Long-read assembly and annotation of rat genomes that are important models of complex genetic disease
大鼠基因组的长读组装和注释是复杂遗传疾病的重要模型
基本信息
- 批准号:10449388
- 负责人:
- 金额:$ 42.53万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-07-12 至 2026-04-30
- 项目状态:未结题
- 来源:
- 关键词:Addictive BehaviorAffectAgricultureAlternative SplicingAmylasesAnimal ModelAnimalsAutomated AnnotationBehaviorBehavioralBehavioral ResearchBiodiversityBiologicalBiological ProcessBiologyBiomedical ResearchBrainBrain DiseasesCarbohydratesCardiovascular PhysiologyCharacteristicsChromosomesCommunitiesComplexDataDepositionDevelopmentDietDigestionDiseaseDisease modelDisease susceptibilityDistantDrug AddictionElementsEnsureEventEvolutionExperimental ModelsFundingGene DuplicationGene ExpressionGenesGeneticGenetic DiseasesGenetic ModelsGenetic VariationGenomeGenomic DNAGenomicsGrainHi-CHumanIGH@ gene clusterInbred BN RatsInbred Strains RatsInbreedingInvestigationKnowledgeLaboratoriesLibrariesLigationLinkLiquid substanceLong-Evans RatsManualsMedicalMethodsModelingMolecular ConformationMusNatureNeurosciencesNorwayOpticsOrganismPathogenesisPhenotypePhysiologyPolishesProcessProteinsRat Genome DatabaseRat StrainsRattusRattus norvegicusRenal functionResearchResearch PersonnelResourcesRodentSamplingSingle Nucleotide PolymorphismSocializationStarchStructureSystemTissuesTranscriptUnited States National Institutes of HealthVariantWorkbasecomparativecostdisorder riskgenome annotationgenome sequencinggenomic toolsgenomic variationhypertensivemRNA sequencingmammalian genomenormotensiverat genomereference genomescaffoldsingle moleculetraittranscriptome sequencingtranscriptomicswhole genome
项目摘要
Project Summary:
The rat is commonly used as an experimental model to investigate a wide diversity of biological processes of
medical relevance. These include neuroscience and brain function, behavioral research, and drug dependency
and addiction. Similarly, aspects of cardiovascular and renal function are more readily investigated in the rat
where the volumes of fluid within these systems are on a much more manageable scale than in smaller rodents.
The utility of rat models for investigation has led to the development of inbred rat strains that harbor medically
relevant phenotypes. Such models have drawn on pre-existing, natural genetic variation to fix genomic diversity
that creates traits such as disease susceptibility. The existence of such models has spurred genetic
investigations that have sought to uncover genetic variation responsible for disease susceptibility traits and to
utilize such knowledge to reveal mechanistic aspects of disease pathogenesis.
However, rat studies can be impeded by the poor quality of existing rat genomic resources. For example, the rat
genome reference sequence is very underdeveloped compared to that of human and mouse. Contiguity of the
genome assembly is an order of magnitude smaller and gene annotation is much reduced. Further, the reference
genome was generated from the Brown Norway inbred rat strain. This strain is biologically remote from many rat
strains used in research.
The rat is recognized as a highly adaptable species. Evolutionary biologists have recognized that an essential
element of adaptation arises from structural variation events in the genome. For example, the adaptation of
humans to high starch diets after the introduction of grain-based agriculture is associated with structural variation
in the amylase gene. This structural variation results from gene duplication events that are adaptive in permitting
increased carbohydrate digestion. These duplication and other large-scale events cannot be observed and
understood simply by alignment of short read genome sequence to the reference genome. Long reads are
required to capture structural variation events.
The objective of our project is to advance rat genomics resources to increase their utility to ongoing studies of
this animal model. To do so, we will use PacBio long read sequencing to capture all genomic variation (SNP and
structural). We will assemble de novo the genomes of 9 widely used rat strains. We will also introduce additional
annotation of the rat genome to increase the numbers of transcripts and proteins associated with the rat
reference genome using long read RNA sequencing. The result of our work will be made available via the Rat
Genome Database and by Ensembl and will provide essential research information to the many laboratories that
employ rat models in their research.
