Genome Assemblies, Analyses, and Comparisons

基因组组装、分析和比较

• 批准号: 9550571
• 负责人: Leonardo Marino-Ramirez
• 金额: $ 42.62万
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9550571
• 关键词: Area; Bacteria; Binding Sites; Biological; Biology; Biomedical Research; Black Currant; Clinical; Collaborations; Colombia; Computing Methodologies; DNA Transposable Elements; DNA sequencing; Data; Databases; Disease; Elements; Gene Expression; Gene Expression Regulation; Generations; Genes; Genetic Transcription; Genome; Genomics; Genotype; Human; Individual; Investigation; Jordan; Knowledge; Methods; Modification; Musa plant; Pathway interactions; Phenotype; Population; Process; Research; Research Personnel; Source; Technology; Transcription Initiation Site; Variant; Vibrio cholerae; falls; genetic variant; human population study; improved; insight; interest; next generation sequencing; plant growth/development; preference; tool; transcription factor; transcriptome

Technological advances in DNA sequencing are enabling new areas of genomic research allowing fine connections between genomic variants and phenotype. We are studying transcriptomes and genomes from a variety of eukaryotic and prokaryotic non model organisms and have contributed to gain biological insights. At the moment we are collaborating with researchers in Corpoica, Colombia to continue the characterization of the Cape gooseberry transcriptome with additional data generated by next-generation sequencing technologies and have finalized the construction of a database using NCBI tools to display the newly assembled Cape gooseberry transcriptome. Additionally, we are in the process of analyzing interactions between plant growth promoting bacteria and banana plants. This is done in collaboration with Richa Agarwala and Roberto Vera Alvarez. In collaboration with John Spouge, we have studied the co-localization of transcription factor binding sites (TFBSs) within regulatory modules (RMs) and found that their tight positional conservation explains much of the TFBS positional preferences near the transcription start site (TSS). In another study related to the investigation of repeated sequences in genomes in collaboration with I. King Jordan we studied the human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. We presented a systematic analysis of the regulatory contributions of polyTE loci that were generated by recent transpositional activity and thereby differ between individuals. We found that the phenotypic impact of human TE activity is not limited to deleterious effects; it also includes the generation of regulatory differences that fall within the scope of naturally occurring human variation and are involved in population-specific gene regulation as well as transcriptional network modification. We contributed to the genome assembly and annotation of 26 genome sequences of Vibrio cholerae strains obtained from clinical and environmental sources. Assemblies were constructed using Illumina and the genomes were annotated with the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP). This research was done in collaboration with I. King Jordan and Brian K. Hammer (Georgia Tech).

DNA测序的技术进步正在使基因组研究的新领域成为可能，从而使基因组变体和表型之间建立良好的联系。我们正在研究各种真核和原核非模式生物的转录组和基因组，并有助于获得生物学的见解。目前，我们正在与哥伦比亚Corpoica的研究人员合作，继续利用下一代测序技术生成的额外数据对Cape gooseberry转录组进行表征，并已完成使用NCBI工具构建数据库以显示新组装的Cape gooseberry转录组。此外，我们正在分析植物生长促进细菌和香蕉植物之间的相互作用。这是与Richa Agarwala和Roberto Vera Alvarez合作完成的。 与John Spouge合作，我们研究了调节模块（RM）内转录因子结合位点（TFBS）的共定位，发现它们的紧密位置保守性解释了转录起始位点（TSS）附近的TFBS位置偏好。在另一项与I.我们用多态性转座元件研究了人类群体特异性基因表达和转录网络修饰。我们提出了一个系统的分析polyTE基因座的监管贡献，产生最近的转座活动，从而不同的个人之间。我们发现，人类TE活性的表型影响不仅限于有害影响;它还包括产生属于自然发生的人类变异范围内的调节差异，并参与群体特异性基因调节以及转录网络修饰。 我们对从临床和环境来源获得的26个霍乱弧菌菌株的基因组序列进行了基因组组装和注释。使用Illumina构建组装体，并用NCBI Proximity Genome Automatic Annotation Pipeline（PGAAP）注释基因组。这项研究是与I。King Jordan和Brian K. Hammer（格鲁吉亚理工大学）。