School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW, 2006, Australia.
Sci Rep. 2024 Feb 18;14(1):3991. doi: 10.1038/s41598-024-54522-x.
The number of genome-level resources for non-model species continues to rapidly expand. However, frog species remain underrepresented, with up to 90% of frog genera having no genomic or transcriptomic data. Here, we assemble the first genomic and transcriptomic resources for the recently described southern stuttering frog (Mixophyes australis). The southern stuttering frog is ground-dwelling, inhabiting naturally vegetated riverbanks in south-eastern Australia. Using PacBio HiFi long-read sequencing and Hi-C scaffolding, we generated a high-quality genome assembly, with a scaffold N50 of 369.3 Mb and 95.1% of the genome contained in twelve scaffolds. Using this assembly, we identified the mitochondrial genome, and assembled six tissue-specific transcriptomes. We also bioinformatically characterised novel sequences of two families of antimicrobial peptides (AMPs) in the southern stuttering frog, the cathelicidins and β-defensins. While traditional peptidomic approaches to peptide discovery have typically identified one or two AMPs in a frog species from skin secretions, our bioinformatic approach discovered 12 cathelicidins and two β-defensins that were expressed in a range of tissues. We investigated the novelty of the peptides and found diverse predicted activities. Our bioinformatic approach highlights the benefits of multi-omics resources in peptide discovery and contributes valuable genomic resources in an under-represented taxon.
非模式物种的基因组资源数量持续快速增长。然而，蛙类的代表性仍然不足，多达 90%的蛙类属没有基因组或转录组数据。在这里，我们为最近描述的南方口吃蛙（Mixophyes australis）组装了第一个基因组和转录组资源。南方口吃蛙是穴居的，栖息在澳大利亚东南部自然植被覆盖的河岸上。我们使用 PacBio HiFi 长读测序和 Hi-C 支架，生成了一个高质量的基因组组装，支架 N50 为 369.3 Mb，95.1%的基因组包含在十二个支架中。利用这个组装，我们鉴定了线粒体基因组，并组装了六个组织特异性转录组。我们还对南方口吃蛙中两种抗菌肽（AMPs）家族的新序列进行了生物信息学特征分析，即 cathelicidins 和 β-defensins。虽然传统的肽组学方法通常可以从皮肤分泌物中鉴定出一个蛙种的一到两种 AMPs，但我们的生物信息学方法发现了 12 种 cathelicidins 和两种 β-defensins，它们在多种组织中表达。我们研究了这些肽的新颖性，发现了多样化的预测活性。我们的生物信息学方法强调了多组学资源在肽发现中的优势，并为代表性不足的分类群提供了有价值的基因组资源。
