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Multi-omic bases of coral disease resistance

珊瑚抗病性的多组学基础

基本信息

批准号：
1924145
负责人：
Steven Vollmer
金额：
$ 99.98万
依托单位：
Northeastern University
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2019
资助国家：
美国
起止时间：
2019-08-15 至 2024-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1924145&HistoricalAwards=false
关键词：
Multi omic bases coral disease

项目摘要

Coral disease outbreaks have radically altered the structure and function of tropical coral reefs worldwide. As progress has been made towards understanding the basic cause of many coral diseases, significant gaps remain in our knowledge of how corals respond to and resist disease infection, even as calls are being made for science to assist in coral evolution by selecting thermal or disease tolerant coral species or genotypes - often called "super corals". This project uses the endangered Caribbean staghorn coral Acropora cervicornis and White Band Disease (WBD) as a host-pathogen system to study the genetics of coral disease resistance. WBD epidemics decimated this key shallow-water Caribbean coral and led to its endangered listing. While the recovery of staghorn corals has been slow, data indicate that up to 15% or more of staghorn corals are highly disease resistant. This project uses modern genomic tools to identify genetic markers for staghorn coral disease resistance. The identification of genetic markers for disease resistance (i) provides needed information on the efficacy of "assisted evolution" for coral resiliency (ii) helps predict how well staghorn coral can resist future disease outbreaks, (iii) assists conservation efforts aimed at identifying and selecting corals with high disease resistance, and (iv) spurs the development of molecular assays for coral disease resistance. This research provides graduate and undergraduate training in the STEM fields of microbiology, genetics, and computational biology. The project is as a platform to develop outreach curricula to teach students about coral diseases and reef health, which are disseminated via Northeastern University's K-12 outreach program and the Smithsonian Tropical Research Institute's outreach program in Panama. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems. It is increasingly becoming clear that the future of coral reefs depends on the resilience of reef-building corals to adapt or acclimate to their changing environment, which in turn requires that key traits like thermal tolerance and disease resistance are genetically heritable, identifiable, and quantifiable. Using staghorn corals and WBD as a model host-pathogen system, this project identifies the genetic underpinnings of disease resistance in Caribbean staghorn corals using state-of-the-art, multi-omic approaches linking patterns of variation across the staghorn coral genome, transcriptome and proteome. For Aim 1, genome-wide SNP variation from 200 staghorn coral genotypes from two populations [100 Florida; 100 Panama] is used to identify genomic regions associated with disease resistance using genome-wide association (GWA) analyses. For Aim 2, tank-based transmission experiments are used to profile key differences in the transcriptomic (mRNA and miRNA) and proteomic response of resistant versus susceptible staghorn corals during disease exposure. Mulit-omic data are analyzed using: (1) eQTL to link SNPs to mRNA expression, (2) miRNA-mRNA interactions and correlation networks to test for post-transcriptional gene regulation, and (3) network-based approaches. For Aim 3, 16s rDNA amplicon sequencing are used to identify changes in the staghorn coral microbiome due to disease resistance and exposure using microbial DNA from the resistant and susceptible corals used in the tank-based experiment (Aim 2). In addition to identify genetic markers associated with coral disease resistance, this study produces (1) the most complete multi-omic analysis of coral immunity and disease resistance to date, and (2) the first functional analyses of miRNA post-translational gene regulation in a cnidarian host-pathogen system. Data on the genetics of coral disease resistance provide valuable information on the efficacy of "assisted evolution" for coral resiliency. By using nursery raised staghorn corals from Florida, this project directly identifies highly disease resistant corals that can be used in the large-scale out planting efforts.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

珊瑚疾病的爆发从根本上改变了世界各地热带珊瑚礁的结构和功能。随着在了解许多珊瑚疾病的基本原因方面取得了进展，我们对珊瑚如何应对和抵抗疾病感染的认识仍然存在重大差距，即使有人呼吁科学通过选择耐热或耐病的珊瑚物种或基因型-通常称为“超级珊瑚”-来协助珊瑚进化。该项目利用濒危的加勒比鹿角珊瑚鹿角珊瑚和白色带状病作为宿主-病原体系统，研究珊瑚抗病性的遗传学。WBD流行病摧毁了这一关键的浅水加勒比珊瑚，并导致其濒危名单。虽然鹿角珊瑚的恢复一直很缓慢，但数据表明，高达15%或更多的鹿角珊瑚具有高度的抗病能力。该项目使用现代基因组工具来确定鹿角珊瑚抗病性的遗传标记。确定抗病遗传标记（一）提供了必要的信息，“辅助进化”的珊瑚弹性的功效（二）有助于预测如何以及鹿角珊瑚可以抵抗未来的疾病爆发，（三）协助保护工作，旨在确定和选择珊瑚高抗病性，和（四）刺激发展的分子测定珊瑚抗病性。这项研究提供了微生物学，遗传学和计算生物学的STEM领域的研究生和本科生培训。该项目是一个平台，以制定外展课程，向学生讲授珊瑚疾病和珊瑚礁健康，这些课程通过东北大学的K-12外展计划和史密森热带研究所在巴拿马的外展计划传播。该项目由海洋科学部的生物海洋学计划和综合有机系统部的共生，防御和自我识别计划共同资助。越来越清楚的是，珊瑚礁的未来取决于造礁珊瑚适应或适应不断变化的环境的弹性，这反过来又要求耐热性和抗病性等关键特征是可遗传的，可识别的和可量化的。使用鹿角珊瑚和WBD作为宿主-病原体系统的模型，该项目使用最先进的多组学方法将鹿角珊瑚基因组，转录组和蛋白质组的变异模式联系起来，确定加勒比鹿角珊瑚抗病性的遗传基础。对于目标1，来自两个种群[100佛罗里达; 100巴拿马]的200个鹿角珊瑚基因型的全基因组SNP变异用于使用全基因组关联（GWA）分析来鉴定与抗病性相关的基因组区域。对于目标2，坦克为基础的传输实验是用来配置文件的关键差异的转录组（mRNA和miRNA）和蛋白质组反应的抵抗与易感鹿角珊瑚在疾病暴露。多组学数据分析使用：（1）eQTL将SNP与mRNA表达联系起来，（2）miRNA-mRNA相互作用和相关网络测试转录后基因调控，以及（3）基于网络的方法。对于目标3，16 s rDNA扩增子测序用于确定鹿角珊瑚微生物组的变化，这是由于使用罐基实验中使用的抗性和易感珊瑚的微生物DNA进行的疾病抗性和暴露所致（目标2）。除了识别与珊瑚抗病性相关的遗传标记外，本研究还产生了（1）迄今为止最完整的珊瑚免疫和抗病性的多组学分析，以及（2）刺胞动物宿主-病原体系统中miRNA翻译后基因调控的第一个功能分析。关于珊瑚抗病性遗传学的数据提供了关于“辅助进化”对珊瑚复原力的效力的宝贵信息。通过使用从佛罗里达的苗圃饲养的鹿角珊瑚，该项目直接识别出可用于大规模外植工作的高度抗病珊瑚。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。