title: Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.
abstract: BACKGROUND
  Dinoflagellates are known for their capacity to form harmful blooms (e.g., "red tides") and as symbiotic, photosynthetic partners for corals. These unicellular eukaryotes have permanently condensed, liquid-crystalline chromosomes and immense nuclear genome sizes, often several times the size of the human genome. Here we describe the first draft assembly of a dinoflagellate nuclear genome, providing insights into its genome organization and gene inventory.
  
  
  RESULTS
  Sequencing reads from Symbiodinium minutum were assembled into 616 Mbp gene-rich DNA regions that represented roughly half of the estimated 1,500 Mbp genome of this species. The assembly encoded ∼42,000 protein-coding genes, consistent with previous dinoflagellate gene number estimates using transcriptomic data. The Symbiodinium genome contains duplicated genes for regulator of chromosome condensation proteins, nearly one-third of which have eukaryotic orthologs, whereas the remainder have most likely been acquired through bacterial horizontal gene transfers. Symbiodinium genes are enriched in spliceosomal introns (mean = 18.6 introns/gene). Donor and acceptor splice sites are unique, with 5' sites utilizing not only GT but also GC and GA, whereas at 3' sites, a conserved G is present after AG. All spliceosomal snRNA genes (U1-U6) are clustered in the genome. Surprisingly, the Symbiodinium genome displays unidirectionally aligned genes throughout the genome, forming a cluster-like gene arrangement.
  
  
  CONCLUSIONS
  We show here that a dinoflagellate genome exhibits unique and divergent characteristics when compared to those of other eukaryotes. Our data elucidate the organization and gene inventory of dinoflagellates and lay the foundation for future studies of this remarkable group of eukaryotes.
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan. eiichi@oist.jp
authors.forename: Eiichi
authors.initials: E
authors.lastname: Shoguchi
authors.forename: Chuya
authors.initials: C
authors.lastname: Shinzato
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawashima
authors.forename: Fuki
authors.initials: F
authors.lastname: Gyoja
authors.forename: Sutada
authors.initials: S
authors.lastname: Mungpakdee
authors.forename: Ryo
authors.initials: R
authors.lastname: Koyanagi
authors.forename: Takeshi
authors.initials: T
authors.lastname: Takeuchi
authors.forename: Kanako
authors.initials: K
authors.lastname: Hisata
authors.forename: Makiko
authors.initials: M
authors.lastname: Tanaka
authors.forename: Mayuki
authors.initials: M
authors.lastname: Fujiwara
authors.forename: Mayuko
authors.initials: M
authors.lastname: Hamada
authors.forename: Azadeh
authors.initials: A
authors.lastname: Seidi
authors.forename: Manabu
authors.initials: M
authors.lastname: Fujie
authors.forename: Takeshi
authors.initials: T
authors.lastname: Usami
authors.forename: Hiroki
authors.initials: H
authors.lastname: Goto
authors.forename: Shinichi
authors.initials: S
authors.lastname: Yamasaki
authors.forename: Nana
authors.initials: N
authors.lastname: Arakaki
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.forename: Yoko
authors.initials: Y
authors.lastname: Kuroki
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Mónica
authors.initials: M
authors.lastname: Medina
authors.forename: Mary Alice
authors.initials: MA
authors.lastname: Coffroth
authors.forename: Debashish
authors.initials: D
authors.lastname: Bhattacharya
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D002843:Chromatin / Q000235:genetics; D004141:Dinoflagellida / Q000235:genetics*; D020440:Gene Duplication; D016678:Genome; D007438:Introns; D008969:Molecular Sequence Data; D012342:RNA, Small Nuclear; D017381:Spliceosomes / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D012342:RNA, Small Nuclear