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

肺鱼是“鱼类”中与所有陆地脊椎动物最近的亲属。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陆生化及其所需适应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过渡。肺鱼还表现出显著的生理适应性，如耐缺氧、夏眠、寿命长和四肢再生能力。肺鱼还拥有动物王国中已知的最大的基因组（40-130 GB），到目前为止，这些基因组在技术上（和经济上）禁止它们的测序和组装。这些巨型基因组的结构和导致其大小的机制仍然知之甚少-突出了更好地理解的必要性，无论是研究四足动物的创新还是巨大基因组的进化和维护。只有通过最近出现的长读测序（PacBio，Oxford Nanopore等）和绘图（Hi-C，BioNano）技术，现在有可能测序，组装和分析肺鱼基因组。我们将通过短读和长读技术和作图方法（例如Bionano）的组合获得澳大利亚肺鱼（Neoceratodus forsteri）的高质量基因组序列，这将提供有关巨型基因组的结构，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。为比较研究提供功能数据。基因组和转录组数据将提供有关四足动物创新以及肺鱼特定适应的信息。

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.