome reveals two novel allergens Der f 37 and Der f 39 |
| title_sort |
chromosome-level assembly of dermatophagoides farinae genome and transcriptome reveals two novel allergens der f 37 and der f 39 |
| publisher |
Elsevier |
| publishDate |
2021 |
| url |
https://doaj.org/article/9ef74f3045eb479f80f66f6a873f750e |
| work_keys_str_mv |
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| _version_ |
1718431306307600384 |