Beyond a single reference: Building high quality graph genomes capturing global diversity

大多数物种在个体和种群之间表现出相当数量的遗传多样性。然而，大量的这种遗传多样性缺失，因此无法使用当前的参考基因组。几乎所有的参考文献都来自一个或少数几个个体，这些个体被折叠成一个单一的伪单倍体表示，这意味着大多数哺乳动物的参考序列中缺失了数百个百万碱基的泛基因组DNA序列。这包括可能与环境适应和疾病耐受性等重要表型相关的区域。这些区域不仅不能在依赖于这些基因组的当前分析中进行研究，而且几项研究已经强调了对这些单倍体参考的依赖如何有害地偏向分析，即使在基因组中存在的区域也是如此。参考图谱偏差影响了与遗传变异调用和基因表达研究一样基础的分析，这最终意味着它们可能会有害地影响每年数以千计的研究。新兴的基因组图领域旨在通过将跨个体观察到的多样性整合到物种全基因组的单一图形表示中来缓解这些问题。这确保了所有基因组区域都可以被捕获，并通过将所有已知的等位基因和单倍型合并为图形的替代路线来缓解诸如映射偏差等问题。尽管它们具有优势，但目前几乎没有高质量的图形基因组可用，主要是因为图形基因组的生成、注释和可视化具有挑战性，为其更广泛的使用提供了障碍。该项目的目的是通过解决这些问题来推动图形基因组的使用。通过生产可重复使用的集装箱管道来生成和处理基因组图，研究人员将能够快速生成和更新他们感兴趣的物种的图基因组。我们将使用这些管道和以前BBR项目的数据来生成和提供第一个高质量的牛基因组图资源，包括从亚种间的大型结构变异到品种内的单核苷酸变异的遗传变异范围。为了确保图表基因组可以被广泛访问，第三个也是最后一个资源将是一个新的门户网站，用于查看注释丰富的基因组图表。通过促进快速创建与相关下游比对和变体调用软件兼容的图形基因组，使其下游可视化，并开发新的牛图形基因组，我们预计该项目将对家畜研究做出重大贡献，范围从绘制与经济重要性状连锁的遗传基因座到理解物种进化的研究。此外，开发的管道将立即转移到其他物种的图形基因组生产中，大大扩大了项目产出的影响。

Most species show substantial amounts of genetic diversity between individuals and populations. However, large amounts of this genetic diversity are missing, and therefore inaccessible, using current reference genomes. Almost all references are derived from just one or a small handful of individuals, which are collapsed into a single pseudo-haploid representation, meaning hundreds of megabases of pan-genome DNA sequence are missing from most mammalian reference sequences. This includes regions likely to be associated with important phenotypes such as environmental adaptation and disease tolerance. Not only can these regions not be studied in current analyses reliant upon these genomes, but several studies have highlighted how reliance on these haploid references deleteriously bias analyses, even in the regions of the genome that are present. Reference mapping biases impact analyses as fundamental as genetic variant calling and gene expression studies, which ultimately means they are likely to be deleteriously affecting thousands of studies a year.The emerging field of genome graphs aims to mitigate these issues by incorporating the diversity observed across individuals into a single graph representation of the species' pan-genome. This ensures all genomic regions can be captured and mitigates issues such as mapping biases by incorporating all known alleles and haplotypes as alternative routes through the graph. Despite their advantages, few high-quality graph genomes are currently available, primarily because the generation, annotation and visualisation of graph genomes is challenging, providing barriers to their wider use. The aim of this project is to drive forward the use of graph genomes by addressing these issues. By producing reusable, containerised pipelines for generating and working with genome graphs, researchers will be able to rapidly generate and update graph genomes for their species of interest. We will use these pipelines and data from previous BBR projects to generate and make available the first high quality cattle graph genome resource, encompassing the spectrum of genetic variants from large structural variants across sub-species to single nucleotide variants within breeds. To ensure graph genomes can be widely accessed the third and final resource will be a new portal for viewing richly annotated genome graphs. By facilitating the rapid creation of graph genomes compatible with relevant downstream alignment and variant calling software freely and publicly accessible, enabling their downstream visualisation, and developing a new cattle graph genome, we expect this project to make a significant contribution to livestock research, ranging from studies mapping genetic loci linked to economically important traits to those understanding the evolution of species. Additionally, the pipelines developed will be immediately transferrable to the production of graph genomes for other species, significantly extending the impact of project outputs.