Genetic and functional analysis of eye degeneration in natural populations of a cave-dwelling crustacean

洞穴甲壳动物自然种群眼睛退化的遗传和功能分析

• 批准号: 9812713
• 负责人: Meredith E Protas
• 金额: $ 33.28万
• 依托单位: DOMINICAN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9812713
• 关键词: Affect; Albinism; Alleles; Animals; Anophthalmos; Biological Models; Birth; Candidate Disease Gene; Clustered Regularly Interspaced Short Palindromic Repeats; Congenital Disorders; Crustacea; DNA Sequence Alteration; Data; Development; Developmental Biology; Disease; Embryo; Evolution; Eye; Eye Development; Genes; Genetic; Human; Hybrids; Invertebrates; Isopoda; Lead; Methods; Microphthalmos; Modeling; Molecular; Morphology; Mus; Mutagenesis; Mutate; Mutation; Natural regeneration; Pathway interactions; Patients; Phenotype; Pigments; Play; Population; Process; Reagent; Research; Role; Sampling; Study models; Surface; Techniques; Testing; Time; Variant; Visual system structure; Work; base; comparative; developmental disease; developmental genetics; differential expression; eye formation; fly; functional loss; gene discovery; genome editing; human disease; human model; mutant; novel; novel strategies; tool; transcriptome; transcriptome sequencing

Abstract: An understanding of eye development is necessary to comprehend proper functioning of the eye, capacity for regeneration, and the developmental basis of disease. Many model systems, both vertebrate and invertebrate, have historically provided much important data about the developmental and genetic basis of eye formation. However, hurdles exist studying eye development in model systems such as inherent biases in mutant screens and the minimal amount of naturally occurring variation in eye size. One novel approach allowing for a greater understanding of the developmental and genetic bases of eye formation is to examine naturally occurring eye size variation in non-model organisms, such as that occurs in cave animals. Our previous work demonstrated the utility of using non-model organisms to model human disease when we found that a commonly mutated gene in cases of human albinism was also responsible for albinism in the cavefish, Astyanax mexicanus. We initially chose the isopod crustacean, Asellus aquaticus as a model for studying eye variation because of the extreme difference in eye size between cave and surface dwelling populations. Our subsequent work on the species demonstrated further advantages including multiple independent mechanisms of eye reduction/ loss within a single cave population, multiple mechanisms of eye loss between different cave populations, and the large genetic component influencing eye size. We have already generated many molecular, developmental, and genetic tools and reagents that will assist in studying this interesting species. Our proposal aims to understand the genetics behind eye degeneration in this species. First, we use comparative transcriptome sequencing of cave and surface embryonic samples as an unbiased method to identify genes and pathways responsible for eye degeneration in the cave form. Second, we sequence transcriptomes of hybrid embryos to identify genes that show allele specific expression and that putatively contain cis-regulatory changes. Next, we validate genes discovered from the transcriptome sequencing using linkage and functional techniques. Our work provides a novel perspective on the developmental and genetic basis of eye size differences and furthers the development of A. aquaticus as an important model for eye degeneration and disease.

摘要： 要理解眼睛的正常功能，就必须了解眼睛的发育。 眼睛、再生能力和疾病的发育基础。多款车型 系统，包括脊椎动物和无脊椎动物，在历史上提供了许多重要的 关于眼睛形成的发育和遗传基础的数据。然而，障碍 在模型系统中研究眼睛发育，例如突变体的固有偏见 屏幕和最小数量的自然发生的眼睛大小差异。一本小说 允许更好地了解发育和遗传基础的方法 眼睛的形成是检查非模型中自然发生的眼睛大小变化 生物体，如出现在洞穴动物体内的生物体。我们以前的工作演示了 使用非模型生物来模拟人类疾病的效用当我们发现一个 人类白化病的常见突变基因也是导致白化病的原因。 在穴居鱼中，墨西哥黄姑鱼Astianax micianus。 我们最初选择等足类甲壳动物水生海鞘作为研究眼睛的模型。 由于洞穴和地表眼睛大小的巨大差异而产生的差异 居住人口。我们随后在该物种上的工作进一步证明了 优势包括多种独立的眼睛减少/丢失机制 单一洞穴群体，不同洞穴间视力损失的多种机制 人口，以及影响眼睛大小的大的遗传成分。我们已经这么做了 产生了许多分子、发育和遗传工具和试剂，将 协助研究这个有趣的物种。我们的建议旨在了解遗传学 在这个物种眼睛退化的背后。首先，我们使用比较转录组 洞穴和表面胚胎样本的测序作为一种无偏见的鉴定方法 负责洞穴形态中眼睛退化的基因和途径。第二，我们 杂交胚胎的序列转录体以确定显示等位基因特异性的基因 该基因可能包含顺式调控变化。接下来，我们验证基因 使用连锁和功能技术从转录组测序中发现。 我们的工作为眼睛的发育和遗传基础提供了一个新的视角 大小差异和进一步发展成为水产养殖的重要模式 眼睛退化和疾病。