Chin J Schisto Control ›› 2020, Vol. 32 ›› Issue (6): 618-.

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Transcriptome sequencing and bioinformatics analysis of Tyrophagus putrescentiae

JIA Hao-Yuan, ZHOU Ying△, CUI Yu-Bao, WANG Ting-Ting*   

  1. Department of Clinical Laboratory, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
  • Online:2020-12-08 Published:2020-12-08



  1. 南京医科大学附属无锡人民医院检验科(无锡214023)
  • 作者简介:贾浩源,女,博士,主管技师。研究方向:支气管哮喘及其环境因素 周颖,女,本科,副主任技师。研究方向:儿童支气管哮喘与免疫调节
  • 基金资助:

Abstract: Objective To obtain the transcriptome data of Tyrophagus putrescentiae, so as to provide insights into the subsequent functional studies. Methods The mixture of male and female T. putrescentiae was sequenced using the Illumina HiSeqTM 2000 high?throughput sequencing platform. Unigenes were obtained after assembling the sequencing data using the Trinity software and compared with the protein sequences in the RefSeq non?redundant protein sequence (NR) database, nucleotide sequence (NT) database, Swiss?Prot database, Kyoto encyclopedia of genes and genomes (KEGG) database and clusters of orthologous groups (COG) database, and the function of the Unigenes was annotated. In addition, the coding DNA sequences (CDS) were predicted through alignment of the Unigenes in NR and Swiss?Prot protein databases. The SSR loci were identified by analysis of the Unigenes in T. putrescentiae with the MISA software, and the SNPs were detected using the SOAPsnp technique. Results A total of 4.67 GB high?quality data were obtained from raw sequencing data. A total of 51 271 Unigenes were obtained after assembling the sequencing data, with a total length of 41 848 995 nucleotide (nt) and a mean length of 816 nt. A total of 29 053 annotated Unigenes were obtained following comparisons with the public protein databases, and 27 443 CDS were predicted. In addition, there were 23 092 SSR loci and 148 027 SNPs identified. Conclusions The database of T. putrescentiae transcriptome is created by sequencing, and a large number of T. putrescentiae transcripts are obtained, which provides a basis for the subsequent functional studies of allergy?related genes.

Key words: Tyrophagus putrescentiae, Transcriptomic sequencing, Bioinformatics analysis

摘要: 目的 获得腐食酪螨转录组数据,为后续基因功能研究奠定基础。方法 基于Illumina HiSeqTM 2000高通量测序平台,对腐食酪螨雌雄混合螨体进行测序,采用Trinity软件组装转录本获得单基因簇(Unigenes)。将单基因簇与非冗余蛋白质序列(RefSeq non?redundant protein sequence,NR)数据库、核苷酸序列(nucleotide sequence database,NT)数据库、Swiss?Prot数据库、京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes,KEGG)数据库、直系同源簇(clusters of orthologous groups,COG)数据库中的蛋白质序列进行比对,对其进行功能注释。将单基因簇按照NR、Swiss?Prot 蛋白库优先级顺序进行编码序列(coding sequence,CDS)比对、预测。利用MISA软件对腐食酪螨Unigenes进行简单重复序列(simple sequence repeats,SSR)位点分析。使用SOAPsnp技术检测螨虫单核苷酸多态性(single nucleotide polymorphism,SNP)。结果 转录组测序数据质控后获得4.67 Gb高质量数据,组装后获得51 271个单基因簇,总长度为41 848 995 个核苷酸(nucleotide,nt)、平均长度为816 nt。将单基因簇与公共数据库进行比对和功能注释后,得到29 053个有功能注释的Unigenes。预测发现27 443条CDS,检测到23 092个SSR位点信息和148 027个SNP位点信息。结论 通过测序技术建立了腐食酪螨转录组数据库,获得了大量腐食酪螨转录本信息,为后续过敏相关基因功能学研究奠定了基础。

关键词: 腐食酪螨, 转录组测序, 生物信息学分析

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