Enhanced genome assembly and a new official gene set for Tribolium castaneum
Enhanced genome assembly and a new official gene set for Tribolium castaneum
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DOI：
10.1186/s12864-019-6394-6
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发表时间：
2020-01-14
期刊：
影响因子：
4.4
通讯作者：
Bucher, Gregor
中科院分区：
文献类型：
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作者：
Herndon, Nicolae;Shelton, Jennifer M.;Bucher, Gregor
赤拟谷盗（Tribolium castaneum）是一种重要的模式生物，在发育和生理学、生态学和进化基因组学、害虫防治等领域具有重要的研究价值。RNA干扰（RNAi）、转基因和基因组编辑已经得到很好的建立，并且用于全基因组RNAi筛选的资源已经在该模型中变得可用。所有这些技术都依赖于高质量的基因组组装和精确的基因模型。然而，基因组组装的第一个版本是通过桑格测序产生的，并且具有限制注释质量的一小组RNA序列数据。结果通过改进赤拟谷盗基因组组装（Tcas 5. 2）和增强基因组注释，构建了赤拟谷盗新的官方基因组（OGS 3），显著提高了赤拟谷盗基因组资源的质量。通过添加大距离跳跃文库DNA测序连接支架和填充小的缺口，基因组组装中的缺口减少，N50增加到4753 kbp。基因模型的精确度通过使用不同生活史阶段和组织类型的大量RNA-Seq读数来提高，从而发现了1452个新基因序列。我们还增加了新的功能，如选择性剪接，明确定义的UTR和microRNA靶点预测。为了进行质量控制，通过人工检查评估了399个基因模型。目前的基因组已提交给Genbank，并被NCBI接受为RefSeq基因组。结论新的基因组拼接（Tcas 5. 2）和官方基因组（OGS 3）为赤拟谷盗的遗传学研究提供了丰富的基因组资源。关于转录起始位点的大量改进的信息支持转基因和基因编辑方法。此外，剪接变体和microRNA靶基因等新型信息为分析提供了额外的可能性。
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.