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: 9976534
• 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 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9976534
• 关键词: Address; Affect; Algae; Area; Biochemical; Bioinformatics; Biological; Biological Process; Biology; Calcium Carbonate; Carbon; Cells; Characteristics; Communities; Comparative Genomic Analysis; Comparative Study; Computer Analysis; Cytosine; DNA Methylation; Data; Development; Epigenetic Process; Expression Profiling; Gene Expression Profile; Gene Family; Gene Proteins; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotype; Goals; Growth; Interdisciplinary Study; Kidney Calculi; Knowledge; Light; Medicine; Methods; Modeling; Modification; Molecular; Northern Blotting; Organism; Osteoporosis; Pathologic; Pattern; Phenotype; Phytoplankton; Play; Process; Research; Resources; Reverse Transcriptase Polymerase Chain Reaction; Rickets; Role; Sculpture; Sister; 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.

项目总结