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

项目摘要 颗石藻是一种海洋植生藻，能产生精美的碳酸钙细胞覆盖物 也就是球孢子虫虽然颗石的形成对材料科学和医学领域具有极大的兴趣， 生物矿化过程的遗传和生物化学基础有关的信息， 颗石藻仍然缺乏。了解调控基因和基因产物的分子机制 参与颗石藻生物成矿过程的分子机制可能有助于了解高等生物的成矿过程， 帮助制定战略，以促进健康的矿化和预防与病理性 诸如佝偻病、肾结石、骨质疏松症和血管组织的异位钙化的病症。这里我们 我建议通过以下方法来提高我们对颗石藻生物矿化中涉及的基因和蛋白质的理解： 对从下一个产生的基因组、转录组和表观遗传数据进行综合比较分析 代测序（NGS）。本研究的系统由三个密切相关的物种组成， 等鞭金藻目（Isochryphalales）的分支：钙化Emiliania huxleyi（E. huxleyi）和Gephyrocapsa oceanica（G. oceanica）和非钙化等鞭金藻Isochrysis galbana（I. galbana），以及E. M217的huxleyi同源株 （钙化）和CCMP 1516（非钙化）。建议的具体目标如下： 目的1：构建高质量的G.奥西尼卡和我利用NGS技术，对galbana的关键基因进行鉴定， 通过比较的综合研究对颗石藻生物矿化必需的蛋白质组 基因组学和转录组学。 目的2：揭示生物矿化基因表达的表观遗传修饰。 本研究将产生大量的NGS数据并进行计算分析，这有助于揭示 基因型的相似性和差异以及表型差异的调控机制 颗石的形成。这里描述的项目将PI目前在生物信息学方面的研究，继续建立 必要的计算基础设施，让更多的研究生和本科生参与到 生物信息学研究在CSUSM，对PI的长期目标，发展一个成功的跨学科 CSUSM的生物信息学研究/教育计划。

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.