title: De novo assembly and characterization of the transcriptome of the newly described dinoflagellate Ansanella granifera: Spotlight on flagellum-associated genes.
abstract: 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.
authors.affiliation: School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.
authors.forename: Se Hyeon
authors.initials: SH
authors.lastname: Jang
authors.affiliation: 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. Electronic address: hjjeong@snu.ac.kr.
authors.forename: Hae Jin
authors.initials: HJ
authors.lastname: Jeong
authors.affiliation: Department of Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea.
authors.forename: Jae Kyung
authors.initials: JK
authors.lastname: Chon
authors.affiliation: School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea.
authors.forename: Sung Yeon
authors.initials: SY
authors.lastname: Lee
mesh_terms: D016208:Databases, Factual; D004141:Dinoflagellida / Q000235:genetics* / Q000648:ultrastructure; D005407:Flagella / Q000235:genetics* / Q000648:ultrastructure; D010802:Phylogeny; D059467:Transcriptome
keywords: Dinoflagellate transcriptome; Flagellar gene; Flagellum phylogeny; Flagellum tree; RNA-Seq