Genome Assemblies, Analyses, and Comparisons

基因组组装、分析和比较

• 批准号: 10004478
• 负责人: Leonardo Marino-Ramirez
• 金额: $ 21.39万
• 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/10004478
• 关键词: Admixture; American; Area; Bacteria; Biological; Biology; Biomedical Research; Black Currant; Collaborations; Colombia; Colombian; Computing Methodologies; Country; DNA sequencing; Data; Databases; Disease; Elements; Genes; Genetic study; Genome; Genomics; Genotype; Health; Jordan; Knowledge; Methods; Musa plant; Pathway interactions; Pattern; Phenotype; Population; Population Group; Research; Research Personnel; Role; Salmonella enterica; Technology; Texas; Universities; genetic variant; health disparity; improved; insight; interest; next generation sequencing; plant growth/development; tool; 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 just completed the analysis of interactions between plant growth promoting bacteria and banana plants, done in collaboration with Rocio Gamez and Roberto Vera Alvarez. In collaboration with I. King Jordan we studied the genetic ancestry and admixture patterns for an Afro-Colombian population and to compare its ancestry to other admixed American populations. We found that at the subcontinental level, the two Colombian populations from Choco and Medellin are far more similar to each other than to any of the other admixed American populations that were analyzed. The shared subcontinental ancestry between Colombian population groups can be taken to have implications for the roles of ethnic and cultural identity in the country. Additionally, we are looking into health determinants in connection with admix genomes to reduce health disparities. We contributed to the genome assembly and annotation of several genome sequences of Salmonella enterica strains in collaboration with Keri Norman at Texas A&M University. Assemblies were constructed using Illumina and the genomes were annotated with the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP).

DNA测序技术的进步使基因组研究的新领域成为可能，使基因组变异和表型之间的精细联系成为可能。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，并为获得生物学见解做出了贡献。目前，我们正在与哥伦比亚Corpoica的研究人员合作，利用下一代测序技术产生的额外数据继续对开普醋栗转录组进行表征，并利用NCBI工具完成了数据库的构建，以显示新组装的开普醋栗转录组。此外，我们刚刚与Rocio Gamez和Roberto Vera Alvarez合作完成了促进植物生长的细菌与香蕉植物之间相互作用的分析。