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

EDGE FGT：鳝鱼的功能基因组学 - 主要脊椎动物转变的发现工具

• 批准号: 2029216
• 负责人: Ingo Braasch
• 金额: $ 162.19万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-11-01 至 2025-10-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2029216&HistoricalAwards=false
• 关键词: EDGE; FGT; Functional; Genomics; Gar

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.

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相比发生了显着变化：四足动物的身体在从鱼类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并获得了数千个额外的基因。这个NSF EDGE项目开发了古老的和独特的信息garfishes（Lepisosteidae）作为研究生物，桥接了四足动物和硬骨鱼的不同世界。它们的基因组在组织上类似于四足动物的基因组，而加尔斯的发育与硬骨鱼非常相似，使加尔斯成为了解脊椎动物进化和我们自己生物起源的“罗塞塔石碑”。该项目将改善雀麦养殖和产卵技术，并开发新的遗传操作方法，如CRISPR基因组编辑，以测试雀麦基因功能。这将使加尔斯可作为实验物种的比较基因组，进化，发育，生理，行为，再生和生态研究之间的广泛的脊椎动物生物学家社区。该项目将通过为K-12和本科生提供实验室经验，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、向水族馆和动物园捐赠动物以及强大的社交媒体将通过强调鱼类对理解进化、遗传和发展的重要性来加强公众的科学素养。因此，该项目将提高人们对雀鳝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获得和丧失。因此，研究具有信息基因组、发育和表型特征的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。该项目将通过为在骨脊椎动物中占据关键系统发育位置的斑点雀鳝（Lepisosteus oculatus）开发基因组-表型组技术，对脊椎动物进化过程中的广泛生物学问题进行调查。加尔斯既作为一个实验上可访问的，“未复制”的外群的硬骨鱼，经历了一个全基因组复制事件在其进化的早期，以及一个外群的叶鳍脊椎动物，包括四足动物。gar基因组组装已用于300多项基因组研究，但目前缺乏能够直接测试gar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工作，以促进基因组使能的gar。待开发的资源和遗传工具包括：1.改进雀鳝产卵技术和基础设施，以在雀鳝中进行分子遗传实验; 2.）用于gar模型的CRISPR基因组编辑、靶向基因沉默和转基因技术的进展;以及3.）通过一个特定项目的在线数据库、两次GAR会议和两次关于功能性脊椎动物Evo-Devo基因组学的讲习班传播项目成果。因此，该项目旨在了解一组选定的gar基因和调控元件的作用，作为原理证明，以释放加尔斯作为比较脊椎动物生物学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，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

项目成果

PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates.

• DOI: 10.1093/nar/gkad152
• 发表时间: 2023-04-24
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Mathavarajah, Sabateeshan;Vergunst, Kathleen L.;Habib, Elias B.;Williams, Shelby K.;He, Raymond;Maliougina, Maria;Park, Mika;Salsman, Jayme;Roy, Stephane;Braasch, Ingo;Roger, Andrew J.;Langelaan, David N.;Dellaire, Graham
• 通讯作者: Dellaire, Graham

Ancient vertebrate dermal armor evolved from trunk neural crest.

• DOI: 10.1073/pnas.2221120120
• 发表时间: 2023-07-25
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Stundl, Jan;Martik, Megan L.;Chen, Donglei;Raja, Desingu Ayyappa;Franek, Roman;Pospisilova, Anna;Psenicka, Martin;Metscher, Brian D.;Braasch, Ingo;Haitina, Tatjana;Cerny, Robert;Ahlberg, Per E.;Bronner, Marianne E.
• 通讯作者: Bronner, Marianne E.

Suppressors of cGAS-STING are downregulated during fin-limb regeneration and aging in aquatic vertebrates.

• DOI: 10.1002/jez.b.23227
• 发表时间: 2023-10
• 期刊: Journal of experimental zoology. Part B, Molecular and developmental evolution
• 作者: Sabateeshan Mathavarajah;Andrew W. Thompson;M. Stoyek;T. A. Quinn;Stéphane Roy;I. Braasch;G. Dellaire

Na+/Cl- cotransporter 2 is not fish-specific and is widely found in amphibians, non-avian reptiles, and select mammals.

Na /Cl-协同转运蛋白 2 不是鱼类特有的，广泛存在于两栖动物、非鸟类爬行动物和特定哺乳动物中。

• DOI: 10.1152/physiolgenomics.00143.2022
• 发表时间: 2023
• 期刊: Physiological genomics
• 影响因子: 4.6
• 作者: Motoshima,Toya;Nagashima,Ayumi;Ota,Chihiro;Oka,Haruka;Hosono,Kohei;Braasch,Ingo;Nishihara,Hidenori;Kato,Akira
• 通讯作者: Kato,Akira

Convergent losses of SCPP genes and ganoid scales among non-teleost actinopterygians

• DOI: 10.1016/j.gene.2021.146091
• 发表时间: 2021-12-08
• 期刊: GENE
• 影响因子: 3.5
• 作者: Mikami, Masato;Ineno, Toshinao;Kawasaki, Kazuhiko
• 通讯作者: Kawasaki, Kazuhiko