State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
PLoS One. 2010 Dec 30;5(12):e15633. doi: 10.1371/journal.pone.0015633.
Locusts exhibit remarkable density-dependent phenotype (phase) changes from the solitary to the gregarious, making them one of the most destructive agricultural pests. This phenotype polyphenism arises from a single genome and diverse transcriptomes in different conditions. Here we report a de novo transcriptome for the migratory locust and a comprehensive, representative core gene set. We carried out assembly of 21.5 Gb Illumina reads, generated 72,977 transcripts with N50 2,275 bp and identified 11,490 locust protein-coding genes. Comparative genomics analysis with eight other sequenced insects was carried out to identify the genomic divergence between hemimetabolous and holometabolous insects for the first time and 18 genes relevant to development was found. We further utilized the quantitative feature of RNA-seq to measure and compare gene expression among libraries. We first discovered how divergence in gene expression between two phases progresses as locusts develop and identified 242 transcripts as candidates for phase marker genes. Together with the detailed analysis of deep sequencing data of the 4(th) instar, we discovered a phase-dependent divergence of biological investment in the molecular level. Solitary locusts have higher activity in biosynthetic pathways while gregarious locusts show higher activity in environmental interaction, in which genes and pathways associated with regulation of neurotransmitter activities, such as neurotransmitter receptors, synthetase, transporters, and GPCR signaling pathways, are strongly involved. Our study, as the largest de novo transcriptome to date, with optimization of sequencing and assembly strategy, can further facilitate the application of de novo transcriptome. The locust transcriptome enriches genetic resources for hemimetabolous insects and our understanding of the origin of insect metamorphosis. Most importantly, we identified genes and pathways that might be involved in locust development and phase change, and may thus benefit pest management.
蝗虫表现出显著的密度依赖性表型（相位）变化，从独居到群居，使其成为最具破坏性的农业害虫之一。这种表型多态性源自单一基因组和不同条件下的多样化转录组。在这里，我们报道了迁徙性蝗虫的从头转录组和一个全面的、有代表性的核心基因集。我们对 21.5 Gb 的 Illumina 读数进行了组装，生成了 72977 个转录本，N50 为 2275 bp，并鉴定了 11490 个蝗虫蛋白质编码基因。与其他八种已测序昆虫的比较基因组学分析首次确定了半变态和全变态昆虫之间的基因组差异，并发现了 18 个与发育相关的基因。我们进一步利用 RNA-seq 的定量特征来测量和比较文库之间的基因表达。我们首先发现了随着蝗虫的发育，两个相位之间的基因表达差异如何进化，并鉴定了 242 个转录本作为相位标记基因的候选基因。结合对 4 龄幼虫的深度测序数据的详细分析，我们发现了分子水平上生物投资的相位依赖性差异。独居蝗虫在生物合成途径中具有更高的活性，而群居蝗虫在环境相互作用中表现出更高的活性，其中与神经递质活性调节相关的基因和途径，如神经递质受体、合成酶、转运体和 GPCR 信号通路，强烈参与其中。我们的研究是迄今为止最大的从头转录组，通过优化测序和组装策略，可以进一步促进从头转录组的应用。蝗虫转录组丰富了半变态昆虫的遗传资源，增进了我们对昆虫变态起源的理解。最重要的是，我们鉴定了可能参与蝗虫发育和相位变化的基因和途径，这可能有助于害虫管理。
