A comparative approarch to genome annotation in Tribolium

谷盗基因组注释的比较方法

• 批准号: 240301934
• 负责人: Professor Dr. Mario Stanke
• 金额: --
• 依托单位: Lehrstuhl für Bioinformatik
• 依托单位国家: 德国
• 项目类别: Research Units
• 财政年份: 2013
• 资助国家: 德国
• 起止时间: 2012-12-31 至 2015-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/240301934?language=en
• 关键词: comparative; approarch; genome; annotation; Tribolium

This project entails the in silico identification of the genes and the dsRNA templates for the RNAi screen of Tribolium castaneum as well as bioinformatics method development for gene-finding. The genome annotation of T. castaneum will be further improved in order to obtain a high success rate for high throughput template generation and of RNAi knockdowns for the remaining roughly 6850 not-yetscreened genes that are harder to correctly predict, because highly expressed and easier to predict genes have been targeted in the first phase of iBeetle already. Likely to be correct fragments of mRNAs will be identified in this project and delivered to the company Eupheria for filtering for regions with high content of efficient siRNAs and minimal off-target effects, for primer design and physical dsRNA template generation. To increase confidence in - and therefore the success rate of - the reported mRNA fragments, a new method for comparative gene finding to supplement expression evidence will be developed and applied to four Tribolium species' genomes that are currently sequenced and assembled in the Brown lab (Kansas State University). The goals of method development will go beyond Tribolium-specific applications and target other genome-dense eukaryotic clades, like vertebrates, too. The new gene prediction tool that will be designed and implemented in this project will identify all genes in all species simultaneously. The iBeetle Gr-Sta1 page 3 of 5 interdependency between the gene structures of different species will be introduced via a graph structure that is based on a multiple genome alignment and a phylogenetic tree in which the nodes are candidate exons

该项目包括赤拟谷盗RNAi筛选的基因和dsRNA模板的计算机鉴定，以及基因发现的生物信息学方法的开发。对T.为了获得高通量模板生成的高成功率和剩余的大约6850个尚未筛选的基因的RNAi敲除，将进一步改进栗的基因，因为高表达和更容易预测的基因已经在iBeetle的第一阶段中被靶向。该项目将识别可能正确的mRNA片段，并交付给Eupheria公司，以过滤具有高含量高效SiRNA和最小脱靶效应的区域，用于引物设计和物理双链RNA模板生成。为了增加对所报道的mRNA片段的信心，从而提高其成功率，将开发一种新的比较基因发现方法，以补充表达证据，并将其应用于目前在布朗实验室（堪萨斯州立大学）测序和组装的四种拟谷盗属物种的基因组。方法开发的目标将超越Tribolium特定的应用，并针对其他基因组密集的真核进化枝，如脊椎动物。该项目将设计和实施的新基因预测工具将同时识别所有物种中的所有基因。iBeetle Gr-Sta 1第3页（共5页）不同物种的基因结构之间的相互依赖性将通过基于多基因组比对和系统发育树（其中节点为候选外显子）的图形结构进行介绍