BACKGROUND The red flour beetle Tribolium castaneum has emerged as an important model organism for the study of gene function in development and physiology, for ecological and evolutionary genomics, for pest control and a plethora of other topics. RNA interference (RNAi), transgenesis and genome editing are well established and the resources for genome-wide RNAi screening have become available in this model. All these techniques depend on a high quality genome assembly and precise gene models. However, the first version of the genome assembly was generated by Sanger sequencing, and with a small set of RNA sequence data limiting annotation quality. RESULTS Here, we present an improved genome assembly (Tcas5.2) and an enhanced genome annotation resulting in a new official gene set (OGS3) for Tribolium castaneum, which significantly increase the quality of the genomic resources. By adding large-distance jumping library DNA sequencing to join scaffolds and fill small gaps, the gaps in the genome assembly were reduced and the N50 increased to 4753kbp. The precision of the gene models was enhanced by the use of a large body of RNA-Seq reads of different life history stages and tissue types, leading to the discovery of 1452 novel gene sequences. We also added new features such as alternative splicing, well defined UTRs and microRNA target predictions. For quality control, 399 gene models were evaluated by manual inspection. The current gene set was submitted to Genbank and accepted as a RefSeq genome by NCBI. CONCLUSIONS The new genome assembly (Tcas5.2) and the official gene set (OGS3) provide enhanced genomic resources for genetic work in Tribolium castaneum. The much improved information on transcription start sites supports transgenic and gene editing approaches. Further, novel types of information such as splice variants and microRNA target genes open additional possibilities for analysis.

中文翻译：

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Tribolium castaneum的增强的基因组组装和新的官方基因集。

背景技术红色面粉甲虫Tribolium castaneum已成为研究发育和生理中的基因功能，生态和进化基因组学，害虫控制和许多其他主题的重要模型生物。RNA干扰（RNAi），转基因和基因组编辑已得到充分确立，并且用于全基因组RNAi筛选的资源已在此模型中可用。所有这些技术都取决于高质量的基因组组装和精确的基因模型。但是，基因组装配的第一个版本是通过Sanger测序生成的，并且具有少量的RNA序列数据，限制了注释的质量。结果在这里，我们提出了一种改进的基因组装配（Tcas5.2）和增强的基因组注释，从而产生了Tribolium castaneum的新官方基因集（OGS3），这大大提高了基因组资源的质量。通过添加远距离跳跃文库DNA测序以加入支架并填补小缺口，基因组装配中的缺口减少，N50增加至4753kbp。通过使用大量不同生活史阶段和组织类型的RNA-Seq读物，提高了基因模型的精确度，从而发现了1452个新基因序列。我们还添加了新功能，例如替代剪接，定义明确的UTR和microRNA靶标预测。为了进行质量控制，通过人工检查评估了399个基因模型。当前的基因组已提交给Genbank，并被NCBI接受为RefSeq基因组。结论新的基因组组装（Tcas5。2）和官方基因集（OGS3）为Tribolium castaneum的遗传工作提供了增强的基因组资源。有关转录起始位点的信息有了很大改进，从而支持转基因和基因编辑方法。此外，新型信息类型，例如剪接变体和microRNA靶基因，为分析提供了更多可能性。