Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8512, Japan.
BMC Genomics. 2014 Mar 10;15(1):183. doi: 10.1186/1471-2164-15-183.
The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in contact with each other. Consequently, P. bursaria is an excellent model for studying cell-cell interaction and the evolution of eukaryotic cells through secondary endosymbiosis between different protists. Despite the importance of this organism, no genomic resources have been identified for P. bursaria to date. This investigation compared gene expressions through RNA-Seq analysis and de novo transcriptome assembly of symbiont-free and symbiont-bearing host cells.
To expedite the process of gene discovery related to the endosymbiosis, we have undertaken Illumina deep sequencing of mRNAs prepared from symbiont-bearing and symbiont-free P. bursaria cells. We assembled the reads de novo to build the transcriptome. Sequencing using Illumina HiSeq2000 platform yielded 232.3 million paired-end sequence reads. Clean reads filtered from the raw reads were assembled into 68,175 contig sequences. Of these, 10,557 representative sequences were retained after removing Chlorella sequences and lowly expressed sequences. Nearly 90% of these transcript sequences were annotated by similarity search against protein databases. We identified differentially expressed genes in the symbiont-bearing P. bursaria cells relative to the symbiont-free cells, including heat shock 70 kDa protein and glutathione S-transferase.
This is the first reported comprehensive sequence resource of Paramecium - Chlorella endosymbiosis. Results provide some keys for the elucidation of secondary endosymbiosis in P. bursaria. We identified P. bursaria genes that are differentially expressed in symbiont-bearing and symbiont-free conditions.
纤毛虫 Paramecium bursaria 的细胞质中容纳了数百个绿藻 Chlorella sp. 的细胞。无论 P. bursaria 与共生藻类之间存在何种相互关系，这两种细胞都保留了在没有伙伴的情况下生长的能力。当它们彼此接触时，它们可以很容易地重新建立共生关系。因此，P. bursaria 是研究细胞间相互作用和通过不同原生生物之间的二次内共生进化的真核细胞的极好模型。尽管该生物体非常重要，但迄今为止尚未确定 P. bursaria 的基因组资源。本研究通过 RNA-Seq 分析和无共生体和有共生体宿主细胞的从头转录组组装比较了基因表达。
为了加速与内共生相关的基因发现过程，我们对带有共生体和无共生体 P. bursaria 细胞的 mRNA 进行了 Illumina 深度测序。我们从头组装读取以构建转录组。使用 Illumina HiSeq2000 平台进行测序生成了 2.323 亿对端序列读取。从原始读取中过滤出的清洁读取被组装成 68175 个连续序列。其中，去除 Chlorella 序列和低表达序列后，保留了 10557 个代表性序列。这些转录序列的近 90%通过与蛋白质数据库的相似性搜索进行注释。我们鉴定了有共生体的 P. bursaria 细胞相对于无共生体细胞中差异表达的基因，包括热休克 70 kDa 蛋白和谷胱甘肽 S-转移酶。
这是首次报道的 Paramecium-Chlorella 内共生的全面序列资源。结果为阐明 P. bursaria 中的二次内共生提供了一些线索。我们鉴定了在有共生体和无共生体条件下差异表达的 P. bursaria 基因。
