Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
Genetics. 2022 Feb 4;220(2). doi: 10.1093/genetics/iyab210.
Procellariiform seabirds rely on their sense of smell for foraging and homing. Both genomes and transcriptomes yield important clues about how olfactory receptor (OR) subgenomes are shaped by natural and sexual selection, yet no transcriptomes have been made of any olfactory epithelium of any bird species thus far. Here, we assembled a high-quality genome and nasal epithelium transcriptome of the Leach's storm-petrel (Oceanodroma leucorhoa) to extensively characterize their OR repertoire. Using a depth-of-coverage-assisted counting method, we estimated over 160 intact OR genes (∼500 including OR fragments). This method reveals the highest number of intact OR genes and the lowest proportion of pseudogenes compared to other waterbirds studied, and suggests that rates of OR gene duplication vary between major clades of birds, with particularly high rates in passerines. OR expression patterns reveal two OR genes (OR6-6 and OR5-11) highly expressed in adults, and four OR genes (OR14-14, OR14-12, OR10-2, and OR14-9) differentially expressed between age classes of storm-petrels. All four genes differentially expressed between age classes were more highly expressed in chicks compared to adults, suggesting that OR genes may exhibit ontogenetic specializations. Three highly differentially expressed OR genes also had high copy number ratios, suggesting that expression variation may be linked to copy number in the genome. We provide better estimates of OR gene number by using a copy number-assisted counting method, and document ontogenetic changes in OR gene expression that may be linked to olfactory specialization. These results provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.
海雀形目海鸟依靠嗅觉觅食和归巢。基因组和转录组都为嗅觉受体 (OR) 亚基因组如何受到自然选择和性选择的影响提供了重要线索,但迄今为止,还没有任何鸟类嗅觉上皮的转录组。在这里,我们组装了一只黑叉尾海燕(Oceanodroma leucorhoa)的高质量基因组和鼻上皮转录组,以广泛描述其 OR 基因库。使用深度覆盖辅助计数方法,我们估计了超过 160 个完整的 OR 基因(包括 OR 片段在内约有 500 个)。与其他研究的水鸟相比,这种方法显示出最高数量的完整 OR 基因和最低比例的假基因,表明 OR 基因复制率在鸟类的主要分支之间存在差异,其中雀形目鸟类的比率特别高。OR 表达模式揭示了两个在成年个体中高表达的 OR 基因(OR6-6 和 OR5-11),以及四个在海燕年龄组之间差异表达的 OR 基因(OR14-14、OR14-12、OR10-2 和 OR14-9)。在年龄组之间差异表达的四个基因在雏鸟中均比在成年个体中表达更高,这表明 OR 基因可能表现出个体发生特化。三个高度差异表达的 OR 基因也具有高拷贝数比,这表明表达变化可能与基因组中的拷贝数有关。我们通过使用拷贝数辅助计数方法提供了更好的 OR 基因数量估计值,并记录了 OR 基因表达的个体发生变化,这些变化可能与嗅觉特化有关。这些结果为海鸟嗅觉的表达、发育和宏进化提供了有价值的见解。