Department of Biology, University of Padova, Padova, Italy.
PeerJ. 2022 May 13;10:e13410. doi: 10.7717/peerj.13410. eCollection 2022.
Nudibranchia is an under-studied taxonomic group of gastropods, including more than 3,000 species with colourful and extravagant body shapes and peculiar predatory and defensive strategies. Although symbiosis with bacteria has been reported, no data are available for the nudibranch microbiome nor regarding viruses possibly associated with these geographically widespread species.
Based on 47 available RNA sequencing datasets including more than two billion reads of 35 nudibranch species, a meta-transcriptome assembly was constructed. Taxonomic searches with DIAMOND, RNA-dependent-RNA-polymerase identification with and viral hallmark genes identification by in combination with were applied to identify genuine viral genomes, which were then annotated using CAT.
A total of 20 viral genomes were identified as viruses, among 552 putative viral contigs resembling both RNA viruses of the Negarnaviricota, Pisuviricota, Kitrinoviricota phyla and actively transcribing DNA viruses of the Cossaviricota and Nucleocytoviricota phyla. The 20 commonly identified viruses showed similarity with RNA viruses identified in other RNA-seq experiments and can be putatively associated with bacteria, plant and arthropod hosts by co-occurence analysis. The RNA samples having the highest viral abundances showed a heterogenous and mostly sample-specific distribution of the identified viruses, suggesting that nudibranchs possess diversified and mostly unknown viral communities.
裸鳃亚目是腹足纲中研究较少的一个分类群，包括超过 3000 种具有丰富多彩和奇特的体型以及独特的捕食和防御策略的物种。虽然已经报道了与细菌的共生关系，但目前还没有关于裸鳃动物微生物组的数据，也没有关于可能与这些地理分布广泛的物种相关的病毒的数据。
基于 47 个可用的 RNA 测序数据集，包括超过 35 种裸鳃动物的超过 20 亿个读段，构建了一个元转录组组装。使用 DIAMOND 进行分类搜索，使用 识别 RNA 依赖性 RNA 聚合酶，并结合 识别病毒特征基因，以鉴定真正的病毒基因组，然后使用 CAT 对其进行注释。
共鉴定出 20 种病毒基因组为 病毒，在 552 个假定的病毒连续体中，既有 Negarnaviricota、Pisuviricota、Kitrinoviricota 门的 RNA 病毒，也有 Cossaviricota 和 Nucleocytoviricota 门的活跃转录 DNA 病毒。这 20 种常见的鉴定病毒与其他 RNA-seq 实验中鉴定的 RNA 病毒具有相似性，通过共现分析，可以推测它们与细菌、植物和节肢动物宿主有关。具有最高病毒丰度的 RNA 样本显示出所鉴定病毒的异质且主要是样本特异性分布，表明裸鳃动物具有多样化且大多未知的病毒群落。
