Applications of high-throughput omics technology in research on dust mite

doi:10.12140/j.issn.1000-7423.2020.05.018

Abstract

Abstract:

House dust mites are one of the most common inhaled allergens worldwide. Since the last 20 years, the prevalence of dust mite allergy has shown a trend of increase. With the advent of the post-genome age, research in life sciences has entered a new stage of systematic, comprehensive and dynamic exploration. High-throughput omics technology has been applied to comprehensively analyze samples at the gene and/or protein levels by sequencing for data mining, and interpreting intrinsic mechanisms of biological processes. This paper reviews the advance in application of high-throughput omics in the genomics, transcriptomics, proteomics and microbiology of dust mites, providing ideas forfurther research on dust mite allergens and allergic diseases and for the development of new control strategies.

Key words: House dust mite, Allergenomics, Genome, Transcriptom, Proteom, Microbiome

CLC Number:

R384.429

LIU Na-na, CUI Yu-bao, YE Lin-hua, HUANG Lu-sheng. Applications of high-throughput omics technology in research on dust mite[J]. CHINESE JOURNAL OF PARASITOLOGY AND PARASITIC DISEASES, 2020, 38(5): 642-646.

Figures/Tables 1

References 30

[1]	Banerjee S, Resch Y, Chen KW, et al. Der p 11 is a major allergen for house dust mite-allergic patients suffering from atopic dermatitis[J]. J Invest Dermatol, 2015,135(1):102-109. doi: 10.1038/jid.2014.271 pmid: 24999597
[2]	He XM, Shao C, Wei QY. Progress in sensitized protein components and subcutaneous specific immunotherapy for dust mites[J]. Int J Pediatrics, 2019(3):198-202. (in Chinese)
	( 何雪梅, 邵婵, 魏庆宇. 尘螨致敏蛋白组份及其皮下特异性免疫治疗的研究进展[J]. 国际儿科学杂志, 2019,46(3):198-202.)
[3]	Li J, Sun B, Huang Y, et al. A multicentre study assessing the prevalence of sensitizations in patients with asthma and/or rhinitis in China[J]. Allergy, 2009,64(7):1083-1092. doi: 10.1111/j.1398-9995.2009.01967.x pmid: 19210346
[4]	Hui Y, Li L, Qian J, et al. Efficacy analysis of three-year subcutaneous SQ-standardized specific immunotherapy in house dust mite-allergic children with asthma[J]. Exp Ther Med, 2014,7(3):630-634.
[5]	Yagami T, Haishima Y, Tsuchiya T, et al. Proteomic analysis of putative latex allergens[J]. Int Arch Allergy Immunol, 2004,135(1):3-11. doi: 10.1159/000080036 pmid: 15286439
[6]	Chan TF, Ji KM, Yim AK, et al. The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens[J]. J Allergy Clin Immunol, 2015,135(2):539-548. doi: 10.1016/j.jaci.2014.09.031 pmid: 25445830
[7]	Parra G, Bradnam K, Korf I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes[J]. Bioinformatics, 2007,23(9):1061-1067. doi: 10.1093/bioinformatics/btm071 pmid: 17332020
[8]	Randall TA, Mullikin JC, Mueller GA. The draft genome assembly of Dermatophagoides pteronyssinus supports identification of novel allergen isoforms in Dermatophagoides species[J]. Int Arch Allergy Immunol, 2018,175(3):136-146. doi: 10.1159/000481989 pmid: 29320781
[9]	Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data[J]. Genomics, 2010,95(6):315-327. doi: 10.1016/j.ygeno.2010.03.001 pmid: 20211242
[10]	Rider SD Jr, Morgan MS, Arlian LG. Allergen homologs in the Euroglyphus maynei draft genome[J]. PLoS One, 2017,12(8):e0183535. doi: 10.1371/journal.pone.0183535 pmid: 28829832
[11]	Waldron R, McGowan J, Gordon N, et al. Draft genome sequence of Dermatophagoides pteronyssinus, the European house dust mite[J]. Genome Announc, 2017,5(32):e00789-e00717. doi: 10.1128/genomeA.00789-17 pmid: 28798186
[12]	Rider SD Jr, Morgan MS, Arlian LG. Draft genome of the Scabies mite[J]. Parasit Vectors, 2015,8:585. doi: 10.1186/s13071-015-1198-2 pmid: 26555130
[13]	Liu XY, Yang KY, Wang MQ, et al. High-quality assembly of Dermatophagoides pteronyssinus genome and transcriptome reveals a wide range of novel allergens[J]. J Allergy Clin Immunol, 2018,141(6):2268-2271. doi: 10.1016/j.jaci.2017.11.038 pmid: 29305317
