ABI Innovation: New Software Tools for Genome Comparisons of Non-Model Organisms

高通量测序技术的最新进展使更多非模式生物的基因组研究成为可能。这些基因组的比较将为不同物种复杂特征的进化提供新的见解。这个项目将开发新的方法来比较十多个新的蜜蜂基因组，以帮助利用进化基因组学来阐明优胜劣汰的分子特征。生态社会物种具有不同层次的社会组织，而相关物种则是独居的，这为研究社会生活的进化提供了一个理想的物种阶梯。直到最近，这种表型的遗传基础在很大程度上还没有被探索出来。在这项研究中，将开发新的工具，通过结合RNA-SEQ数据和来自相关生物基因组序列的信息来更好地注释基因模型。该方法在注释基因模型时将充分利用剪接变体。还将开发方法，为蜜蜂基因组中的编码区和非编码区建立高质量的跨物种序列比对。此外，原始基因组组装中的错误将得到纠正，以提高质量。随着数据的获得，这个项目的见解可以应用到其他物种和支系。这项研究涉及计算生物学家和实验生物学家之间的互动。该项目将开发计算生物学课程，并培训研究生跨学科研究方法。在这个项目中开发的研究将被整合到现有的推广计划中(如G.A.M.E.S.夏令营和伊利诺伊大学的SING研讨会)，以鼓励本科生在科学和工程领域从事职业。项目中产生的工具和数据将通过项目网站提供。

Recent advances in high-throughput sequencing technologies have allowed study of the genomes of many more non-model organisms. The comparisons of these genomes will provide new insights into the evolution of complex traits of different species. This project will develop new methods to compare more than ten new bee genomes to help elucidate the molecular signatures of eusociality using evolutionary genomics. Eusocial species have different levels of social organization while related species are solitary, providing an ideal "ladder" of species to study the evolution of social life. The genetic basis for such phenotypes has remained largely unexplored until very recently. In this research, new tools will be developed to better annotate the gene models by incorporating both RNA-seq data and information from genome sequences of related organisms. The method will fully utilize splice variants when annotating the gene models. Methods will also be developed to build high-quality cross-species sequence alignments for both coding and non-coding regions in the bee genomes. Additionally, errors in the original genome assemblies will be corrected to improve quality. Insights from this project can be applied to other species and clades as the data becomes available.This research involves interactions between computational and experimental biologists. The project will develop computational biology curricula and train graduate students in interdisciplinary research methods. The research developed in this project will be integrated into existing outreach programs (such as the G.A.M.E.S. camp and the SING workshop at the University of Illinois) to encourage undergraduate students to pursue careers in science and engineering. The tools and data produced in the project will be made available through a project website.