Understanding Biomineralization in Coccolithophores by Comparative Genomic, Transcriptomic and Epigenetic Analyses

通过比较基因组、转录组和表观遗传学分析了解颗石藻的生物矿化

• 批准号: 9279616
• 负责人: Xiaoyu Zhang
• 金额: $ 10.44万
• 依托单位: CALIFORNIA STATE UNIVERSITY SAN MARCOS
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2021-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9279616
• 关键词: Address; Affect; Algae; Area; Biochemical; Bioinformatics; Biological; Biological Process; Biology; Calcified; Calcium Carbonate; Carbon; Cells; Characteristics; Communities; Comparative Genomic Analysis; Comparative Study; Computer Analysis; Cytosine; DNA Methylation; Data; Development; Epigenetic Process; Gene Expression Profile; Gene Family; Gene Proteins; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotype; Goals; Growth; Interdisciplinary Study; Kidney Calculi; Knowledge; Light; Marines; Medicine; Methods; Modeling; Modification; Molecular; Molecular Profiling; Northern Blotting; Organism; Osteoporosis; Pathologic; Pattern; Phenotype; Phytoplankton; Play; Process; Research; Resources; Reverse Transcriptase Polymerase Chain Reaction; Rickets; Role; Sculpture; Sister; Staining method; Stains; System; Technology; Time; Tissues; Vascular calcification; base; biomineralization; bisulfite sequencing; calcification; comparative genomics; computer infrastructure; cost; design; differential expression; epigenome; experimental study; gene product; genomic variation; graduate student; improved; interest; materials science; member; mineralization; next generation sequencing; prevent; programs; reference genome; response; transcriptome; transcriptome sequencing; transcriptomics; undergraduate student; whole genome

Project Summary Coccolithophores are marine phytoplanktons that produce elegantly sculptured calcium carbonate cell coverings known as coccoliths. While coccolith formation is of great interest to areas of material science and medicine, information relating to the genetic and biochemical underpinnings of the biomineralization process in coccolithophores is still lacking. Knowledge of the molecular mechanisms regulating genes and gene products involved in the biomineralization process of coccolithophores may shed light on that of higher organisms, and help to develop strategies to promote healthy mineralization and prevent problems associated with pathological conditions such as rickets, kidney stones, osteoporosis, and ectopic calcification of vascular tissues. Here we propose to improve our understanding of genes and proteins involved in coccolithophorean biomineralization by performing integrated comparative analyses of genomic, transcriptomic and epigenetic data generated from next generation sequencing (NGS). The system for this study consists of three closely related species of Isochrysidales clade of haptophytes: calcifying Emiliania huxleyi (E. huxleyi) and Gephyrocapsa oceanica (G. oceanica), and non-calcifying Isochrysis galbana (I. galbana), as well as E. huxleyi isogeneic strains of M217 (calcifying) and CCMP1516 (non-calcifying). The following specific aims are proposed: Aim 1: Assemble high-quality genomes of G. oceanica and I. galbana by using NGS, and identify key gene and protein groups essential to coccolithophorean biomineralization through integrated study of comparative genomics and transcriptomics. Aim 2: Uncover epigenetic modifications critical to the expression of biomineralization genes. A large amount of NGS data will be generated and computationally analyzed for this study, which help to uncover the genotypic similarity and differences as well as regulatory mechanisms underlying the phenotypic diversities of coccolith formations. The project described here will PI’s current research in bioinformatics, continue to build necessary computational infrastructure and involve more graduate and undergraduate students into bioinformatics research at CSUSM, towards PI’s long-term goal of developing a successful interdisciplinary research/educational program of bioinformatics at CSUSM.

项目摘要 球石生物体是海洋浮游植物，能产生优雅雕刻的碳酸钙细胞覆盖物。 被称为球石。虽然球石的形成对材料科学和医学领域非常感兴趣， 与生物矿化过程的遗传和生化基础有关的信息 球石发育体仍然缺乏。对调控基因和基因产物的分子机制的认识 参与球藻生物体的生物矿化过程可能有助于揭示高等生物的矿化过程，以及 帮助制定促进健康矿化的策略，并防止与病理相关的问题 软骨病、肾结石、骨质疏松症和血管组织异位钙化等情况。在这里我们 建议通过以下方式提高我们对球石原生物矿化相关基因和蛋白质的理解 对NEXT产生的基因组、转录组和表观遗传学数据进行综合比较分析 世代排序(NGS)。这项研究的系统由三个密切相关的物种组成 等鞭毛目：钙化的埃米利亚尼亚huxleyi(E.huxleyi)和大洋小球藻Gephy rocapsa Ocean anica(G. Ocean)和非钙化等鞭金藻(I.galbana)，以及湖北乳杆菌M217的同源菌株 (钙化)和CCMP1516(非钙化)。提出了以下具体目标： 目的1：利用NGS技术构建海洋棉和球藻的高质量基因组，并鉴定关键基因和关键基因 通过比较研究综合研究球虫石原生物矿化所必需的蛋白质组 基因组学和转录组学。 目的2：揭示对生物矿化基因表达至关重要的表观遗传修饰。 本研究将产生大量的NGS数据并进行计算分析，这些数据有助于揭示 表型多样性的基因相似性和差异性及其调控机制 球石的形成。这里描述的项目将继续建设Pi目前在生物信息学方面的研究 必要的计算基础设施，并让更多的研究生和本科生参与到 CSUSM的生物信息学研究，朝着PI发展成功的跨学科的长期目标迈进 南加州州立大学生物信息学研究/教育计划。