EDGE FGT: Functional Genomics in Gar - Discovery Tools for Major Vertebrate Transitions

脊椎动物的生物多样性包括30,000种陆地脊椎动物(四足动物，包括人类)以及30,000种现代鱼类(硬骨鱼)。直接比较这两个群体仍然具有挑战性，因为它们与4.5亿年前的共同祖先发生了重大变化：四足动物从鱼类中出现并开始生活在陆地上时，经历了重大转变；硬骨鱼彻底改变了它们的基因组组织，获得了数千个额外的基因。这个NSF EDGE项目开发了古老而独特的信息量丰富的加尔鱼(Lesssteidae)，作为连接四足动物和硬骨鱼不同世界的研究有机体。它们的基因组在组织上类似于四足动物的基因组，而GAR的发育与硬骨鱼非常相似，这使得GAR成为了解脊椎动物进化和我们自己的生物起源的一块“罗塞塔石头”。该项目将改进GAR饲养和产卵技术，并开发新的遗传操作方法，如CRISPR基因组编辑，以测试GAR基因功能。这将使GAR作为实验物种在广泛的脊椎动物生物学家社区中进行比较基因组、进化、发育、生理、行为、再生和生态学研究。该项目将通过K-12和本科生的实验室经验、GAR会议和脊椎动物进化遗传学研讨会来培训下一代脊椎动物生物学家。公共研讨会、对水族馆和动物园的动物捐赠以及强大的社交媒体存在将通过强调鱼类对理解进化、遗传和发育的重要性来加强普通公众的科学素养。因此，该项目将提高人们对甘蔗种群减少的生态意义的认识。脊椎动物的进化伴随着特定谱系的基因和形态结构的得失。因此，具有信息丰富的基因组、发育和表型特征的研究生物对于了解脊椎动物的起源、主要转变、生物多样性和基因组功能至关重要。该项目将通过开发斑点石蒜(Lesssteus Oculatus)的基因组到表型组技术，使研究脊椎动物进化过程中的广泛生物学问题成为可能。斑点石蒜在多骨脊椎动物中占有关键的系统发育地位。对于在进化早期经历了全基因组复制事件的硬骨鱼来说，GAR既是一个实验上可到达的、未复制的外类群，也是包括四足类在内的叶鳍脊椎动物的外类群。GAR基因组组合已经用于300多个基因组研究，但目前还缺乏能够直接测试GAR的基因型与表型关系的功能遗传学研究。该项目利用正在进行的研究努力，以促进GAR的基因组使能。待开发的资源和遗传工具包括：1.)改进GAR产卵技术和基础设施，以便在GAR中进行分子遗传学实验；2)CRISPR基因组编辑、靶向基因沉默和GAR模型转基因技术的进展；以及3.通过一个特定于项目的在线数据库、两次GAR会议和两次关于功能脊椎动物Evo-Devo基因组学的讲习班传播项目成果。因此，该项目试图了解一组精选的GAR基因和调控元件作为原则证明的作用，以释放GAR作为比较脊椎动物生物学中广泛研究问题的模式生物的全部潜力。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The biodiversity of vertebrate animals includes 30,000 land vertebrates (tetrapods, including humans) as well as 30,000 species of modern fishes (teleosts). It remains challenging to compare the two groups directly because they significantly changed from their common ancestor 450 million years ago: tetrapod bodies underwent major transitions when they emerged from fishes and began to live on land; teleosts drastically changed their genome organization and gained thousands of extra genes. This NSF EDGE project develops the archaic and uniquely informative garfishes (Lepisosteidae) as research organisms that bridge the disparate worlds of tetrapods and teleosts. Their genome resembles the tetrapod genome in its organization while gars develop very similar to teleosts, making gars a “Rosetta Stone” to understand vertebrate evolution and our own biological origins. The project will improve gar husbandry and spawning techniques and develop novel methodologies for genetic manipulations such as CRISPR genome editing to test gar gene functions. This will make gars available as experimental species for comparative genomic, evolutionary, developmental, physiological, behavioral, regeneration, and ecological research among the broad community of vertebrate biologists. The project will train the next generation of vertebrate biologists through laboratory experiences for K-12 and undergraduate students, gar conferences, and workshops on vertebrate evolutionary genetics. Public seminars, animal donations to aquaria and zoos, and strong social media presence will strengthen scientific literacy of the general public by emphasizing the importance of fishes for understanding evolution, genetics, and development. Thereby, the project will raise awareness for the ecological significance of declining gar populations.The evolution of vertebrates has been accompanied by lineage-specific gains and losses of genes and morphological structures. Research organisms with informative genomes, development, and phenotypic traits are thus essential to understand vertebrate origins, major transitions, their biodiversity, and genome functions. This project will enable the investigation of broad biological questions across vertebrate evolution by developing genome-to-phenome technologies for the spotted gar (Lepisosteus oculatus) that occupies a key phylogenetic position among bony vertebrates. Gars serve both as an experimentally accessible, "unduplicated" outgroup to the teleost fishes that went through a whole genome duplication event early in their evolution as well as an outgroup to lobe-finned vertebrates including tetrapods. The gar genome assembly has been used in 300+ genomic studies, but functional genetic investigations that enable direct testing of genotype-to-phenotype relations in gar are currently lacking. This project leverages ongoing research efforts in order to facilitate the genome enablement of gar. Resources and genetic tools to be developed include: 1.) improvements in gar spawning techniques and infrastructure to perform molecular genetic experiments in gar; 2.) advances in CRISPR genome editing, targeted gene silencing, and transgenic technologies for the gar model; and 3.) dissemination of project results through a project-specific online database, two Gar Conferences, and two Workshops on Functional Vertebrate Evo-Devo Genomics. The project thereby seeks to understand the role of a select set of gar genes and regulatory elements as proof-of-principle to unlock the full potential of gars as model organisms for broad research questions in comparative vertebrate biology.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.