PDF(Pubmed)
Abstract：
Living species vary significantly in phenotype and genomic content. Sophisticated statistical methods linking genes with phenotypes within a species have led to breakthroughs in complex genetic diseases and genetic breeding. Despite the abundance of genomic and phenotypic data available for thousands of species, finding genotype-phenotype associations across species is challenging due to the non-independence of species data resulting from common ancestry. To address this, we present CALANGO (comparative analysis with annotation-based genomic components), a phylogeny-aware comparative genomics tool to find homologous regions and biological roles associated with quantitative phenotypes across species. In two case studies, CALANGO identified both known and previously unidentified genotype-phenotype associations. The first study revealed unknown aspects of the ecological interaction between Escherichia coli, its integrated bacteriophages, and the pathogenicity phenotype. The second identified an association between maximum height in angiosperms and the expansion of a reproductive mechanism that prevents inbreeding and increases genetic diversity, with implications for conservation biology and agriculture.
摘要：
生物物种在表型和基因组含量上差异很大。复杂的统计方法将基因与物种内的表型联系起来，导致了复杂遗传疾病和遗传育种的突破。尽管基因组和表型数据丰富，可用于成千上万的物种，由于来自共同祖先的物种数据的非独立性，因此在物种中发现基因型-表型关联具有挑战性。为了解决这个问题，我们介绍了CALANGO(与基于注释的基因组成分的比较分析)，一种具有系统发育意识的比较基因组学工具，用于发现与跨物种的定量表型相关的同源区域和生物学作用。在两个案例研究中，CALANGO鉴定了已知和先前未鉴定的基因型-表型关联。第一项研究揭示了大肠杆菌之间生态相互作用的未知方面，它的整合噬菌体，和致病性表型。第二个发现了被子植物的最大高度与防止近亲繁殖和增加遗传多样性的生殖机制的扩展之间的关联，对保护生物学和农业有影响。