项目总结:
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
数据更新时间:{{ journalArticles.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ monograph.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ sciAawards.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ conferencePapers.updateTime }}
{{ item.title }}
- 作者:
{{ item.author }}
数据更新时间:{{ patent.updateTime }}
PETER A DORIS其他文献
PETER A DORIS的其他文献
{{
item.title }}
{{ item.translation_title }}
- DOI:
{{ item.doi }} - 发表时间:
{{ item.publish_year }} - 期刊:
- 影响因子:{{ item.factor }}
- 作者:
{{ item.authors }} - 通讯作者:
{{ item.author }}
{{ truncateString('PETER A DORIS', 18)}}的其他基金
Long-read assembly and annotation of rat genomes that are important models of complex genetic disease
大鼠基因组的长读组装和注释是复杂遗传疾病的重要模型
- 批准号:
10211748 - 财政年份:2021
- 资助金额:
$ 42.53万 - 项目类别:
Long-read assembly and annotation of rat genomes that are important models of complex genetic disease
大鼠基因组的长读组装和注释是复杂遗传疾病的重要模型
- 批准号:
10615135 - 财政年份:2021
- 资助金额:
$ 42.53万 - 项目类别:
Immunogenetics of Common Polygenic Renal Disease
常见多基因肾病的免疫遗传学
- 批准号:
10471535 - 财政年份:2017
- 资助金额:
$ 42.53万 - 项目类别:
相似海外基金
RII Track-4:NSF: From the Ground Up to the Air Above Coastal Dunes: How Groundwater and Evaporation Affect the Mechanism of Wind Erosion
RII Track-4:NSF:从地面到沿海沙丘上方的空气:地下水和蒸发如何影响风蚀机制
- 批准号:
2327346 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Standard Grant
BRC-BIO: Establishing Astrangia poculata as a study system to understand how multi-partner symbiotic interactions affect pathogen response in cnidarians
BRC-BIO:建立 Astrangia poculata 作为研究系统,以了解多伙伴共生相互作用如何影响刺胞动物的病原体反应
- 批准号:
2312555 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Standard Grant
How Does Particle Material Properties Insoluble and Partially Soluble Affect Sensory Perception Of Fat based Products
不溶性和部分可溶的颗粒材料特性如何影响脂肪基产品的感官知觉
- 批准号:
BB/Z514391/1 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Training Grant
Graduating in Austerity: Do Welfare Cuts Affect the Career Path of University Students?
紧缩毕业:福利削减会影响大学生的职业道路吗?
- 批准号:
ES/Z502595/1 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Fellowship
Insecure lives and the policy disconnect: How multiple insecurities affect Levelling Up and what joined-up policy can do to help
不安全的生活和政策脱节:多种不安全因素如何影响升级以及联合政策可以提供哪些帮助
- 批准号:
ES/Z000149/1 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Research Grant
感性個人差指標 Affect-X の構築とビスポークAIサービスの基盤確立
建立个人敏感度指数 Affect-X 并为定制人工智能服务奠定基础
- 批准号:
23K24936 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Grant-in-Aid for Scientific Research (B)
How does metal binding affect the function of proteins targeted by a devastating pathogen of cereal crops?
金属结合如何影响谷类作物毁灭性病原体靶向的蛋白质的功能?
- 批准号:
2901648 - 财政年份:2024
- 资助金额:
$ 42.53万 - 项目类别:
Studentship
ERI: Developing a Trust-supporting Design Framework with Affect for Human-AI Collaboration
ERI:开发一个支持信任的设计框架,影响人类与人工智能的协作
- 批准号:
2301846 - 财政年份:2023
- 资助金额:
$ 42.53万 - 项目类别:
Standard Grant
Investigating how double-negative T cells affect anti-leukemic and GvHD-inducing activities of conventional T cells
研究双阴性 T 细胞如何影响传统 T 细胞的抗白血病和 GvHD 诱导活性
- 批准号:
488039 - 财政年份:2023
- 资助金额:
$ 42.53万 - 项目类别:
Operating Grants
How motor impairments due to neurodegenerative diseases affect masticatory movements
神经退行性疾病引起的运动障碍如何影响咀嚼运动
- 批准号:
23K16076 - 财政年份:2023
- 资助金额:
$ 42.53万 - 项目类别:
Grant-in-Aid for Early-Career Scientists