Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
Genome Res. 2023 Jan;33(1):112-128. doi: 10.1101/gr.277070.122. Epub 2023 Jan 18.
Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650-750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.
线虫包含超过 24000 种已描述的物种，几乎存在于所有生态生境中，占土壤后生动物分类多样性的 >80%。线虫的最后一个共同祖先被认为可以追溯到约 6.5 亿至 7.5 亿年前，产生了一个庞大且系统发育多样的群体有待探索。然而，对于大多数物种来说，高质量的基因注释并不全面或缺失。我们将短读 RNA 测序与基于质谱的蛋白质组学以及机器学习质量控制相结合，这种方法称为蛋白质转录组学，从而改进了 9 个基因组测序线虫物种的基因注释，并为另外 3 个没有基因组组装的物种提供了新的基因注释。我们的方法强调了其敏感性，为模式生物中两个迄今未被描述的基因提供了证据。使用这种全面的蛋白质组注释进行广泛的系统发育分析，为后生动物群体的进化过程提供了新的见解。
