De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences.
De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences.
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使用转录组序列在储存产品害虫 Liposcelis entophila (Enderlein) 中进行从头组装、基因注释和标记发现
DOI：
10.1371/journal.pone.0080046
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Wang JJ
中科院分区：
文献类型：
--
作者：
Wei DD;Chen EH;Ding TB;Chen SC;Dou W;Wang JJ
研究背景嗜虫书虱是粮食仓储系统的主要害虫，对多种杀虫剂产生了很高的抗性。然而，耐药性和环境胁迫的分子机制尚未得到表征。迄今为止，缺乏该物种的基因组信息。因此，研究旨在剖析L。昆虫转录组的研究将有助于在分子水平上更好地了解昆虫的生物学功能。方法/主要发现我们应用Illumina测序技术对L.虫媒共获得54，406，328个干净的读段，并且从头组装成54，220个单基因，平均长度为571 bp。通过相似性搜索，33，404（61.61%）个单基因与NCBI非冗余（Nr）蛋白质数据库中的已知蛋白质匹配。这些unigenes进一步的功能注释与基因本体论（GO），蛋白质的直链组簇（COG），和京都基因和基因组百科全书（KEGG）数据库。大量的基因可能参与杀虫剂抗性人工策划，包括68个推定的细胞色素P450基因，37个推定的谷胱甘肽S-转移酶（GST）基因，19个推定的羧基/胆碱酯酶（CCE）基因，和其他126个转录本含有靶位点序列或编码解毒基因代表8种类型的抗性酶。此外，为了深入了解L。对嗜虫热激蛋白（Hsp）基因进行了克隆和序列分析，共鉴定出25个Hsp基因。此外，共检测到1,100个SSR标记和57,757个SNPs，设计了231对SSR引物，为进一步的遗传多样性研究奠定了基础。结论/意义我们建立了一个全面的L.虫媒这些序列和推测的分子标记将进一步促进我们对杀虫剂抗性或环境胁迫的分子机制的理解，并将有助于研究群体遗传学，以及为未来的功能基因组研究提供有用的信息。
Background As a major stored-product pest insect, Liposcelis entomophila has developed high levels of resistance to various insecticides in grain storage systems. However, the molecular mechanisms underlying resistance and environmental stress have not been characterized. To date, there is a lack of genomic information for this species. Therefore, studies aimed at profiling the L. entomophila transcriptome would provide a better understanding of the biological functions at the molecular levels. Methodology/Principal Findings We applied Illumina sequencing technology to sequence the transcriptome of L. entomophila. A total of 54,406,328 clean reads were obtained and that de novo assembled into 54,220 unigenes, with an average length of 571 bp. Through a similarity search, 33,404 (61.61%) unigenes were matched to known proteins in the NCBI non-redundant (Nr) protein database. These unigenes were further functionally annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of genes potentially involved in insecticide resistance were manually curated, including 68 putative cytochrome P450 genes, 37 putative glutathione S-transferase (GST) genes, 19 putative carboxyl/cholinesterase (CCE) genes, and other 126 transcripts to contain target site sequences or encoding detoxification genes representing eight types of resistance enzymes. Furthermore, to gain insight into the molecular basis of the L. entomophila toward thermal stresses, 25 heat shock protein (Hsp) genes were identified. In addition, 1,100 SSRs and 57,757 SNPs were detected and 231 pairs of SSR primes were designed for investigating the genetic diversity in future. Conclusions/Significance We developed a comprehensive transcriptomic database for L. entomophila. These sequences and putative molecular markers would further promote our understanding of the molecular mechanisms underlying insecticide resistance or environmental stress, and will facilitate studies on population genetics for psocids, as well as providing useful information for functional genomic research in the future.
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