[14]	Koren S, Walenz BP, Berlin K, et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation[J]. Genome Res, 2017,27(5):722-736. doi: 10.1101/gr.215087.116 pmid: 28298431
[15]	Cui Y, Yu L, Teng F, et al. Transcriptomic/proteomic identification of allergens in the mite Tyrophagus putrescentiae[J]. Allergy, 2016,71(11):1635-1639. doi: 10.1111/all.12999 pmid: 27496383
[16]	Bordas-Le Floch V, Le Mignon M, Bussières L, et al. A combined transcriptome and proteome analysis extends the allergome of house dust mite Dermatophagoides species[J]. PLoS One, 2017,12(10):e0185830. doi: 10.1371/journal.pone.0185830 pmid: 28982170
[17]	Zhou Y, Li L, Qian J, et al. Identification of three aquaporin subgroups from Blomia tropicalis by transcriptomics[J]. Int J Mol Med, 2018,42(6):3551-3561. doi: 10.3892/ijmm.2018.3877 pmid: 30221673
[18]	Haas BJ, Papanicolaou A, Yassour M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis[J]. Nat Protoc, 2013,8(8):1494-1512. doi: 10.1038/nprot.2013.084 pmid: 23845962
[19]	Zhao QP, Jiang MS. Proteomics and its application in parasitology[J]. Chin J Parasitol Parasit Dis, 2006,24(2):136-139. (in Chinese)
	( 赵琴平, 蒋明森. 蛋白质组学及其在寄生虫学研究中的应用[J]. 中国寄生虫学与寄生虫病杂志, 2006,24(2):136-139.)
[20]	He DG. Proteomics and its application in parasitology[J]. Chin Trop Med, 2003,3(4):507-512. (in Chinese)
	( 何东苟. 蛋白质组学研究及其在寄生虫学上的应用[J]. 中国热带医学, 2003,3(4):507-512.)
[21]	An S, Chen LL, Long CB, et al. Dermatophagoides farinae allergens diversity identification by proteomics[J]. Mol Cell Proteomics, 2013,12(7):1818-1828. doi: 10.1074/mcp.M112.027136 pmid: 23481662
[22]	Choopong J, Reamtong O, Sookrung N, et al. Proteome, allergenome, and novel allergens of house dust mite, Dermatophagoides farinae[J]. J Proteome Res, 2016,15(2):422-430. doi: 10.1021/acs.jproteome.5b00663 pmid: 26754146
[23]	Kim JY, Yi MH, Hwang Y, et al. 16S rRNA profiling of the Dermatophagoides farinae core microbiome: Enterococcus and Bartonella[J]. Clin Exp Allergy, 2018,48(5):607-610. doi: 10.1111/cea.13104 pmid: 29381238
[24]	Hubert J, Kopecky J, Perotti MA, et al. Detection and identification of species-specific bacteria associated with synanthropic mites[J]. Microb Ecol, 2012,63(4):919-928. doi: 10.1007/s00248-011-9969-6 pmid: 22057398
[25]	Kopecky J, Perotti MA, Nesvorna M, et al. Cardinium endosymbionts are widespread in synanthropic mite species (Acari: Astigmata)[J]. J Invertebr Pathol, 2013,112(1):20-23. doi: 10.1016/j.jip.2012.11.001 pmid: 23147105
[26]	Santos-Garcia D, Rollat-Farnier PA, Beitia F, et al. The genome of Cardinium cBtQ1 provides insights into genome reduction, symbiont motility, and its settlement in Bemisiatabaci[J]. Genome Biol Evol, 2014,6(4):1013-1030. doi: 10.1093/gbe/evu077 pmid: 24723729
[27]	Penz T, Schmitz-Esser S, Kelly SE, et al. Comparative genomics suggests an independent origin of cytoplasmic incompatibility in cardinium hertigii[J]. PLoS Genet, 2012,8(10):e1003012. doi: 10.1371/journal.pgen.1003012 pmid: 23133394
[28]	Hubert J, Nesvorna M, Kopecky J, et al. Population and culture age influence the microbiome profiles of house dust mites[J]. Microb Ecol, 2019,77(4):1048-1066. pmid: 30465068
[29]	Valerio CR, Murray P, Arlian LG, et al. Bacterial 16S ribosomal DNA in house dust mite cultures[J]. J Allergy Clin Immunol, 2005,116(6):1296-1300. doi: 10.1016/j.jaci.2005.09.046 pmid: 16337462
[30]	Erban T, Ledvinka O, Nesvorna M, et al. Experimental manipulation shows a greater influence of population than dietary perturbation on the microbiome of Tyrophagus putrescentiae[J]. Appl Environ Microbiol, 2017,83(9):e00128-e00117. pmid: 28235879

种名	拉丁文	基因组大小/Mb	支架N50	支架	预测蛋白数	基因组NCBI登录号	参考文献
粉尘螨	Dermatophagoides farina	53.5	187 kb	515	16 376	GCA_000767015.1	[6]
屋尘螨	D. pteronyssinus	52.5	376 kb	834	19 368	-	[8]
梅氏嗜霉螨	Euroglyphus maynei	59	480 nt	-	15 000	-	[10]
屋尘螨	D. pteronyssinus	70.76	450 kb	332	-	GCA_001901225.2	[11]
屋尘螨	D. pteronyssinus	66.8	80 kb	634	-	GCA_003076615.1	[13]