Jang Se Hyeon, Jeong Hae Jin, Chon Jae Kyung, Lee Sung Yeon
School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.
School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, Republic of Korea.
Mar Genomics. 2017 Jun;33:47-55. doi: 10.1016/j.margen.2017.01.003. Epub 2017 Jan 19.
Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known. Thus, a de novo assembly and characterization of the transcriptome of the fast-swimming dinoflagellate Ansanella granifera were conducted and its flagellum genes were compared with those of other dinoflagellates, motile small flagellates, and non-motile protist species. Based on assembled data using Trinity/CLC combined strategy, 83,652 transcripts of A. granifera were identified. The assembled consensus sequences were annotated to the NCBI non-redundant (nr), InterProScan, Gene Ontology (GO), and KEGG pathway analyses. Moreover, 71 structural and 35 functional flagellum-associated genes expressed were identified. The number of expressed flagellar structural and functional genes of A. granifera was not markedly different from those of other dinoflagellates or motile small flagellates, but much greater than those of non-motile species. Furthermore, in both phylogenetic trees based on the outer dynein arm (ODA1, ODA9, and DLC1) and inner dynein arm (IDA4, IDA7, and BOP5) flagellum genes of dinoflagellates, the problem of the long-branch attraction artifacts of Oxyrrhis marina which has been reported in the phylogenetic trees based on ribosomal DNA was removed. Moreover, in both phylogenetic trees based on the ODA and IDA flagellum genes, the species in the order Peridiniales or Gymnodiniales were revealed to belong to a big clade of each order. Therefore, the phylogenetic tree based on the flagellum genes is likely to give a clue to resolve the problem of separation in a big clade of a dinoflagellate order which has also been reported in the phylogenetic trees based on ribosomal DNA.
许多甲藻已知会引发赤潮，并且常常通过在光照良好的表层水和富营养化的深层水之间进行活跃的垂直迁移，和/或通过定位并摄取猎物细胞，从而超过不具运动能力的硅藻和具运动能力的小型鞭毛虫。它们的鞭毛在这两种关键行为中发挥着重要作用。然而，甲藻鞭毛的结构和功能基因却鲜为人知。因此，对快速游动的甲藻粒突安山藻的转录组进行了从头组装和表征，并将其鞭毛基因与其他甲藻、具运动能力的小型鞭毛虫以及不具运动能力的原生生物物种的鞭毛基因进行了比较。基于使用Trinity/CLC联合策略的组装数据，鉴定出了粒突安山藻的83,652条转录本。对组装得到的共有序列进行了NCBI非冗余（nr）注释、InterProScan注释、基因本体（GO）注释和KEGG通路分析。此外，还鉴定出了71个表达的与鞭毛相关的结构基因和35个功能基因。粒突安山藻表达的鞭毛结构和功能基因数量与其他甲藻或具运动能力的小型鞭毛虫相比并无显著差异，但远多于不具运动能力的物种。此外，在基于甲藻外动力蛋白臂（ODA1、ODA9和DLC1）和内动力蛋白臂（IDA4、IDA7和BOP5）鞭毛基因构建的系统发育树中，基于核糖体DNA构建的系统发育树中所报道的海洋尖鼻藻长枝吸引假象问题得以消除。此外，在基于ODA和IDA鞭毛基因构建的两个系统发育树中，多甲藻目或裸甲藻目的物种都被揭示属于每个目的一个大分支。因此，基于鞭毛基因构建的系统发育树可能为解决在基于核糖体DNA构建的系统发育树中也有报道的甲藻目一个大分支内的分类问题提供线索。
