Department of Biology, East Carolina University, E 5th Street, Greenville, NC 27858, USA.
Integr Comp Biol. 2021 Oct 14;61(4):1281-1290. doi: 10.1093/icb/icab150.
Third-generation (long-read-based) sequencing technologies are reshaping our understanding of genome structure and function. One of the most persistent challenges in genome biology has been confidently reconstructing radiations of complex gene families. Olfactory receptors (ORs) represent just such a gene family with upward of thousands of receptors in some mammalian taxa. Whereas in birds olfaction was historically an overlooked sensory modality, new studies have revealed an important role for smell. Chromosome-level assemblies for birds allow a new opportunity to characterize patterns of OR diversity among major bird lineages. Previous studies of short-read-based (second-generation) genome assemblies have associated OR gene family size with avian ecology, but such conclusions could be premature especially when new assembly methods reshape our understanding of avian OR evolution. Here we provide a fundamental characterization of OR repertoires in five recent genome assemblies, including the most recent assembly of golden-collared manakin (Manacus vitellinus). We find that short read-based assemblies systematically undercount the avian-specific gamma-c OR subfamily, a subfamily that comprises over 65% of avian OR diversity. Therefore, in contrast to previous studies, we find a high diversity of gamma-c ORs across the avian tree of life. Building on these findings, ongoing sequencing efforts and improved genome assemblies will clarify the relationship between OR diversity and avian ecology.
第三代(长读长测序)测序技术正在改变我们对基因组结构和功能的认识。在基因组生物学中,最持久的挑战之一是如何自信地重建复杂基因家族的辐射。嗅觉受体(ORs)就是这样一个基因家族,在一些哺乳动物分类群中,OR 受体的数量多达数千个。虽然在鸟类中,嗅觉在历史上一直被忽视,但新的研究揭示了嗅觉的重要作用。鸟类的染色体水平组装为研究主要鸟类谱系之间的 OR 多样性模式提供了一个新的机会。以前基于短读长(第二代)基因组组装的研究将 OR 基因家族的大小与鸟类生态学联系起来,但这些结论可能还为时过早,尤其是当新的组装方法改变了我们对鸟类 OR 进化的理解时。在这里,我们对五个最近的基因组组装中的 OR 库进行了基本特征描述,包括金颈丛-manakin(Manacus vitellinus)的最新组装。我们发现,基于短读长的组装系统地低估了鸟类特异性的 gamma-c OR 亚家族,这个亚家族构成了超过 65%的鸟类 OR 多样性。因此,与以前的研究相比,我们在整个鸟类生命之树上发现了 gamma-c OR 的高度多样性。基于这些发现,正在进行的测序工作和改进的基因组组装将澄清 OR 多样性与鸟类生态学之间的关系。