Department of Evolution, Ecology, and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
BMC Genomics. 2011 Oct 20;12:519. doi: 10.1186/1471-2164-12-519.
The heterotrophic dinoflagellate Oxyrrhis marina is increasingly studied in experimental, ecological and evolutionary contexts. Its basal phylogenetic position within the dinoflagellates make O. marina useful for understanding the origin of numerous unusual features of the dinoflagellate lineage; its broad distribution has lent O. marina to the study of protist biogeography; and nutritive flexibility and eurytopy have made it a common lab rat for the investigation of physiological responses of marine heterotrophic flagellates. Nevertheless, genome-scale resources for O. marina are scarce. Here we present a 454-based transcriptome survey for this organism. In addition, we assess sequence read abundance, as a proxy for gene expression, in response to salinity, an environmental factor potentially important in determining O. marina spatial distributions.
Sequencing generated 57 Mbp of data which assembled into 7, 398 contigs. Approximately 24% of contigs were nominally identified by BLAST. A further clustering of contigs (at ≥ 90% identity) revealed 164 transcript variant clusters, the largest of which (Phosphoribosylaminoimidazole-succinocarboxamide synthase) was composed of 28 variants displaying predominately synonymous variation. In a genomic context, a sample of 5 different genes were demonstrated to occur as tandem repeats, separated by short (200-340 bp) inter-genic regions. For HSP90 several intergenic variants were detected suggesting a potentially complex genomic arrangement. In response to salinity, analysis of 454 read abundance highlighted 9 and 20 genes over or under expressed at 50 PSU, respectively. However, 454 read abundance and subsequent qPCR validation did not correlate well - suggesting that measures of gene expression via ad hoc analysis of sequence read abundance require careful interpretation.
Here we indicate that tandem gene arrangements and the occurrence of multiple transcribed gene variants are common and indicate potentially complex genomic arrangements in O. marina. Comparison of the reported data set with existing O. marina and other dinoflagellates ESTs indicates little sequence overlap likely as a result of the relatively limited extent of genome scale sequence data currently available for the dinoflagellates. This is one of the first 454-based transcriptome surveys of an ancestral dinoflagellate taxon and will undoubtedly prove useful for future comparative studies aimed at reconstructing the origin of novel features of the dinoflagellates.
异养腰鞭毛目原生动物海洋游仆虫在实验、生态和进化等方面的研究日益增多。海洋游仆虫在腰鞭毛目中的基本系统发育地位使其成为研究腰鞭毛目众多独特特征起源的有用工具；其广泛的分布使其成为原生生物生物地理学研究的对象；营养灵活性和广适性使其成为海洋异养鞭毛虫生理反应研究的常见实验动物。然而，海洋游仆虫的基因组规模资源却很少。在这里，我们对该生物进行了基于 454 的转录组调查。此外，我们评估了序列读取丰度（作为基因表达的替代物）对盐度的响应，盐度是决定海洋游仆虫空间分布的一个潜在重要环境因素。
测序生成了约 57 Mbp 的数据，这些数据组装成 7398 个连续序列。大约 24%的连续序列通过 BLAST 进行了名义上的鉴定。进一步对连续序列（相似度≥90%）进行聚类，揭示了 164 个转录变体簇，其中最大的（磷酸核糖基氨基咪唑琥珀酰胺合酶）由 28 个变体组成，主要是同义变异。在基因组背景下，证明了 5 个不同基因的样本以串联重复的形式出现，由短（~200-340bp）基因间区隔开。在 HSP90 方面，检测到几个基因间变体，表明可能存在复杂的基因组排列。对盐度的响应分析表明，在 50 PSU 时，分别有 9 个和 20 个基因的 454 读取丰度升高或降低。然而，454 读取丰度和随后的 qPCR 验证相关性不好-表明通过临时分析序列读取丰度来衡量基因表达需要仔细解释。
本文表明，串联基因排列和多个转录基因变体的出现是常见的，并表明海洋游仆虫可能存在复杂的基因组排列。与现有的海洋游仆虫和其他腰鞭毛目 EST 报告数据集的比较表明，重叠序列很少，可能是由于目前可用的腰鞭毛目基因组规模序列数据相对有限。这是对原始腰鞭毛目生物进行的第一个基于 454 的转录组调查之一，无疑将有助于未来旨在重建腰鞭毛目新特征起源的比较研究。
