Comparative Chloroplast Genomics: Integrating Computational Methods, Molecular Evolution, and Phylogeny

0120709 Jansen，Raubeson，and Warnow一个生物复杂性研究基金已被授予来自德克萨斯大学、中央华盛顿大学、新墨西哥州大学、美国能源部联合基因组研究所和宾夕法尼亚州立大学的跨学科研究小组，对来自50多种有代表性的陆地植物的完整叶绿体基因组进行比较进化分析。 该团队由四名生物学家（Jansen，Raubeson，Boore和dePamelo）和五名计算机科学家（Warnow，Moret，Bader，Sankoff和米勒）组成，将在生物学和计算机科学的交叉点上解决三个领域的一些重要问题：陆地植物的遗传学，叶绿体基因组进化和计算基因组学。 将产生55个完整的基因组序列（大大增加了现在已知的10个左右），将设计和实施使用基因组数据检查关系的新计算方法，并开发基因组学的生物信息学工具和资源。 然后，这些数据和方法将用于研究植物之间的关系以及突变的模式和过程，因为它们影响叶绿体基因组。这些结果将提供给科学界和非科学界。 此外，学生在计算生物学，生物信息学，系统发育分析和基因组学领域将得到培训。了解生物体之间的关系是生物科学所有领域的必要前提，包括生态学，进化，法医学，医学和分子生物学等不同领域。本研究的重点是陆地植物，包括30多万种，构成陆地生态系统的基础。 这个重要的生物群的系统发育史，只有不完全理解，将澄清这项研究。 该项目也将为我们理解叶绿体基因组内的突变机制和进化过程做出重大贡献。 该基因组包含植物功能所必需的基因;研究其进化应该为植物科学家提供具有根本重要性的基本信息。 最后，这个项目将对计算生物学产生重要影响，计算生物学是当今发展最快的科学领域之一。 这包括开发和测试比较基因组学中的新算法，如基因顺序改变，这将增加理论计算生物学的范围。 该小组开发的所有软件都将免费提供。

0120709Jansen, Raubeson, and Warnow A Biocomplexity grant has been awarded to an interdisciplinary team ofresearchers from the University of Texas, Central Washington University,University of New Mexico, the DoE Joint Genomics Institute, and Penn StateUniversity to undertake comparative evolutionary analyses of complete chloroplast genomes from more than 50 representative land plants. The team of four biologists (Jansen, Raubeson, Boore and dePamphilis) and five computer scientists (Warnow, Moret, Bader, Sankoff and Miller) will address a number of important issues in three areas at the intersection of biology and computer science: phylogeny of land plants, chloroplast genome evolution, and computational genomics. Fifty-five complete genomic sequences will be generated (greatly augmenting the 10 or so now known), new computational approaches for examining relationships using genomic data will be designed andimplemented, and bioinformatic tools and resources for genomics will bedeveloped. Then, the data and approaches will be used to study the relationships of plants and the patterns and processes of mutation as they affect the chloroplast genome. These results will be made available to both the scientific and lay communities. In addition, students in the fields of computational biology, bioinformatics, phylogenetic analysis, and genomics will be trained. Understanding relationships among organisms is an essential prerequisite for all areas of Biological Science, including such diverse fields as ecology, evolution, forensics, medicine, and molecular biology. Land plants, the focus of this study, include over 300,000 species and form the basis of terrestrial ecosystems. The phylogenetic history of this important group of organisms, only imperfectly understood, will be clarified by this research. This project also will make major contributions to our understanding of the mutational mechanisms and evolutionary processes acting within the chloroplast genome. This genome contains genes essential to plant function; studying its evolution should provide basic information of fundamental importance to plant scientists. Finally, this project will have important implications for computational biology, one of thefastest growing fields of science today. This includes the development andtesting of new algorithms in comparative genomics, such as gene-order changes, that will increase the scope of theoretical computational biology. All software developed by the team will be made freely available.