Lungfish Mega-Genomes: Analysis of the Largest Vertebrate Genomes and the Evolution of Tetrapod Adaptations

肺鱼巨型基因组：最大脊椎动物基因组的分析和四足动物适应的进化

• 批准号: 418085836
• 负责人: Professor Dr. Thorsten Burmester
• 金额: --
• 依托单位: Arbeitsbereich Molekulare Tierphysiologie
• 依托单位国家: 德国
• 项目类别: Research Grants
• 财政年份: 2019
• 资助国家: 德国
• 起止时间: 2018-12-31 至 2023-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/418085836?language=en
• 关键词: Lungfish; Mega; Genomes; Analysis; Largest

Lungfish are the closest living relatives to all land vertebrates among the "fishes". Their phylogenetic position is crucial for the investigation of both tetrapod evolution and innovations associated with the terrestrialization of vertebrates and its required adaptations. The project aims to better understand the transition from fish to tetrapod adaptations to a terrestrial environment. Lungfish also show remarkable physiological adaptations, such as hypoxia tolerance, aestivation, longevity, and the ability of regeneration of entire limbs. Lungfish also have the largest genomes (40-130 GB) known in the animal kingdom that prohibited their sequencing and assembly technically (and financially) so far. The structure of these megagenomes and the mechanisms that have led to their size are still poorly understood - highlighting the need for a better understanding, both to study tetrapod innovations and the evolution and maintenance of huge genomes. Only through the recent advent of long-read sequencing (PacBio, Oxford Nanopore, etc.) and mapping (Hi-C, BioNano) technologies, is it now possible to sequence, assemble and analyze the lungfish genome. We will obtain a high-quality genomic sequence of the Australian lungfish (Neoceratodus forsteri) through a combination of short-read and long-read technologies and mapping methods (e.g. Bionano), which will provide information on the structure, composition, and origin of megagenomes. Tissue-specific transcriptomes from all six lungfish species (1 Australian, 1 South American and 4 African) will aid in the assembly, annotation and analysis of gene and gene family evolution (gains, losses, selection, etc.) and provide functional data for comparative studies. The genomic and transcriptomic data will provide information on tetrapod innovations as well as on lungfish-specific adaptations.

肺鱼是“鱼类”中与所有陆地脊椎动物最接近的近亲。它们的系统发育位置对于研究四足动物的进化和与脊椎动物的陆地化及其所需的适应性相关的创新至关重要。该项目旨在更好地了解从鱼类到四足动物适应陆地环境的转变。肺鱼还表现出显著的生理适应性，如耐缺氧、耐寒、长寿和全肢再生能力。肺鱼还拥有动物王国中已知的最大的基因组（40-130 GB），这使得迄今为止在技术上（和经济上）禁止对它们进行测序和组装。这些大基因组的结构和导致其大小的机制仍然知之甚少-突出表明需要更好地理解，无论是研究四足动物的创新，还是研究巨大基因组的进化和维持。只有通过最近出现的长读测序（PacBio， Oxford Nanopore等）和制图（Hi-C, BioNano）技术，现在才有可能对肺鱼基因组进行测序，组装和分析。我们将通过结合短读和长读技术和定位方法（如Bionano）获得澳大利亚肺鱼（Neoceratodus forsteri）的高质量基因组序列，这将提供关于大基因组结构、组成和起源的信息。来自所有六种肺鱼（1种澳大利亚，1种南美和4种非洲）的组织特异性转录组将有助于基因和基因家族进化（获得，损失，选择等）的组装，注释和分析，并为比较研究提供功能数据。基因组学和转录组学数据将提供有关四足动物创新以及肺鱼特异性适应的信息。