Kyslík Jiří, Kosakyan Anush, Nenarokov Serafim, Holzer Astrid S, Fiala Ivan
Institute of Parasitology, Biology Centre, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic.
Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
BMC Genomics. 2021 Mar 20;22(1):198. doi: 10.1186/s12864-021-07515-3.
Lineage-specific gene expansions represent one of the driving forces in the evolutionary dynamics of unique phylum traits. Myxozoa, a cnidarian subphylum of obligate parasites, are evolutionarily altered and highly reduced organisms with a simple body plan including cnidarian-specific organelles and polar capsules (a type of nematocyst). Minicollagens, a group of structural proteins, are prominent constituents of nematocysts linking Myxozoa and Cnidaria. Despite recent advances in the identification of minicollagens in Myxozoa, the evolutionary history and diversity of minicollagens in Myxozoa and Cnidaria remain elusive.
We generated new transcriptomes of two myxozoan species using a novel pipeline for filtering of closely related contaminant species in RNA-seq data. Mining of our transcriptomes and published omics data confirmed the existence of myxozoan Ncol-4, reported only once previously, and revealed a novel noncanonical minicollagen, Ncol-5, which is exclusive to Myxozoa. Phylogenetic analyses support a close relationship between myxozoan Ncol-1-3 with minicollagens of Polypodium hydriforme, but suggest independent evolution in the case of the myxozoan minicollagens Ncol-4 and Ncol-5. Additional genome- and transcriptome-wide searches of cnidarian minicollagens expanded the dataset to better clarify the evolutionary trajectories of minicollagen.
The development of a new approach for the handling of next-generation data contaminated by closely related species represents a useful tool for future applications beyond the field of myxozoan research. This data processing pipeline allowed us to expand the dataset and study the evolution and diversity of minicollagen genes in Myxozoa and Cnidaria. We identified a novel type of minicollagen in Myxozoa (Ncol-5). We suggest that the large number of minicollagen paralogs in some cnidarians is a result of several recent large gene multiplication events. We revealed close juxtaposition of minicollagens Ncol-1 and Ncol-4 in myxozoan genomes, suggesting their common evolutionary history. The unique gene structure of myxozoan Ncol-5 suggests a specific function in the myxozoan polar capsule or tubule. Despite the fact that myxozoans possess only one type of nematocyst, their gene repertoire is similar to those of other cnidarians.
谱系特异性基因扩增是独特门特征进化动态的驱动力之一。粘孢子虫是刺胞动物门下的一个专性寄生亚门，是进化上发生改变且高度简化的生物，具有简单的身体结构，包括刺胞动物特有的细胞器和极囊（一种刺丝囊）。微小胶原蛋白是一组结构蛋白，是连接粘孢子虫和刺胞动物的刺丝囊的主要成分。尽管最近在粘孢子虫中微小胶原蛋白的鉴定方面取得了进展，但粘孢子虫和刺胞动物中微小胶原蛋白的进化历史和多样性仍然难以捉摸。
我们使用一种新的流程来过滤RNA测序数据中密切相关的污染物种，生成了两种粘孢子虫物种的新转录组。对我们的转录组和已发表的组学数据进行挖掘，证实了粘孢子虫Ncol-4的存在（此前仅报道过一次），并揭示了一种新的非经典微小胶原蛋白Ncol-5，它是粘孢子虫特有的。系统发育分析支持粘孢子虫Ncol-1-3与多态水螅微小胶原蛋白之间的密切关系，但表明粘孢子虫微小胶原蛋白Ncol-4和Ncol-5是独立进化的。对刺胞动物微小胶原蛋白进行的全基因组和转录组范围的额外搜索扩展了数据集，以更好地阐明微小胶原蛋白的进化轨迹。
一种处理受密切相关物种污染的下一代数据的新方法的开发，是粘孢子虫研究领域之外未来应用的有用工具。这种数据处理流程使我们能够扩展数据集，并研究粘孢子虫和刺胞动物中微小胶原蛋白基因的进化和多样性。我们在粘孢子虫中鉴定出一种新型微小胶原蛋白（Ncol-5）。我们认为，一些刺胞动物中大量的微小胶原蛋白旁系同源物是近期几次大的基因倍增事件的结果。我们揭示了粘孢子虫基因组中微小胶原蛋白Ncol-1和Ncol-4的紧密并列，表明它们有共同的进化历史。粘孢子虫Ncol-5独特的基因结构表明其在粘孢子虫极囊或小管中具有特定功能。尽管粘孢子虫仅拥有一种类型的刺丝囊，但其基因库与其他刺胞动物相似。
