A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species
Background. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. Methods. We achieved a chromosome-level assembly of D. farinae’s genome by integrating PacB...
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| Format: | Article |
| Language: | English |
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Wiley
2024-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2024/3779688 |
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| author | Rongxuan Hu Haifeng Huang Ying Zhou Yanshan Liu Yaning Ren Yuanfen Liao Cunyin Yuan Xiaohong Gu Yubao Cui |
| author_facet | Rongxuan Hu Haifeng Huang Ying Zhou Yanshan Liu Yaning Ren Yuanfen Liao Cunyin Yuan Xiaohong Gu Yubao Cui |
| author_sort | Rongxuan Hu |
| collection | DOAJ |
| description | Background. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. Methods. We achieved a chromosome-level assembly of D. farinae’s genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. Results. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. Conclusion. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing D. farinae allergy research and treatment strategies. |
| format | Article |
| id | doaj-art-625c2f33bd214cf18229995b6127bc22 |
| institution | Kabale University |
| issn | 2314-4378 |
| language | English |
| publishDate | 2024-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-625c2f33bd214cf18229995b6127bc222025-02-03T05:55:21ZengWileyInternational Journal of Genomics2314-43782024-01-01202410.1155/2024/3779688A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite SpeciesRongxuan Hu0Haifeng Huang1Ying Zhou2Yanshan Liu3Yaning Ren4Yuanfen Liao5Cunyin Yuan6Xiaohong Gu7Yubao Cui8Department of RheumatologyDermatological DepartmentDepartment of Pediatrics LaboratoryDepartment of Pediatrics LaboratoryClinical Research CenterClinical Research CenterClinical Research CenterRespiratory DepartmentClinical Research CenterBackground. Genome data have been used to find novel allergen from house dust mites. Here, we aim to construct a chromosome-level genome assembly of Dermatophagoides farinae, a common allergenic mite species. Methods. We achieved a chromosome-level assembly of D. farinae’s genome by integrating PacBio single-molecule real-time sequencing, Illumina paired-end sequencing, and Hi-C technology, followed by annotating allergens and mapping them to specific chromosomes. Results. A 62.43 Mb genome was assembled with a 0.52% heterozygosity rate and a 36.11 Merqury-estimated quality value. The assembled genome represents 92.1% completeness benchmarking universal single-copy orthologs with a scaffold N50 value of 7.11 Mb. Hi-C scaffolding of the genome resulted in construction of 10 pseudochromosomes. The genome comprises 13.01% (7.66 Mb) repetitive sequences and predicts 10,709 protein-coding genes, 96.57% of which are functionally annotated. Moreover, we identified and located 36 allergen groups on specific chromosomes, including allergens Der f 1, Der f 2, Der f 23, Der f 4, Der f 5, Der f 7, and Der f 21 located on chromosomes 2, 1, 7, 3, 4, 6, and 4, respectively. Conclusion. This comprehensive genomic data provides valuable insights into mite biology and evolutionary adaptations, potentially advancing D. farinae allergy research and treatment strategies.http://dx.doi.org/10.1155/2024/3779688 |
| spellingShingle | Rongxuan Hu Haifeng Huang Ying Zhou Yanshan Liu Yaning Ren Yuanfen Liao Cunyin Yuan Xiaohong Gu Yubao Cui A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species International Journal of Genomics |
| title | A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species |
| title_full | A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species |
| title_fullStr | A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species |
| title_full_unstemmed | A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species |
| title_short | A Chromosomal-Level Genome of Dermatophagoides farinae, a Common Allergenic Mite Species |
| title_sort | chromosomal level genome of dermatophagoides farinae a common allergenic mite species |
| url | http://dx.doi.org/10.1155/2024/3779688 |
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